PyPI - mafutils - Versions diffs - 0.2.1__tar.gz → 0.3.0__tar.gz - Mend

mafutils 0.2.1tar.gz → 0.3.0tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (87) hide show

mafutils-0.3.0/.github/workflows/tests.yml ADDED Viewed

@@ -0,0 +1,28 @@
+name: Tests
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+jobs:
+  test:
+    name: pytest
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out source
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install package and pytest
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e . pytest
+      - name: Run tests
+        run: pytest tests/ -v

{mafutils-0.2.1 → mafutils-0.3.0}/DEVELOPMENT.md RENAMED Viewed

@@ -187,7 +187,24 @@ pytest tests/
 per-command parallel/sequential/fallback logic) across all three compression
 types. `tests/test_validate.py` covers index integrity (size/mtime/hash
 header fields, `mafutils validate`'s three-way verdict, and `--verify-hash`
-on `fetch`/`stats`/`gc`).
+on `fetch`/`stats`/`gc`). `tests/test_stats.py` checks `mafutils stats`'s
+computed `overall.tsv`/`species.tsv` values against numbers hand-derived
+directly from `tests/example.maf`'s raw content (not just "doesn't crash"),
+including a regression guard that the sequential (`-p 1`, no
+`ProcessPoolExecutor`) and real multi-worker (`-p 2`+) paths produce
+identical output.
+`tests/test_real_data.py` runs `stats`/`gc`/`fetch` against
+`tests/real-excerpt.maf` -- 8 real, complete alignment blocks extracted
+read-only from gwct's actual ~42GB production MAF
+(`data/hamsters/uncompressed/...`), not hand-crafted. Unlike
+`example.maf`-based tests (which verify exact hand-computed values),
+these check plausibility/robustness on genuinely real data -- real
+species-naming conventions, real gap patterns, real block-size
+distribution -- since a hand-crafted fixture wouldn't think to include
+whatever real data actually looks like. This is deliberately still a
+tiny, committed fixture, not the real dataset itself: `data/hamsters/`
+stays untouched and out of git (see the `.gitignore` `data/` entry).
 ## Releasing to PyPI

{mafutils-0.2.1 → mafutils-0.3.0}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mafutils
-Version: 0.2.1
+Version: 0.3.0
 Summary: Utilities for indexing, fetching, and summarizing MAFs.
 Author: Gregg Thomas
 License: MIT License
@@ -214,6 +214,7 @@ Options:
 | `--fasta-dedupe` | FASTA duplicate handling: `none` or `most-seq` |
 | `--processes`, `-p` | Number of worker processes (see Compression above — plain gzip always runs single-process) |
 | `--mode`, `-m` | Fetch mode: `block` or `scaffold` |
+| `--scaffold-subdirs` | Group output files into subfolders named by reference scaffold (`<output>/<scaffold>/<basename>`) instead of one flat directory |
 | `--verbose` | Emit warning lines from each completed batch |
 | `--profile` | Log internal timing breakdowns |
 | `--verify-hash` | Verify the index's stored content hash against the MAF file (see Index Integrity above) |

{mafutils-0.2.1 → mafutils-0.3.0}/README.md RENAMED Viewed

@@ -177,6 +177,7 @@ Options:
 | `--fasta-dedupe` | FASTA duplicate handling: `none` or `most-seq` |
 | `--processes`, `-p` | Number of worker processes (see Compression above — plain gzip always runs single-process) |
 | `--mode`, `-m` | Fetch mode: `block` or `scaffold` |
+| `--scaffold-subdirs` | Group output files into subfolders named by reference scaffold (`<output>/<scaffold>/<basename>`) instead of one flat directory |
 | `--verbose` | Emit warning lines from each completed batch |
 | `--profile` | Log internal timing breakdowns |
 | `--verify-hash` | Verify the index's stored content hash against the MAF file (see Index Integrity above) |

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils/_version.py RENAMED Viewed

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
-__version__ = version = '0.2.1'
-__version_tuple__ = version_tuple = (0, 2, 1)
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)
-__commit_id__ = commit_id = 'g5c611ce9e'
+__commit_id__ = commit_id = 'g694487dcd'

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils/fetch.py RENAMED Viewed

@@ -90,6 +90,7 @@ WORKER_MAF_COMPRESSION = None
 WORKER_INDEX = None
 WORKER_OUTPUT = None
 WORKER_SINGLE_OUTPUT = None
+WORKER_SCAFFOLD_SUBDIRS = None
 WORKER_AS_FASTA = None
 WORKER_FASTA_HEADER = None
 WORKER_EXPECTED_SPECIES = None
@@ -174,6 +175,7 @@ def initBatchWorker(
     verbose,
     profile,
     prefetched_cache=None,
+    scaffold_subdirs=False,
 ):
     global WORKER_HEADER
     global WORKER_MAF_FILE
@@ -181,6 +183,7 @@ def initBatchWorker(
     global WORKER_INDEX
     global WORKER_OUTPUT
     global WORKER_SINGLE_OUTPUT
+    global WORKER_SCAFFOLD_SUBDIRS
     global WORKER_AS_FASTA
     global WORKER_FASTA_HEADER
     global WORKER_EXPECTED_SPECIES
@@ -196,6 +199,7 @@ def initBatchWorker(
     WORKER_INDEX = index
     WORKER_OUTPUT = output
     WORKER_SINGLE_OUTPUT = single_output
+    WORKER_SCAFFOLD_SUBDIRS = scaffold_subdirs
     WORKER_AS_FASTA = as_fasta
     WORKER_FASTA_HEADER = fasta_header
     WORKER_EXPECTED_SPECIES = expected_species
@@ -714,6 +718,20 @@ def trimMafBlock(block_text, bed_start, bed_end, BATCHLOG, verbose=False, warnin
 #############################################################################
+def buildOutputPath(output_dir, scaffold, out_basename, ext, scaffold_subdirs):
+    """
+    Shared per-output-file path builder for block mode (fetchByRegion) and
+    scaffold mode (fetchByScaffold/fetchScaffoldsSequential). The scaffold
+    subdirectory itself is never created here -- callers must pre-create
+    every needed one upfront (see run_fetch) before any of these paths are
+    actually opened for writing.
+    """
+    if scaffold_subdirs:
+        return os.path.join(output_dir, scaffold, out_basename + ext)
+    return os.path.join(output_dir, out_basename + ext)
+#############################################################################
 def fetchByRegion(
     region,
     header,
@@ -729,6 +747,7 @@ def fetchByRegion(
     verbose=False,
     warning_state=None,
     profile_state=None,
+    scaffold_subdirs=False,
 ):
     """
     Worker function to process a single BED region:
@@ -760,7 +779,7 @@ def fetchByRegion(
         fill_cache = {}
     # For fasta output, hold sequences per species
-    output_filename = os.path.join(output, out_basename + (".fa" if as_fasta else ".maf"))
+    output_filename = buildOutputPath(output, scaffold, out_basename, ".fa" if as_fasta else ".maf", scaffold_subdirs)
     out_stream = None
     if single_output:
@@ -997,6 +1016,7 @@ def fetchByBatch(
             verbose=WORKER_VERBOSE,
             warning_state=warning_state,
             profile_state=profile_state,
+            scaffold_subdirs=WORKER_SCAFFOLD_SUBDIRS,
         )
         batch_results[result_idx] = region_result
         if not WORKER_SINGLE_OUTPUT:
@@ -1027,13 +1047,13 @@ def fetchByBatch(
 #############################################################################
-def fetchByScaffold(scaffold, start_end, maf_file, maf_header, maf_compression, out_dir, LOG):
+def fetchByScaffold(scaffold, start_end, maf_file, maf_header, maf_compression, out_dir, LOG, scaffold_subdirs=False):
     """
     Worker function to extract one scaffold from the MAF file.
     start_end is a tuple (start_byte, end_byte).
     """
     start, end = start_end
-    output_path = os.path.join(out_dir, f"{scaffold}.maf")
+    output_path = buildOutputPath(out_dir, scaffold, scaffold, ".maf", scaffold_subdirs)
     try:
         with COMMON.openMaf(maf_file, maf_compression, "rb") as mfp, open(output_path, "wb") as outfp:
@@ -1047,7 +1067,7 @@ def fetchByScaffold(scaffold, start_end, maf_file, maf_header, maf_compression,
     return f"{output_path}: Wrote {scaffold}";
-def fetchScaffoldsSequential(ordered_scaffolds, index, maf_file, maf_header, maf_compression, out_dir, LOG):
+def fetchScaffoldsSequential(ordered_scaffolds, index, maf_file, maf_header, maf_compression, out_dir, LOG, scaffold_subdirs=False):
     """
     Extracts multiple scaffolds using a single open MAF handle, in the given
     (ascending file-offset) order. Used for gzip input: reusing one handle
@@ -1058,7 +1078,7 @@ def fetchScaffoldsSequential(ordered_scaffolds, index, maf_file, maf_header, maf
     with COMMON.openMaf(maf_file, maf_compression, "rb") as mfp:
         for scaffold in ordered_scaffolds:
             start, end = index[scaffold]
-            output_path = os.path.join(out_dir, f"{scaffold}.maf")
+            output_path = buildOutputPath(out_dir, scaffold, scaffold, ".maf", scaffold_subdirs)
             try:
                 LOG.info(f">>> Scaffold {scaffold}");
                 data = COMMON.readMafBlockBytes(mfp, maf_compression, start, end)
@@ -1101,6 +1121,13 @@ def run_fetch(args, cmdline="mafutils fetch"):
         LOG.error(f"Invalid mode: '{args.mode}'. Must be 'block' or 'scaffold'.")
         sys.exit(1)
     # Validate mode
+    if args.scaffold_subdirs and args.single_output:
+        LOG.error("--scaffold-subdirs cannot be used with --single-output.")
+        sys.exit(1)
+    # --single-output collects blocks into one combined file and never uses
+    # per-region output_basename/output_filename at all, so it doesn't
+    # compose with grouping per-region files into scaffold subfolders.
     # if args.max_no_overlap_regions < -1:
     #     LOG.error("--max-no-overlap-regions must be >= -1.")
     #     sys.exit(1)
@@ -1171,6 +1198,12 @@ def run_fetch(args, cmdline="mafutils fetch"):
                 sys.exit(1)
         LOG.info(f"Extracting {len(scaffold_set)} scaffolds from scaffold index: {scaffold_set}");
+        if args.scaffold_subdirs:
+            # Pre-create upfront in the main process, same rationale as
+            # block mode below -- avoids any per-worker/cross-process race.
+            for scaffold in scaffold_set:
+                os.makedirs(os.path.join(args.output, scaffold), exist_ok=True)
         # Process scaffolds in ascending file-offset order; for gzip this is
         # what lets a single reused handle avoid ever seeking backward.
         ordered_scaffolds = sorted(scaffold_set, key=lambda s: index[s][0])
@@ -1182,7 +1215,7 @@ def run_fetch(args, cmdline="mafutils fetch"):
                     "gzip-compressed files; --processes will be ignored. (Use a bgzip-compressed MAF "
                     "for real parallel speedup on compressed input.)"
                 )
-            for result in fetchScaffoldsSequential(ordered_scaffolds, index, args.maf_file, maf_header, maf_compression, args.output, LOG):
+            for result in fetchScaffoldsSequential(ordered_scaffolds, index, args.maf_file, maf_header, maf_compression, args.output, LOG, scaffold_subdirs=args.scaffold_subdirs):
                 LOG.info(result)
         else:
             # Extract from MAF using the region index for matching scaffolds
@@ -1198,7 +1231,8 @@ def run_fetch(args, cmdline="mafutils fetch"):
                         maf_header,
                         maf_compression,
                         args.output,
-                        LOG
+                        LOG,
+                        args.scaffold_subdirs,
                     ))
                 for future in futures:
                     result = future.result()
@@ -1273,6 +1307,15 @@ def run_fetch(args, cmdline="mafutils fetch"):
         else: # basename_mode == "coords":
             region["output_basename"] = f"{scaffold}-{start}-{end}"
+    if args.scaffold_subdirs:
+        # Pre-create every needed scaffold subdirectory upfront, in the main
+        # process, mirroring the single os.makedirs(args.output, ...) above --
+        # block-mode writes happen inside ProcessPoolExecutor workers, and
+        # nothing per-worker creates directories today, so doing this here
+        # avoids needing any cross-process race handling at write time.
+        for scaffold in {region["scaffold"] for region in regions}:
+            os.makedirs(os.path.join(args.output, scaffold), exist_ok=True)
     info_outfile = os.path.join(args.output, "maf_fetch_summary.tsv")
     # if args.fasta_header and not args.fasta:
@@ -1303,6 +1346,7 @@ def run_fetch(args, cmdline="mafutils fetch"):
             args.verbose,
             args.profile,
             prefetch_cache,
+            args.scaffold_subdirs,
         ),
     ) as executor, open(info_outfile, "w") as info_out:
         summary_headers = ["scaffold", "start", "end", "basename", "n.overlapping.blocks", "block.lengths", "interblock.distances", "n.sequences"]
@@ -1462,6 +1506,7 @@ def fetch_command(
     fasta_dedupe: Annotated[FastaDedupeMode, typer.Option("--fasta-dedupe", help="When outputting FASTA, collapse duplicate species per block; 'most-seq' keeps the copy with most non-gap bases.")] = FastaDedupeMode.none,
     processes: Annotated[int, typer.Option("--processes", "-p", help="Number of parallel processes to use (default: 1)")] = 1,
     mode: Annotated[FetchMode, typer.Option("--mode", "-m", help="Mode: 'block' to trim by regions, 'scaffold' to extract whole scaffolds (default: block)")] = FetchMode.block,
+    scaffold_subdirs: Annotated[bool, typer.Option("--scaffold-subdirs", help="Group output files into subfolders named by reference scaffold (<output>/<scaffold>/<basename>) instead of one flat directory.")] = False,
     single_output: Annotated[bool, typer.Option("--single-output", hidden=True)] = False,
     verbose: Annotated[bool, typer.Option("--verbose", help="Print every warning line after each batch completes.")] = False,
     profile: Annotated[bool, typer.Option("--profile", help="Log aggregate timing breakdowns for internal fetch steps.")] = False,
@@ -1480,6 +1525,7 @@ def fetch_command(
         fasta_dedupe=fasta_dedupe.value,
         processes=processes,
         mode=mode.value,
+        scaffold_subdirs=scaffold_subdirs,
         single_output=single_output,
         verbose=verbose,
         profile=profile,

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mafutils
-Version: 0.2.1
+Version: 0.3.0
 Summary: Utilities for indexing, fetching, and summarizing MAFs.
 Author: Gregg Thomas
 License: MIT License
@@ -214,6 +214,7 @@ Options:
 | `--fasta-dedupe` | FASTA duplicate handling: `none` or `most-seq` |
 | `--processes`, `-p` | Number of worker processes (see Compression above — plain gzip always runs single-process) |
 | `--mode`, `-m` | Fetch mode: `block` or `scaffold` |
+| `--scaffold-subdirs` | Group output files into subfolders named by reference scaffold (`<output>/<scaffold>/<basename>`) instead of one flat directory |
 | `--verbose` | Emit warning lines from each completed batch |
 | `--profile` | Log internal timing breakdowns |
 | `--verify-hash` | Verify the index's stored content hash against the MAF file (see Index Integrity above) |

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils.egg-info/SOURCES.txt RENAMED Viewed

@@ -7,6 +7,7 @@ README.md
 THIRD_PARTY_LICENSES.md
 pyproject.toml
 .github/workflows/publish-pypi.yml
+.github/workflows/tests.yml
 benchmarks/README.md
 benchmarks/Snakefile
 benchmarks/baseline-manual-timings.txt
@@ -53,9 +54,14 @@ tests/example.maf.gz.block.idx
 tests/example.maf.gz.scaffold.idx
 tests/example.maf.scaffold.idx
 tests/example.maf.scaffold.regenerated.idx
+tests/real-excerpt.maf
+tests/real-excerpt.maf.block.idx
+tests/real-excerpt.maf.scaffold.idx
 tests/test_compression.py
 tests/test_fetch.py
 tests/test_gc.py
+tests/test_real_data.py
+tests/test_stats.py
 tests/test_validate.py
 tests/expected-fasta/01-singleblock-gap.fa
 tests/expected-fasta/02-truncatedblock.fa

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils.egg-info/scm_file_list.json RENAMED Viewed

@@ -17,6 +17,7 @@
     "benchmarks/notebook.ipynb",
     "benchmarks/config.yaml",
     "benchmarks/profiles/slurm/config.yaml",
+    ".github/workflows/tests.yml",
     ".github/workflows/publish-pypi.yml",
     "mafutils/validate.py",
     "mafutils/fetch.py",
@@ -30,9 +31,13 @@
     "mafutils/lib/loginit.py",
     "mafutils/lib/common.py",
     "mafutils/lib/__init__.py",
+    "tests/real-excerpt.maf.scaffold.idx",
+    "tests/test_stats.py",
     "tests/example.maf.gz",
     "tests/example.maf.bgz",
+    "tests/real-excerpt.maf",
     "tests/test_compression.py",
+    "tests/real-excerpt.maf.block.idx",
     "tests/test_validate.py",
     "tests/example.maf.block.idx",
     "tests/example.maf.gz.scaffold.idx",
@@ -40,6 +45,7 @@
     "tests/example-tabs.maf.block.idx",
     "tests/test_gc.py",
     "tests/example-tabs.maf.scaffold.idx",
+    "tests/test_real_data.py",
     "tests/test_fetch.py",
     "tests/crossblocks.bed",
     "tests/example-tabs.maf",

{mafutils-0.2.1 → mafutils-0.3.0}/mafutils.egg-info/scm_version.json RENAMED Viewed

@@ -1,7 +1,7 @@
 {
-  "tag": "0.2.1",
+  "tag": "0.3.0",
   "distance": 0,
-  "node": "g5c611ce9e5d735e4f0eec333e1c8b906eb815005",
+  "node": "g694487dcd86f14f29285ea1b51261b03fe3cc45d",
   "dirty": false,
   "branch": "HEAD",
   "node_date": "2026-07-21"

mafutils-0.3.0/tests/real-excerpt.maf ADDED Viewed

@@ -0,0 +1,131 @@
+##maf version=1
+a
+s	Mus_musculus.CM000994.3	125888838	82	+	195154279	TCC-ATCTACTCAAACCTAATTCTTTACGATTCACTGAAGAAATCCCCTCCAGGAAGAAATCCTGATC-TTTGATTCTTCTTTC
+s	Phodopus_campbelli.chr12	18452278	5	-	32442325	T----------------------------------------------------------------------------TCCA---
+s	Phodopus_sungorus_new.chr12	17334137	5	-	31225933	T----------------------------------------------------------------------------TCCA---
+s	Phodopus_roborovskii.JAEOAF010000031.1	16485673	8	+	29770300	T----------------------------------------------------------------------------TACATCT
+s	Cricetus_cricetus.OZ199631.1	140166140	8	-	205530201	T----------------------------------------------------------------------------TTTTTTT
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6038229	4	-	8539717	A----------------------------------------------------------------------------TTT----
+s	Arvicola_amphibius.NC_052058.2	72668393	4	-	166747489	A----------------------------------------------------------------------------CTT----
+s	Microtus_pennsylvanicus.CM073176.1	20976023	4	+	113485825	A----------------------------------------------------------------------------cct----
+s	Microtus_arvalis.JAHRII010002323.1	111060626	4	+	200229077	A----------------------------------------------------------------------------CTT----
+s	Neotoma_floridana.CM113793.1	27921528	83	-	95303938	TCC-ATCTTCTCAAACCTAATACTTCAAGATTCACCTAAGAAATCACCTCCAGGAAGAAACCCTGATTACTTAATTCCTTTTTC
+s	Onychomys_torridus.LR877198.1	72220278	83	+	93020901	CCC-ACCTACTCAAACCTAATTCTTCAAGATTCATCTAAGAAATTATCTCTAGGAAGAAACTCTGATTACTTAATTCCTTTTTC
+s	Peromyscus_californicus.VALE03000237.1	12778336	84	+	80346014	TCCCATCTACTCAAACCTAATTCTTCAAGATTCACCTAAGAAATTACCTCCAGGAAGAAACCCTGATTACTTAATTCCTTTTTC
+s	Peromyscus_maniculatus_North.CM113205.1	35699024	84	+	104458120	TCCCATCTACTCAAACCTAATTCTTCAAGATTCACCTAAGAAATTACCTCCAGGAAGAAACCCTGATTACTTAATTCCTTTTTC
+a
+s	Mus_musculus.CM000994.3	125888920	187	+	195154279	TTGGGAATCAAGTTGAGTGCTCAGTTTCAGTAGATACAGACAACCC-CCA---CC---C----AGCC--TTGTACTCAATATTCCATAATTGTGTCATATTTGTACTGTGTTTGGGATCTATTGT-----------CTTCCTA-GGACAATCGGAAGGGACAAAAGAAGGTAATAGCAACAAGGTCACCATCAGC----------T-CTCAGATCTCAGAGGA
+s	Phodopus_campbelli.chr12	18452286	180	-	32442325	TAAAGGA-------------------CCAGTGGTCACAGACAATCCTCCC---CC---CCAACACCCTTTTTTAGTCAATAGTCCATAA-------ACCTGTGTTCTATTCTTGGAATCCAATGGGAAATATCATACTTCCT-GGGACAACCAGAACTGGAAGAGGAGGATAATAGCAATG---TCACC------ATCAGCA-AAATCTTAAGTGCTGCGGGA
+s	Phodopus_sungorus_new.chr12	17334145	152	-	31225933	TAAAGGA-------------------CCAGTGGTCACAGACAATCCTCCA---CC---CCAACAGCCTTTTTTAGTCAATAGTCCATAA-------ACCTGTGTCCTATTCTTGGAATCCAATGTGAAATATCATACTTC-T-GGGACAACCAGAACTGGAAGAGTTGGATAATAGCAATG---TCACC----------------------------------
+s	Phodopus_roborovskii.JAEOAF010000031.1	16485768	182	+	29770300	TAAAGGA-------------------CCAGTGTTAACAGACAATCCTTTC---CTCCACCAACAGCC--TTTTAGTCAATATCCCATAA-------ACATTTGCCCTATACTTGGAATCCAATGTGAAAAATCATACTCCCT-GGAACAACCAGAGCAGGCAGAGTTGGATAATAGCAATG---TCACC------ATCAGCAGAAAACTTAAGTGCTGTGGGA
+s	Cricetus_cricetus.OZ199631.1	140166148	180	-	205530201	TAAAGGA-------------------TCAGTGATCACAGACAATCC-CCATGCCT---CCAGTAGCC--TTTTAGTCAATATTCCATAA-------GCATTCATCCTGTAGTTGGAATCCAATATGAAATATCATACTTCCT--GGACAACCAGAATGGGCAGAGTAGGATAATAGTAACA---TCACC------ACCAGCAGAAAACTTAAGTGTTATGGGA
+s	Neotoma_floridana.CM113793.1	27921611	174	-	95303938	TTAAGGA-------------------TCAGTGGTTCCAGACAATCCCCCA---CA---C----AGCC--TT-TAGTCAATATTCCATAA-------ACATTTGTCCTGTACTTGGAATCCAATATGAAATATCATACTTCCTG-GGATGACCAGAATGGTCAGAGGAAGATAATAGCAACA---TCACCATCAGC------AGAAAACTTAAGTGTTATGGGA
+s	Onychomys_torridus.LR877198.1	72220361	175	+	93020901	TTAAGGA-------------------TCAGTGGTCACAGACAATCCTCCA---CA---C----AGCCT-TT-TAGCCAATATCCCATAA-------ACATTTGTCCTGTACTGGGAACCTAATATGAAATATCATACTTCCTG-GGACAACCAGAATGGTCAGAGGAAGATAATAGCAGCA---TCACCATCAGC------AGAAAACTTAAAAGTTATGGGA
+s	Peromyscus_californicus.VALE03000237.1	12778420	175	+	80346014	TTAAGGA-------------------TCAGTGGTCACAGACAATCCTCCA---CA---C----AGCCT-TT-TAGCCAATATTCCATAA-------ACATTTGTCCTGTACTTGGAATCTAATATGAAATATCATCCTTCCTG-GGACAACCAGAATGGTCAGAGGAAGATAACAGCCACA---TCACCATCAGC------AGAAAACTTAAATGTTATGGGA
+s	Peromyscus_maniculatus_North.CM113205.1	35699108	175	+	104458120	TTAAGCA-------------------TCAGTGGTCACAGACAATCCTCCA---CA---C----AGCCT-TT-TAGCCAATATTCCATAA-------ACATTTGTCCTGTACTTGGAATCTAATATGAAATATCATCCTTCCTG-GGACAACCAGAATGGTCAGAGGAAGATAACAGCCACA---TCACCATCAGC------AGAAAACTTAAATGTTATGGGA
+a
+s	Mus_musculus.CM000994.3	125889107	10	+	195154279	G---------------------GGGCATCTG
+s	Phodopus_campbelli.chr12	18452505	18	-	32442325	TT-------------TTGCAATGAtcatctc
+s	Phodopus_sungorus_new.chr12	17334315	18	-	31225933	TT-------------TTGCAATGATCATCTC
+s	Phodopus_roborovskii.JAEOAF010000031.1	16485989	18	+	29770300	TT-------------CTGCAATGATCATCTT
+s	Cricetus_cricetus.OZ199631.1	140166328	31	-	205530201	TTCTAGAAGAGGGGCTTGTAATGATCATCTG
+s	Neotoma_floridana.CM113793.1	27921822	18	-	95303938	TT-------------TTGCAATGATCATCTC
+s	Onychomys_torridus.LR877198.1	72220576	18	+	93020901	TT-------------TTGCAATGAACATCTC
+s	Peromyscus_californicus.VALE03000237.1	12778635	18	+	80346014	TT-------------TTGCAATGATCATCTC
+s	Peromyscus_maniculatus_North.CM113205.1	35699323	18	+	104458120	TT-------------TTGCAATGACCATCTC
+a
+s	Mus_musculus.CM000994.3	125889117	440	+	195154279	CATGTCTGACAAAGCACTTGCT---TG---ACACAGGACAATAAAATTCTGTCATGAACTATCATGAAGT-ATGTGACAGGATGACAAAGCATGGGTGAAAAGGAAGTTG---TGTCACATTTGGGTGGCACTT-ATATGCTTCTGGTAATGATGGTGGC----------TCTT--TAAAGTTTCTTATGACTTCTTTGTAACTAGCGAGTAAGCTCTGTGGGCA--------TTGCAGGCTATCACCTTCCTCTTCATAACAGCACTGA-AGTTCATGTCtgtgaggctcaatctctgttgtcaaccagatggcattaagtctgtccatgaaaacagacctctgggg----------atgtctgtgatagaggttaggctatttaaagttgaaagacccaccctaa-tctgagtggtaccagttcatgggctggggttctag-act---gaaagaaagagagaaaggaagctgagccctagcctta
+s	Phodopus_campbelli.chr12	18452900	426	-	32442325	CA----------TGTACTTTCT---T----AC--AGGACAATAAAATCCTAGCATGGGCTATCATGAAGTTATGTGACAAGACGGTAAGGCATGGATGGAAAGGAGCCCATGTC---ATGTTCAGG-GGCACTT-ACATGCTGCTGGCA---------GTGATCGTTGAGTCTTTATAAAGTTTCTTGTGTTTTCTCTGTAACTAGCCTGTAAGCTCTGTGGGCAGGGATGCATTGCATGCTGTCCCCTCCCTACTCCAAACAGCACTAA-GCTTCATGTCTGTACGGCTTAATCGTGACTGTCAACCAGATGGGACAAAGTCTGTCTATGAAAACAA--------------------ATGTCTGTGAGGGATATCAGGCtaactgaggttggaagacccactctaaAtctgagtggcaccaatctatgggcttgtgagct-gGaat---aagcaaggagaa---agtaagctgagccccagcattc
+s	Phodopus_sungorus_new.chr12	17334333	426	-	31225933	CA----------AGTACTTACT---T----AC--AGGACAATAAAATCCTAGCATGGGCTATCATGAAGTTATGTGACATGACGATAAGGCATGGATGGAAAGGAGCCCATGTC---ATGTTCAGG-GGCACTT-ACATGCTGCTGGCA---------GTGATCGTTGAGTCTTTATAAAGTTTCTTGTGTTTTCTCTGTAACTAGCCTGTAAGCTCTGTGGGCAGAGATGCATTGCATGCTGTCCCCTTCCTACTCCAAACAGCACCAA-GCTTCATGTCTGTACGGCTTAATCGTGACTGTCAACCAGATGGGACAAAGTCTGTCTATGAAAACAA--------------------ATGTCTGTGAGGGACATCAGGCTAACTGAGGTTTGAAGACACACTCTAAATTTGAGTGGCACCAATCTATGGGCttgtgagct-gGaat---aagcaaggagaa---agtgagctgagccccagcattc
+s	Phodopus_roborovskii.JAEOAF010000031.1	16486007	437	+	29770300	CA----------AGTACTTACTTGAT----AC--AGGACAATAAAATCCTAGCATAGGCTATCATGAAGTTATGTGACAAGATGATAAAGCATGGGTGGAAAGGAG-CCATGTC---ATGTTCAGG-GGCATTT-ACATGCTGTTGGCA---------GTGATCGTTGAGTCTTTATAACGTTTCCTGTGTTTTCTCTGTAACTAGCCTGTAAGCTCTGTGGGCAGGAATCCATTGCATGCTGTCTCCTTCCTACTCCCAACAGCACCAA-GCTTCATGTCtgtaaggcttcatcgtgactgtcaaccagatggaataaagtctgtctatgaaaacaa----------ATATCTGGGGatgtctgtgagggacatcgggctaactgaggttggaagacccactctaaAtctaagtgacaccaatct-tgggcttgtgagct-gGaat---aaacaaggagaa---agtgagctgagccccagcattc
+s	Cricetus_cricetus.OZ199631.1	140166359	437	-	205530201	CA----------AGTACTTACT---T-GACAC--AGGACAATAAAATCCTAGCATGGACTATCATCCAGTTATGTGACAAGATGATAAGGTATGGGTGGAAAGGAACCCAAGTC---ATTTTCGGG-GACACTTAACATGCTATTGGTA---------GTGATTG-TGAGTCTT--TAAAGTTTCTCATGCCTTCTCTGTAACTAGCCTGTAAGCTCTGTGGGCAGGACTGCATTGCATGCTGTCTCCCTCCTACTCCTAACAGCACCAA-GCTTCCTGTCtgtgaggcttaatcatgactgtcaaccagacgggataaagtctgcctatgaaaacaa----------ATGTCTGGGCatgtctgtgagggacatcatgctaattgaggttggaaggcccaccctaaAtctgagtgacaccaatccatgtgctggtgtgct-gGaat---gaacaaagagga---agtgagctgagatccagcattc
+s	Cricetulus_griseus.NC_048598.1	130954973	1	-	193770019	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------c
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6038233	79	-	8539717	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTAAGCCTGAGTTAcaccaatccatgggctggtgtgct-aGaat---gaa---acaggagaaagtgagctgagctccagcattc
+s	Arvicola_amphibius.NC_052058.2	72668397	79	-	166747489	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctctaaAcccgagttacaccaatccatgggctggtgtgct-gGaat---gag---aaaggagaaagtgagctgagccccagcagtc
+s	Microtus_pennsylvanicus.CM073176.1	20976027	78	+	113485825	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ccctaaAcctgagttacaccaatccatgagttggtgtgct-gGaat---gag---aa-ggagaaagtgagctgagccccagcatgc
+s	Microtus_arvalis.JAHRII010002323.1	111060630	76	+	200229077	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctctaaAcctgagttacatcaatccatggactg---tgcc-gAaat---gag---aaaggagaaagtgagctgagccccagcatgc
+s	Neotoma_floridana.CM113793.1	27921840	432	-	95303938	CA----------AGCACTTACT---T----ACATAGGACAATCAAATCCTATCATGGACTATCATGAAGTTATATGACAAGATGATAAGGCATGGATGGAAAAGAGTCTGCATC---ATATTTTGG-GGCACTC-ACATGCTGCTGGTA---------GC----------TCTT--TAAATTTTCTTGTGTCTTCTCTGTAACTAGCCTGTAAGCTCTGTGGGCAGGACTGCATTGCATGCTGTCTCCTTCCTATTCCCAATAGCACCAA-GCTTCATGTCtgtgaggcttaatcttgactgtcatccagatgagataaagtctgtctgtgaaaacaaacgtctgggg----------atgcctgtgagggagatcaggctaatggaggatgggagacccgccctaaAtctgaagggcaccaatccatgggctgctctgct-gGaatATAgagaaaaaaccagaaagtgagctgagtcccagcattc
+s	Onychomys_torridus.LR877198.1	72220594	423	+	93020901	CA----------AGTACTTACT---T-G--ACATAGGACAATAAAATCCTATCATGGACTATCATGAAGTTATGTGACAAGATGATAAGGCATGGGTGGAAAGGAGT--G---T---ATATTTTGG-GGCCCT--AAATGCTGCTGGTA---------GC----------TCTT--TAAATTTCCTTGTGTCTTCTCTGTAACTAGCCTGTAAGCTCTGTCCTCAGGGCTGCCCTGCGTGCTGTCTCCTTCCTGCTCTCAAGGGCACCAA-GCTTCAGGTCtgtgaggcttaatcttgactgtcaacaagaagggataaagtctgtctatgcaaacaaacatctgggg----------atggctgtgagggagatcaggctaatggaggttggaggacctgccctaaAtctgagtggcaccattctatgggctggtgagct-gGaat---gaacaaaaaa-aggaagggagctgagccccagcattc
+s	Peromyscus_californicus.VALE03000237.1	12778653	427	+	80346014	CA----------AGTACTTACT---T-G--ACATAGGACAATAAAATCTTGTCATGGACTATCATGAAGTTATATGACAAGATGATAAGGCATGGATAGAAAGGAGTCTG---T---ATATTTTGG-GGCCCTT-ATATGCTGCTGGTA---------GC----------TCTT--TAAATTTCCT-GTGTCTTCTCTATAACTCGCCTGTAAGCTCTGTGGGCAGGCCTACATTACGTGCTGTCTCCTTCCTGCTCCCAAAAGCACCAAAGCTTCATGTCTGtgaggcttaatcttgactgtcaaccagaagggataaagtctgtctatgaaaacaaatgtctgagg----------atgtctgtgagggagatcaggctaatggaggttggaaggcctgccctaaAtctgagcggcaccattccatgggctggtgagct-gGaat---aaacaaaaaggagaaagtgagctgggtcccagtattc
+s	Peromyscus_maniculatus_North.CM113205.1	35699341	427	+	104458120	CA----------AGTACTTACT---T-G--ACATAGGACAATAAAATCCTATCATGGACTATCATGAAGTTATGTGACAAGGTGATAAGGCATGGATGGAAAGGAGTCTG---T---ATGTTTTGG-GGCCCTT-ACATGCTGCTGGTA---------GC----------TCTT--TCAATTTCCTTGTGTCTTCTCTGTCACTCGCCTGGAAGCTCTGTGAGCAGGGCTGCATTACGTGCTGTCTCCTTCCTGCTCCCCAAAGCACCGAACCTTCATGTCtgtgaggcttaatcttgactgtcaaccagaagggataaagtccgtctatgaaaacaaatgtctgagg----------atgtctgagagggagatcaggctaatggaggttggaaggcctgccctacAtctaagcggcaccactccatgggctggtgagct-g-aat---gaacaaaaaggagaaagtgagctgagtcccagtattc
+a
+s	Mus_musculus.CM000994.3	125889557	280	+	195154279	gtt-ctgcctgcttcctgactgtggatgccaagtgaccagctgtctctcatgctggctgccatgccttcttcaggatgaactgtgtccctccagac--atgtgagt---------------------gcaaaac------------accctccctccctccct-ccctccctccctctcccttccttctttaggatgcttttcttag---c--ttttgttacagtattcagaaaagtgacAATTCATAGAGAGTCTTCAACAGGTCCTCACCAAGCA-----CTTATGGAATCATAGCAGGC------------T-AA-A-----------TG----GGCTAAAAATCCTCCTCCT
+s	Rattus_norvegicus.CM070403.1	39970935	170	+	109350286	-----------------------------------------------------------------------------------------------------------------------------------------------------ctcccttcctctttAttttccctccc---cccttcttcccttaggttgctttccttag---cCAttttgtcacagtaaccagaaaagtgacAACTCAC--AGAGTCTCCAACAGATCCTCACCAAGCG-----CCCATGGAATCACAGCAGGCAGAGGAGTCACTT-AA-A-----------AG----GGCTAAAAATCC-------
+s	Phodopus_campbelli.chr12	18453724	270	-	32442325	acaGctccctgcttcctggctgcggatggcatgtgaccagcttcctcctgttcttgctgccatgccctcctcatgatggactgtattcctttggaaCTctg--agtAAAGCAACAACCACAACAACAacaacaa------------g--c-----------------------------TCTTTGTCCTTTAAGTTGCTGA--GTCA-GCA--CTTTGTCCCTGTACTCAGAAAAGGGACA-TTCATAGTGAGTCTCCTTCGGGTCCTCACCAGGCA-----CACA--GGATTGTGGCGGGCAGGGGATTCACTT-AG-CT----------CC----TCCT-----CCG-------
+s	Phodopus_sungorus_new.chr12	17335144	282	-	31225933	acaGctccctgcttcctggctgcggatggcatgtgaccagcttcctcctgttcttgctgccatgccctcctcatgatggactgtatccctttggaaCTctg--agtAAAGCAACAACAACAACAACAacaacaaCAACAACAACAAg--c-----------------------------tctttgtcccttaagttgctta--gtCA-GTA--CTTTGTCACTGTACTCAGAAAAGGGACA-TTCATAGTGAGTCTCCTTCGGGTCCTCACCAGGCA-----CACA--GGATTGTGGCGGGCAGAGGATTCACTT-AA-CT----------CC----TCCT-----CCG-------
+s	Phodopus_roborovskii.JAEOAF010000031.1	16486444	261	+	29770300	attGctctctgcttcctggctgtggatggcccgtgaccagcttcc-cccattcttgctgccgtgtcctcctcctgatggactctatcactttggaa--ctg--agtAAAACAACAA-------CAAA-----aa------------g--c-----------------------------tctttgttccttaagttgcttt--gtca-GTa--ttttgtcactgtactcagaaaAGGGGCAGTTCATAGTGAGTCTCCTTCAGGTCCTCATCAGGTCCTCATCACA--GAATTGTGGCAGGTAGAGGATTCACTT-AA-AT----------CC----TCCT-----CCT-------
+s	Cricetus_cricetus.OZ199631.1	140166796	266	-	205530201	attGctctctgcttcctgattgtggatgccatgtgaccacctgcctcctattcttgctgctatgcctttcccatgatggactgtatccttttggaa--ctgtgatgT---AAAAAACA--AAGCAAAacaaaac------------a--c-----------------------------acttggtttcttaagttgcttt--gtga-GTa--gtttgtcactgtaatcagaaaagGGAGAGTTCATAGTGAGTCTCCGACAGGTCCTCACCAAGCA-----CACA--GAGCGGGGGCAGGGAGAGGATTCACTT-AA-AA----------CC----TCCT-----CCT-------
+s	Cricetulus_griseus.NC_048598.1	130954974	265	-	193770019	attGctctctgcttcctgactgtggatgccatgtgaccacctgcctcctattcttgctgccatgcctttcccatgatggactgtatccctttggaa--ctgtgaggTAAAAAC----A--AAACAAAacaaaac------------a--c-----------------------------actttgtttcttaagttgcatt--gtga-GTa--ttttgttactgtaatcagaaaagGGACAGTTCATAGTGAGTCTCCGACAGGTCCTCACCAAGCA-----CACA--GAGTGGTGGCAGGTAGAGGATTCACTT-AA-AA----------CC----TCCT-----CCT-------
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6038312	259	-	8539717	actGctctctgcttcctgactgtgg-tgccatgtgactagccagctcctactcttgctgctgtgccttccccatgacaaactgtgtccctctggaa--ctgtgagtTCAAAAACAG-------GAAAggaaaaa------------a--a-----------------------------ccttccctccttaaggttcttt--gccaGGTa--ttttgtcatggtagtcagaaaagtgacaattcATGGCAAGTCTCCATCAGGTCCTCACCAAGCA-----CACACGGAACTGTGACCGGT------------------AGAGGACATGC-C----TCCT-----TTT-------
+s	Arvicola_amphibius.NC_052058.2	72668476	265	-	166747489	actGctctctgcttcctgactgtgggtgccaagtgactagccagctcctactcttgctgtcatgccttccccatgacagactatatccccctaaga--ctgtgagtTCAAAAA----A--AAGAAAAggaaaaa------------a--c-----------------------------ccttccctccttaaggtccttt--gccaGGTa--ttttgtcatggtagtcagaaaagtgacAACTCATGGTGAGTCTCAATCAGGTCCTCACCAAGCA-----CACACAGAATCGTGGCAGGA------------------AGAGGATTCGC-TTAAGTCCT-----TTT-------
+s	Microtus_pennsylvanicus.CM073176.1	20976105	241	+	113485825	actGctctctgcttcctgactgtgggtgccatgtgaccagccagctcctactcttgctgtcatgccttccccatgacagacgatttccccctagaa--ctgtgagtTCAAAAAGAG-------AAATggaaaaa------------a--c-----------------------------ccttccctccttaaggtcgttt--gccaGGTa--ttttgtcacggcagttagaaaagtgacAGTTGATGGCAAGTCTCCATCAGGTCCTCACCAAGCA-----CACACAGAATTGTGGCAGGC------------------------------------------------------
+s	Microtus_arvalis.JAHRII010002323.1	111060706	260	+	200229077	actGctctctgcttcctgactgttggtgccatgtgaccagccagctcctactcttgctgctgtgctttccccatgacaaactgtgtccccctagga--ctgtgagtTCAAAAAAAG-------AAAAgaaaaaa------------a--c-----------------------------ccttgcctccttaaggtccttt--gccaGGTa--ttttgtcacggtagttagaaaAGTGACAGTTCATGGCAAGTCTCCATCAGGTCCTCACCAAGCA-----CACACAGAATTGTGACTGGT------------------AGAGGATATGC-C----TCCT-----CTT-------
+s	Neotoma_floridana.CM113793.1	27922272	255	-	95303938	attGctctctgcttcctgactgcagatgccgtgtgaccagct----------------gccacgccttccccatgatggactctatccctctggaa--ctgtgagtTCAAAAACAACA--AACAAACaaacaaa------------g--c-----------------------------ccttccttccttaagctgcctctgtcag-GTa--ctttacgactgtaaccagagaagTGATGGTTCATGGGGAGTCTCCA--AGGTTGTCCCCAAGCA-----CATACAGAATTGTGGCATGCAGTAGATTCACTTAAA-T-----------TC----TCCT-----CCT-------
+s	Onychomys_torridus.LR877198.1	72221017	244	+	93020901	attActctctgcttcctgactgtggaggccatgtgaccagctgcctcctactctttcagccatgccttccccatgatggactgcattcctgtggaa--ttg--agtCCCAAAACAGCA--AACAAACaaa---g---------------t-----------------------------ccttccttccttaagctgccttcatcag----------gtcactgtaaccagaaaagtgacGGTTCATGGGGAGTC---------------ACAAGCA-----CACATAGAATCATGGCAGGCAGAGGATTCACTT-AA-T-----------CC----TCCT-----CCT-------
+s	Peromyscus_californicus.VALE03000237.1	12779080	263	+	80346014	attActctctgcttcctgactgtggaggccatgggaccagctgcctcctgctctttcagccacgccctcctcatgatggactgtgtccctgtggaa--ctgtgagtTCAAAAACAACA--AACAGACaaaccaa---------------t-----------------------------ccttccttccttaagctgccttcgtcag----------gtcactgtaaccagaaGAGTGATGATTCATGGGGAGTCTCCA--AGGTCGTCCCCAAGCA-----CACACAGAATCATGGCAGGCAGAGGGTTCACTT-AAAT-----------CC----TCCT-----CCT-------
+s	Peromyscus_maniculatus_North.CM113205.1	35699768	259	+	104458120	attActctctgctacctgactgtggaggccacgtgaccagctgcctcctcctctttcggccacgccttccccatgatggattggatccctgtggaa--ctgtgagtCCACAAACAACA--AAGAAACaaacaaa---------------g--------------------------------tccttccttaagcggcctttgtcag----------gtcactgtcaccagaagagtGCTGATTCATGGGGAGTCTCCA--AGGTCGTCCCCAAGCA-----CACACAGAATCATGGCAGGCAGAGGATTCACTT-AA-A-----------CC----TCCT-----CCT-------
+a
+s	Mus_musculus.CM000994.3	125889837	333	+	195154279	ACCCACATTTCCTTTCCTAAAGTGTATTCAGGTCAGCAATGAAAGTTCTCCAAAGGCAACTGCCTGGGGACAGAAAGACAGCAATGCACATGGATCCTCAGGATGCCACTGCAAACACAGGACCACCCTTTACTTGCATGTGGACCTGAGGAACCTTTGTAATTAATCACCCCTTAAGCTGAATGACTGATGTAGGAAACGCTAGACAGGGGTGAGAGCCTCAGGCCAGTCAGTTAATCACATCA-AGAAGAAATGGAGATAAATTCATCTTACCC-ACTTAGCAATTACCTCATTCACACTTGCCAAT-AAAAGAAACTAATTGTTCTGCCCTTT
+s	Rattus_norvegicus.CM070403.1	39971105	325	+	109350286	ACACACATTCCCTTTCCTTGTATGTGTTCAGGTCAGCAATGAAAGTTCTCCAAAGGCAATCACACAGGGACAGAAGGACAGCATGCC-CATGAGTCCTCAGGATGCCACCGCAAAGAAAGGATCCGCCTTTACTTGCATGTG-------GGATTCTTTATAATTAATCATACCTTATGGTAAATGACTGATGTAGCAAATTCTAGACAGGGGTGAGAGCCTCAGGCTACTCAGTTAATCACATCA-TGAAGAAATGGAGATAAATTCATCTTACCC-AGTTACCAATTACCTCTTTCACAGTTGCCAAT-AAAAGAAACTAATCGTTCTGCCCTTT
+s	Phodopus_campbelli.chr12	18453994	318	-	32442325	GC-CATGTTTCCTTTTCTTGAGTGTCTTCAGGTTAGTAATGAAAGCCCTGCAAAGACAATTACACCGGGACAGGAGGACAGAATACC-CGTGAATCCTCAGGATGCCCGGGCAAACATAGGGCCTCCTGTCACTTGCATGTGGGCCAAAGAAGCATTTGTAATTAATTGTACTTGATGGTGAATGACTAATGTAGCGAACTCTAGACAGGGGTGAGAGCTTCAGGCCAGC--------------AATGAAGCAATGGAGATAAATTCATCTTACTC-AGTTACCAATTACCTCTTTCATACTTGGCAAT-AAAATAAACTGATTGTTATGCCCTTT
+s	Phodopus_sungorus_new.chr12	17335426	318	-	31225933	GC-CGTGTTTCCTTTTCTTGAGTGTCTTCAGGTTAGCAATGAAAGCCCTGCAAAGACAATTACACCAGGACAGGAGGACAGAATACC-CGTGAATCCTCAGGATGCCCGGGCAAACATAGGGCCTCCTGTCACTTGCATGTGGGCCAAAGAAGCATTTGTAATTAATTGTACTTGATGGTGAATGACTAATGTAGCGAACTCTAGACAGGGGTGAGAACTTCAGGCCAGC--------------AATGAAGCAATGGAAATAAATTCATCTTACTC-AGTTACCAATTACCTCTTTCATACTTGGCAAT-AAAATAAACTGATTGTTATGCCCTTT
+s	Phodopus_roborovskii.JAEOAF010000031.1	16486705	319	+	29770300	GCACGTGTTTCCTTTTCTTGAGTGTCTTCAGGTTAGCAATGAAAGTCCTGCAAAGGCAATTACACCGGGACAGGAGGACAGAATACC-CGTGAATCCTCAGGATGCCTGGACAAACAAAGGGCCTCCCTTTACTTGCATGTGGGCCTAAGAAGCATTTGTAATTAATTGTACTTGATGGTGAATGACTAATGTAGCGAACTCTAGACAGGGGTGAGAGCTTTAGGCCAGC--------------AATGAAGCAATGGAGACAAATTCATCTTACTC-AGTTACCAATTACCTCTTTCATACTTGGCAAT-AAAATAAACTGATTGTTGTGCCCTTT
+s	Cricetus_cricetus.OZ199631.1	140167062	318	-	205530201	GTGCATGTTTCCTTTTCTTGTGTGCCTTCAGGTTAGCAATGAAAGTCCTGCAAAGGCAATTACA-CAGGACAGAAGGACAGAATACC-CACAAATCCTCAGGATGACAGTGCAAACAAATGGCCTCCCTTTACTTACATGTGGGCCTAAGAAGCATTTGTAATTAATTGCACTTGATGGTGAATGACTAATGTAGCAAACTCTAGACAGGGGTGAGAGCTTCAGGCCATC--------------AGTGAAGCAATGGAGATAAATTCATCTTACCC-AGTTACCAATTACCTCTTTCATACTTGGCAAT-AAAATAAACTGATTGTTCTGCCCTTT
+s	Cricetulus_griseus.NC_048598.1	130955239	319	-	193770019	GTGCATGTTTCCTTTTCTTGTGTGCCTTCAGGTTAGCAATGAAAGTCCCGAAAAGGCAATTACACAGGGACAGAAGGACAGAATACC-CACGAATCCTCAGGATGACAGTGCAAACAAATGGCCTCCCTTTACTTACATGTGGGCCTAAGAAGCATTTGTAATTAATTGCACTTGATGGTGAATGACTAATGTAGCAAACTCTAGACAGGGGTGAGAGCTTCAGGCCATC--------------AATGAAGCAATGGAGATAAATTCATCTTACCC-AGTTACCAATTACCTCTTTCATACTTGGCAAT-AAAATAAACTAATTGTTCTGCCCTTT
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6038571	314	-	8539717	GCACACATTTCCTTTCCTTGTGTGTCTTCAGGTT--------------------GGCAGTTACATAGGGACAGAAGGACAGCATAAC-CAAGAATCCTCAGGATAACACTGCAATCAAAGGGCCTCTCTTTATTTGTATGTGGGCCTAAGAAGCATTTGTAATTAATCACACCTGATGGCAAATGACTGATGTAGGAAACTCTAGGCAGGGGTGAGAGCTTCAGGCTAGCCAGTTAATCACAGCAATGAAGAAACAGAGATAAATTCATCTTACCC-AGTTACCAATCACCCCTCTCACACTTGGCGATAAAAAGGAACTGATTGTTCTGCCTGTT
+s	Arvicola_amphibius.NC_052058.2	72668744	313	-	166747489	ACACACATTTCTTCTCCTTGTGAGTCTTCAGGCT--------------------GGCAGTTACATAGGGACAGAAGGACAGCAGACC-CAAGAATCCTCAGGATACCACTGCTATCAAAGGGCCTCTCGTTGTTTGCATGTGGGCCTAAGAAGCATTTGTAATTAATCACACCTGATGGCAAATGACTGATGTAGCAAACTCTTGGCAGGGGTGAGAGCTTCAGGCCAGCCGGTTAATCACAGCAATGAAGAAACGGAGATGAATTCATCTTACCC-AGTTACCAATCACCTCGTTCACACTTGCCGAT-AAAAGAAACTGATTGTTCTGCCCTTT
+s	Microtus_pennsylvanicus.CM073176.1	20976356	287	+	113485825	--------------------TGAGTCTTCAGGTT--------------------GGCAGTTACATAGGGACAG-AGGACAGCAGACC-CAAGAATCCTCAGGATAG------GATCAAAGGGCCTCTCGTTATTTGCATGTGGGCCTAAGAAGCATTTGTAATTAATCACACCCCATGGCAAATGACTGATGTAGCAAACTCTAGGCAGGGGGGAGAGCTTCAGGCCAGCCAGTTAATCACAGCAATGAAGAAACAGAGATAAATTCATCTTACCCCAGTTACCAATCACCTCTTTCACACTTGGCAAT-AAAAGGAACTGATTGTTCTGCCTGTT
+s	Microtus_arvalis.JAHRII010002323.1	111060966	306	+	200229077	GCACACATTTCCTTTCCTTGTGAGTCTTCAGGTT--------------------GGCAGTTACATAGGGACAG-AGGACAGCAGACC-CAAGAATCCTCAGGATTG------GATCAAAGGGCCTCCCTTCATTTGCATGTGGGCCGAAGAAGCATTTGTAATTTATCACACCCAATGGCAAATGACTGATGTAGCAAACTCTAGGCAGGGGTGAGAGCTTCAGGTCAGCCAGTTAATCACAGCAATGAAGAAACGGAGATGAATTCATCTTACCC-AGGTACCAATCACCTCTTTCACACTTGGCAAT-AAAAGGAATTGATTGTTCTGcccatt
+s	Neotoma_floridana.CM113793.1	27922527	333	-	95303938	GCACACGCTGCCTTTTCTTGTGTGTCTTCACATCAGCAATGAAAGTCCTCCACAGGCAAATACATAGGGACAGAAGGACAGCATACT-CATGCATCCTTAGGATGCCAGTGCAATCTAAAGGCCCCCCTTTACCTGCAGGTGTACCTAAGAAGCATTTGCAATTAATCGCACCTGATGGTGAGTGACTGATGTAGCAAACTCTCGACAGGGGTGAGAGCTTCAGGCCGGGCAGTTAATCATGGCAATGAAGAAATGGAGATAAATTTATCTTACCC-AGTAACCAATTGCCTCTTTCACATTTGGCAAT-AAAAGAAACTGATTGCTCTGCCCTTT
+s	Onychomys_torridus.LR877198.1	72221261	332	+	93020901	GCACCTGTTGCCTTTTCTTGTGTGTCTCCAAGTCAGCAATGGACGTCCCCTACAGGTAATTACACAGGGACAGAGGAACAGCACAGC-CACACGACCTCAAGATGCCAGTACAAACTAAAGGCCTC-CTTGCCCTGCATATGTGCCTAAGAAGCATTTGTAATTAATCGCACCTGATGGTGAGTGACTGATGTAGCAAACTCTAGACAGGGGTgagagcttcaggccagccagttaatcacagcaAtgaagaaatggagacaaattcATCTTATCC-AGTTACCAATGGTGTCTTTCACACTTGGCAAT-AAAAGAAACTGATTGCTCTGCCCTTT
+s	Peromyscus_californicus.VALE03000237.1	12779343	332	+	80346014	ACACATGCTGCCTTTTCTTGTGTGTCTTCAAGTCAGCAATGAAAGTCCCCCACAGGCAATTGCACAGGGACAAAAGGACAGCGCAGC-CATGCATCCTCAAGATGCCGGTGCAAACTAAAGGCCTC-CTTTTCCTGCTTGTGTGCCTAAGAAGCATTTGTAATTAACCGCACCTGATGGTGAGTGACGGATGTAGCAAACTCCAGACAGGGGTGAGAGCTTCCGGCCAGCCagttaatcacagcaAtgaagaaatggagacaaattcaTCTTATCC-GGTTAGCAATGGCCTCTTTCACACTCGGCAAT-AAAAGCAACTGATTGCTCTGCCCTTT
+s	Peromyscus_maniculatus_North.CM113205.1	35700027	332	+	104458120	GTACACGCTGCCTTTTCTTGTGTGTCTTCAAGTCAGCAATGAAAATCCTCCACAGGCAATTGCACAGGGACAGAAGGACAGCGTAGC-CATGTATCCTCAAGATGCCGGTGCAAACTAAAGGCCTC-CTTTCCCTGCATGTGTGCCTAAGAAGCATTTGTAATTAACCACACCTGATGGTGAGTGACGGCTGGAGCCAACTCCAGACAGGGGTGAGAGCTTCCAGCCAGCCAGTTAATCACAGCAATGAAGAAATGGAGACAAATTCATCTTATCC-GGTTACCAATGGCTTCTTTCACACTCGGCCAT-AAAAGCAACTGATTGCTCTGCCCTTT
+a
+s	Mus_musculus.CM000994.3	125890170	1154	+	195154279	ATCTTTTTAATATGAAAGTGATTTAAGACAACTGTAAAGCCAAGTTTTTTTTTTTTaaatgggctagggatgcagctctgtggtagagcactggcccagcaagcatgaggtcttgt-tttattctacagg-at----cacacatacacagaCCACACTCCCACAGCACACATAAGGCACACA-----------GTAGATCCACTGTAGACAACACATGGT------------------------GTGTACACAACAGATGAGCAGCAGGCACACAACAGATGTATACAACATAG-------------CACAGAAACAATGAATAAATGTAATAGACATATACATAACATGAacacaacacacata--tac-cattcacaccg-cacacactc-aagacattcattgtacacacaatatacacaacagataca--TATAACA--G--ATATTCAAC--AGAT--ATATAAC-ATACAATAAGTGTAGCACACACAAACAAAA---TTAGAAAAACACTCATATAAAAATTAC-----------------------ATAAATAAAACAAAATTACATATATAAAACAAAAACTA--CTGTGTACTCATATGTAAAG-ATCAAA-----AGCAAAGCACAAAGTCACTAGAAGAACTGTGACGTTTTAAAAATTAACTCAGGAATAGGGAAGCTTTTGGTTCAAAACAACTGGTGTTTGACCATTATAAAAATAAAACGTATACAAGCATGAACTTCCCATGTG-ATATCATAAGCAAATGGAGGTCCCTGCACGAAAAATGAAGG-AGGGGA-AATCCTCCCTAACTCTGAAGAGATTCTGGAAACCATGATGACACAGACTAACAAGACGAGTGAAAACTCAGTCAC------CAGCAGAAGGTTCACAGG--GAGGAATACAG-CCATCTCTGTGTACACATTTGAGGGTGG-TTCCAGAGATGA-----CTACATCGTCAGGACTCTGA-CCACTAAATCCTTTACTCCATTGATTGCCACATCACTGAAATAGATTATCAGGAAGTGGGAAAACTGAGGAAAAAGGGAGAAGATTGAAGGCAGTTGGTCAGCAGGT-A-GG-G-CGCACGCCCAAGGGCAATATCTTGCCCTTTCCTGTTGTGGCTCCTCTCTGCTCCATGCCTACCAAGATATGAGCT----CCTCTATTTG-----------TCTCCTCcatggactgaatcccctgaaaccaa-gagcaaagtcaatccattctccct-------------taagttgttcccattgg---------cta-tttc--gttacagGT--A
+s	Rattus_norvegicus.CM070403.1	39971430	1107	+	109350286	ATCTTTTTAATATGAAAGTGATTTAAGACAATTGCAAAGCCAAGTTTTTTTTTT---AATAggctagggaggcaactttgtggtagagcactcacccagcaagcatgagcccttgtGtttattctacagg-at----caca-atacacagatTACA--TCCACAGCATGCATAATGCACACA-----------ATAGATCCACTATAGACAACACACGAT------------------------GTATACATAACACCCATACCACAGATACACAACAGATGTATACAACATAGTTAACACAGAAACAGCAA----------------------------ACATAACATTCACACGAC--------------------------------------ACATTCAATATACACTCAACATACACAAAAGACACT--CATAACC--G--ATACAGAAC--AGAT--GTATAAC-ACACAACACTTGTAACAAACAC--ACAAAA---TT---AAAACACTCATACAA-AATTATTATTCTCACACAACACACAGCATATACACAAAACACA--TG--TCTGTAAGGCAAAAACTA--CTTTGCATTCCTATAAAAAG-ATAAAA-----TCCAAGGCACAAAGATTCTAGAAGAACTGTTAAGTTTTAAAAACTAACTCAGGAATAGGGCAAAGTTTGGTCTGAAACAGTTGGTGTTTGACCATGATAAAAATAAAACATGTACACGCATGAACTTCCTATGTG-ATGTCATAGGCAAATGGAGGTCCCTCTATGATACATGAAGG-AGGGGA-AACCCTTCCTGACTCTGAAGAGTTTATAGAAACTGTGATGACACAGACTAACAAGGCAAATGAAAACTCAGAGAC------CAAAAG-ATGTTCACAGA--GAGGAATACAG-CTACCTCTGTGTATATATTTGAGGGCGG-TTCTTGAGATGA-----C-ACATCATCAGGACTCTGA-CCACT-----CTTTACTCCATTGATGGACTCAGCACTGAAATAGATTATCAGGAAGTGGGGCCACTCGGGAAGATGGGAGCAGATTGAAGGTAACTGGTCAGCAGGT-A-AG-G-GGCACGCCCAACGGCAATATTTTGCCCTTTCCTGTTACGGCTCCACTCTGCTTCCTGCCTACCAAGATATGCgct----gctctatctg-----------tctcctccatgggctgaaacccctgaaaccat-gagcaaagtaaatctgttctccct-------------taagttgttcccattgg---------cta-tttt--gttacagGT--A
+s	Phodopus_campbelli.chr12	18454312	1133	-	32442325	ATCTTTTTAATATGAAAGTGATTTAAGACAActgca--------------------------------g------cccagtggtagagcatttacccagcGAGTATGAGGCCGTAGGTTTATTCTACAGT-AT----CACACATACACAGGAAACACACCCAC---------AA--CACACATAAGACATGCAATAGACATACTGCAGACAACATGTGAC------------------------ATGTACACAACA-----------ATCATACAACAGATATACACAACATAGACAACAC-AAAGCAGTAGAAACAACAGACGTACATACCAGACATATatgtaacatgcacacaacaca----CAtaa-cattcacacaa-cacatacta-gagaaatATAATACACATAGAACATATACAACAGA--CACATATAATA--G--ATACAGAAC--AGAT--ATATAAC-ACACAACACTTGCAACAGACAC--ACACAAAACCC---AAAACA----TACAATAATCACAGCTCTCATACAATATATAGCACACATAAAATACACA--TACATACCCAG--GAAAAATTA--CTTTGTATTTATATATAAAG-ATAAAA-----CCTAAAGCACAAAGATACTAGGAGAATTATGGAACTTTATAAATTAATTTGCGAATAGAAGAGAGTTTGGTCAGAAGTAATCGATGTTTGACCATTATAAAAATAAAACATACACAAACAAGAACTTCTCATGTA-AAGTCATAGGCAAATGGAAACCCCTGTATGGCAAATGAAGG-AGGGAATAACCCTCCCTGACTGTGAAGAATTTATTGAAACTCTGATGACAAAGACTAACAAGGC-AGTGCAA--------ACAGTCACCAGCAGAAGGTTCATAGACACAGGCACGCAGGCCACGTCTGTGTGCACCTGTGAGGGAGG-TTCCAGCGATGA-----CGACATC-TCAGGACTC-GAGCCAGTGGAAGGTTTACTCTACTGACTGACTCAGCATTGGAACAGATTACTGGGAAGTGACAGAACTGGAGATAATGGAACCAGATTGGAGGTAGCTGGTC-GGGGGT-A-AG-GGGACATGCCTACGGGCAGTATCTTG----------TTAGGGTTCCACTCTCCTTCCTGCTAACCATGATATGAGCT----GCTCTATCTGCCAGACCCTCACCTCCTTCATGGTCTGAAACCTCTAAAACCAT-GAGCAAAGTAAATACATTCTCCTTTAAGTTGTTCACAT-------------TAG---------CTA-TTTTT-GTCACAGGTGCA
+s	Phodopus_sungorus_new.chr12	17335744	1130	-	31225933	ATCTTTTTAATATGAAAGTGATTTAAGACAactgca--------------------------------g------ctcagtggtagagcatttacccagcaagtatgaggccgtagGtttattctacagt-at----cacacatacacaggaaacacacccac---------aa--cacacaTAAGACATGCAatagacatactgcagacaacatgtgac------------------------atgtacacaaca-----------ggcatacaacagatatacacaacatagACAACAC-AGAGCaatagaaacaacagacatacataccagacatatatgtaacatgcacacaacaca------taa-cattcacacaa-cacatacta-GAGACATATAATACACACAGAACATATACAACAGA--CA--TATAATA--G--ATACAGAAC--AGGT--ATATAAC-ACACAACACTTGCAACAGACAC--ACACAAAACCC---AAAACA----TACAATAATTACAGCTCTCATACAATATATAGCACACATAAGATACACA--CACATACCCAG--GAAAAATTA--CTTTGTATTTATGTATAAAG-ATAAAA-----CCTAAAGCACAAAGACACTAGGAGAATTATGGAACTTTATAAATTAATTTGCGAATAGAGGAGAATTTGGTCAGAAGTAATCGATGTTTGACCATTATAAAAATAAAACATACACAAACAAGAACTTTACATGTA-AAGTCATAGGCAAATGGAAACCCCTGCATGACAAATGAAGG-AGGGAATAACCCTCCCTGACTGTGAAGAATTTATTGAAACTCTGATGACAAAGACTAACAAGGC-AGTGCAA--------ACAGTCACCAGCAGAAGGTTCATAGACACAGGCACGCAGGCCACGTCTGTGTGCACCTGTGAGGGAGG-TTCCAGAGATGA-----CGACATC-TCAGGACTC-GAGCCAGTGGAAGGTTTACTCTACTGACTGACTCAGCATTGGAACAGATTACTGGGAAGTGACAGAACTGGAGATAATGGAACCAGATTGGAGGTAGCTGGTC-GGGGGT-A-AG-GGGACATGCCTACGGGCAGCATCTTG----------TTAGGGTTCCACTCTCCTTCCTGCTAACCATGATATGAGCT----GCTCTATCTGCCAGACCCTCACCTCCATCatggtctgaaacctctgaaaccat-gagcaaagtaaatacattctccttTAAGTTGTTCACAt-------------tag---------ctt-ttttTTGTCACAGGTGCA
+s	Phodopus_roborovskii.JAEOAF010000031.1	16487024	1036	+	29770300	ATCTTCTTAATATGAAAGTGATTTAAGACAACTGCAAAGGCAATT-----------------GTTGAG------------------------------------ATGAGGCCGTGTGTTTATTCTACAAT-AT----catacatacacaggaaacacatccac---------aacacacacaCAAGATATGCAatagacacactgtagacaacatgtgac------------------------atgtagacaata-----------ggcatacaacagatatacacagcatagATAACAC-AAAGCaacagaaataacaga-atacataccagatatacatgtaacatgcacacaacaca----CAtaa-cattcacctaa-cacatacta-gagacatataatatacacacaacatatacagcaga--c----ataata--g--atacagaac--agat--atataac-actca-------------acac--acacaaAACcc---aaaaca----tacaataatcaaAGCTCTCCTACATTATACAGCATacataagatacaca--tacatacccaG--GAAAAATTA--CTTTGCATTTATATATAAAG-ATAAAA-----CCTAAAGCACAGAGATAGTAGGAGAATTGTGAAACTTTATAAATTAATTTGTGAATAGAGGAGAGTTTGGTCAGAAACAATTGATGTTTGACCATCATAAAAATAAAACATACACAAACATGAACTCCACATGTA-ATGTCACAGGCAAATGGAAAGCCCTGTATGACAAATGAAGG-AGGGAATAAGCCTCCCTGACTGTGAAGAACTTATTGAAACTGTGATGACAAAGAATAATAAGGCAAGTGGAAACCCAATGACAGTCACCAGCAGAAGGTTCATAGACATAGGCATACAGGCCACATGTGTGTGCAT-----------------------------------------------------------------------CTGGCTGACTCAGCATTGGAATATATTGCTGGGAAGTTGGAGAAGTGGAGATAACGGGACCAGATTGGACGTAGCTGGTCAGGGGGT-A-AG-GGGACATGCCTAAAGGCAGTGTCTTG----------TTAGGGTGCCACTCCCCTTTCTGCTAACCATGATATGAGCT----GCTCTATCTGCCAGACCCTCACctccttcatggtctgaaacctctgaaaccat-gagcaaagtaaatagtctctcctt-------------t-------------tag---------cta-ttttT-gtcaCCAGTGCA
+s	Cricetus_cricetus.OZ199631.1	140167380	1129	-	205530201	ATCTTTTTAATATGAAAGTGATTTAAgccaactgcaaagccagct-----------------gctgggggtacagctcagtggtagagcacttgtccagcaagcatgaggcagtgtAtttattctacaat-at----ctcacacacacagaaaacacacccac---------aagacatgca-----------atagacacattgttgacaatacatgac------------------------atgtacacaata-----------ggcatataacagttatacacgacatagATAACAC-AAAGCaacagaaactacagacctacataccagacatatatgtaacatgcatacaacacacacaCAcaa-cattcacacaaCcacatatga-gagacttataatatacacagaacatatacagcagacaca--tataata--g--atacagaac--agat--atgtaaa-atgcaacacttgcaacagacac--acaagAAACCA---AAAACA----TACAATAACCACAGCTCTCATACAATATACAGAATACATATAATGTATG--TACATACACAG--CAAAAA-TA--CTTTGCATTTATGTATAAAG-ATAAAA-----TCTAAAGCACAAAGATACTAGGAGAATTATGAAACTTTATCAATTCATTTGGGAAAAGAAGAGATTTTAGTCAGAATTAATTGATGTTTGGCCATTACAAAAATAAAACATACACAAACATGAACTCCACCTGTA-ATGTCATGGGCAAATG--------------ACAAATGAAGG-AGGAAA-ACCCCTCCTTGACTCTGAAGAGCTTATGGAAACCGTGATGACAAAGACTAACAAGGAAAGTGAAAACTCAGTGATAGTCACCAGCAGAAGGTTCATAGACATAGCGATACAGGCCACCTCTGTGTGCACCTATGAAGGTGG-TTCCAGAGTTGA-----TGACATCATCAGGACTCTGAGCCAGTAAAAGGTTTACTCTATGGATTGACTCAACACTGGAATAGATTACCAGGAAGTGAGAGAACTGGGGATGATGGAACCAGATTGGAGGTAGTTGGTCAGGAGGT-A-GG-GTGGCATGCCTAGGGGTAATATCT---------------------------CCTTCCTGTCTACCATGATATGAGCT----GCTCTATCTGATAGACCCTTGcctccatcatggtctgaaacctctgtaaccat-gagcaaagaaaatactttctccct-------------taagtttttcacattag---------ctg-ttttT-gtcacaggtGCa
+s	Cricetulus_griseus.NC_048598.1	130955558	1135	-	193770019	ATCTTTTTAATATGAAAGTGATTTAAGCCAACTGCAAAGCCAACT-----------------gctgggggtacagctctgtggtagagcacttgcccagaaagcatgaggcagtgtAtttattctacaat-atCACAcacacacacacagaaaacacacccac---------aagacatgca-----------atagatacattgttgacaatacatgac------------------------atgtacacaata-----------ggcatataacagttatacacaacatagATAACAC-AAAGCaacagaaactacagacctacataccagacatatatgtaacatgcatacaacacacacaCGtaa-cattcacacaa-cacatatga-gagacttataatatacacagaccatatacaacagacaca--tataata--gATatacagaac--agat--atataaa-acgcaacacttgcaacagacac--acaaaaAACca---aaaaca----tacaataatcacAGCTCTCATACAATATACAGAGTacatataatgtata--tacatacatag--CAAAAATTA--CTTTGCATTTATATATAAAG-ATAAAA-----CCTAAAGCACAAAGATACTAGGAGAGTTATGAAACTTTATAAATTAATTTGGGAAAAGAAGAGATTTTAGTCAGAAATAATTGATGTTTGACCATTACAAAAATAAAACATACACAAACATGAACTCCACTTGTA-ATGTCATAGGCAAATG--------------ACAAATGGAGG-AGGAAA-ACCCCTCCCTGACTCTGAAGAGCTTATGGAAACTGTGATGACAAAGACTAACAAGGAAAGTGAAAACTCAGTGACAGTTACCAGCAGAAGGTTCATAGACATAGGCATACAGGCCACCTCTGTGTGTACCTATGAAGGCGG-TTCCAGAGATGA-----TGACATCATCAGGACTCTGAGCCAGTAAAAGGTTTACTCTATCGATTGACTCAACACTGGAATAGATTACCAGGAAGTGAGAGAACTGGGGATGATGGAACCAGATTGGAGGTAGTTGGTCAGGAGGC-A-GG-GTGGCATGCCTAGGGGTAATATCT---------------------------CCTTCCTGCCTACCATGATATGAGCT----GCTCTAGCTGATAGACCCTTGCCTCCatcatggtctgaaacctctgtaaccat-gagcaaagaaaatactttctcctt-------------taagtttttcacattag---------ctg-ttttT-gtcacagGTGCA
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6038885	1118	-	8539717	ATCTTTTTAATATGAAAGTGATTTACGGCAACTGCAAAACCAGCT-----------------GC-ggggatgcagctcagaggtagagcacttgctcagtgagcatgaggctttctGtttattctacaat-at----cacacataaacagacaacacacccgc---------agcacataca-----------atagagacattatggacaatacatgac------------------------at-----------------------------------atacacaacatagATAACACAAAAAGaacagaaaaaacagacatacataacaga-atatatgtaacatacacacaacacatacaCAtaa-catttacacaa-cacatacga-gagacatataatatacacagaacatatacaacagatgca--tataata--g--atatacaac--aaat--atgtaac-atacatcacttgcaacagacat--aaataaAACtc---aaagcacttacacaataatcatAGCTCTCATACAATATATAGCATacatataagacaca--tgtatacacag--caaatatta--ctttgtattcatatataaat-ataaaa-----cctaaagcacaaaggcacaaggagaattatgaaactttataaattaacttgGGAATAGAGAAGATTTTGGTCAGGAATAATTGATGTTTGGCCATTATAAAAATTAAACAAACACAAACATAAACTCCACATGTGGACATCATAGGCAGATGGAAATCCCTGCATG-CAAATGAAGG-AGGGA----CCCTACTTGACTCTGAAGAGCTTATGCAAACTGTGATGACAAAGACTAACAAGGCAAGTGAGAACTCAGTGACAGTTACCAGCAGAAGGCTCACAGATACAGGCATACAGGCCACCTCCGTGTGCATCTGTGAGGGTGG-TTCCAGAGACGA-----TGGCACCATCAGGACCCTGAGCCAGTAAAAGGTTTACTCCACTGATCGACTCAAGATTAGAACAGATTACCAGTGAGTTTGAGAACTGGGGAAGATGGGACCAGATTGGAAACAGTGGTTCAGGGCAT-G-GC-GGGGCATGCCTAGGGGCAAAATCTGA----------TCAGGGCTCCACTCTGTTTCCTGCCTACCA-GATATGAgct----gctctatc--TT-----CCAGcctccttcatggact---------gaaaccat-gagcaaagtaaattctttctccct-------------cgagtttttcacagtgg---------ctg-tttt--gtcacagggGCa
+s	Arvicola_amphibius.NC_052058.2	72669057	1139	-	166747489	ATCTTTTT-ATATGAACGTGATCGAGGAGAACTGCAAAACCAACG-----------------GC-ggggatgctgctcagaggtagagcacttgctcagtgagcatgaggccttgtGtttattctacaat-at----cacacataaacagacagcgcacccac---------agcacatgca-----------atagacacactgtggacaatacatgacATATATACAACAGGCACAACACAGat-----------------------------------atatacaacatagATAGCACAAAAACaacagaaaccacagacatacataacaga-atgtatgtaacatacacacaacacacaca--taa-cattcatacaa-cacatacaa-gacacatataacatacacagaacatatacaacagatgca--tattata--g--acataca----agat--atataac-atacattacttg-aacagacat--acacaaAATtc---aaaa-acccatacaataatcatAGCTCTCATATAATATACAGCATgcatataacacaca--tgtatacacag--caaaaatta--ctttgtattcatatataaatAaaAAAA-----CCTAAAGCACAAAGTCACTAGGAGAATTATGAAGCTTTATAAATTAACTTGGGAATAAGGGAGATTTTGGTCAGGAATAATTGATGTTTGACCATTACAGAAATTAAACATACACAAACATAAACTCCACGTGTGGATATCATAGGCAGATGGAAATCCCTGTATGACAAATGAAGG-AGGGA----CCCTCCTTGACTCTGAAGAGCTTATGCAAACTGTGATGACAAAGACCAACAAGGCAAGTGAGAACTCAgtgacAGTCACcagcagaaggctcacagaCAcacgcatacagGccacctctgtgtgcacctgtgagGGTGG-TTCCAGAGATGA-----TGGCATCATCAGGACCCGGAGCCAGTAAAAGGGTTACTCCAATGATCGACTCAAGATTAGAACAGATTACCAGGAAGTTTGAGAA-CAGGGAAGATGGGACCAGATTGGAGATAGTGGTTCAGGGGGTGG-GGGGGGGCATGCCTAGGGGCAAAATCTGG----------TCAGGGCTTCGCTCTGCTTCCTGCCTACCA-GATATGAACT----GCTCTATC--CT-----CCAGCCTCCTTCATGGACT---------GAAACCATGGAGCAAAGTAAATTCTTTCTCTCG-------------CGAGCTTTTCACAGTGG---------CTG-TTTT--GTCACGAGTGCa
+s	Microtus_pennsylvanicus.CM073176.1	20976643	1100	+	113485825	ATCTTTTTAATATGAAAGTGATCTAGGATAACTGCAAAACCAGCT-----------------gc-ggggatgcagctcagaggtagagcacttgctcagcgagcatgaggccttgtGtttattctacaat-at----cacacataaacagacaacacacccac---------agtgcataca-----------acat-caca-tgtggacaatacatgac------------------------at-----------------------------------atacacaacacagATAACACAAAAACaacagaaacaacagacatacatagcgga-atatatgtaacatacacacaacacacaca--taa-cattca------------------cacatgtaatatacacagaacatatacaacatatgca--tatgata--g--atatacaacATatat--atataat-atatatcacttgcaacagacat--acataaAACtc---aaagcacttgtacaataatcatAGCTCTCATACAATATATAGCACacatataacagaca--tgtatacacaG--CAAAAATTA--CTTTGTGTTCATATATAAAT-ATAATA-----CCTAAAACACAAAGGCACTTGGAGAATTAGGAAGCCTTATAAATTAACTTGGGAATAGGGGAGATTTTGGTCAGGAATAATTGATGTTTGACCATTATAAAAATTAAAGATACACAAACATAAACTCTACATGTGCATATCATAGGCAAGTAGAAATCCCTGAATGACAAATGAAGG-AGGGA----CCCTCCTTGA--CTGAAGAGTTTATGCAAACTGTGATGACAAAGACTAAAAAGGCAAGTGAGAACTCAGTGACAGTCACCAGCAGAAGGCTCACAGACACAGGCATACAGGTCACCTCTGTGTGCACCTGGGAGGGTGG-TTCCAGAGACGA-----TGGCATCATCAGGACCCAGAGCCAGTAAAGGGGTTACTCCACTAATCGACTCAAGATTAGAACAGATTACCAGGAAGTTTGAGAACCAGGGAAGATGGGACCAGATTGGAGACAGTGGTTCAGGGGGT-A-GGAGGGGCAAGCCTAGGGGAAAAATCTGG----------TCAGGAATTCActctgcttcctacctatca-gatgtgaact----gctctatc--CT-----CCAGcctccttcatggact---------gaaaccat-gagctaagtaaattctttctccct-------------cgagtttttcacagtgg---------ctg-tttt--atcacaAGTGCA
+s	Microtus_arvalis.JAHRII010002323.1	111061327	1117	+	200229077	atctttttaatatgaaagtgatctaggataactgcaaaaccagct-----------------gc-agggatgcagctcagaggtagagcatttgctcagtgagcttgaggccttgtGtttattctacaat-at----tacacataaacagacaacatacccac---------agtacataca-----------acat-caca-tgtggacaatacatgac------------------------at-----------------------------------atacacaacatagATAACACAAAAACaacagaaacaacagacatacataacaga-atatatgtaacatatacacaacacacata--taa-cattcacacaa-cacatacaa-gagacatataatatacacagaacatatacaacagatgca--tatgata--g--atatacaacATatatGTatataac-atatatcacttgcaacagacat--acataaAACtc---aaagcacttatacaataatcatAGCTCTCATACAATATATAGCACacatataacagaca--tgtaTACACAG--CAAAAATTA--CTTTGTGTTCATATATAAAT-AAA-TA-----CCTAAAACACAAAGGCACTAGGAGAATTATGAAGCCTTATAAATTAACTTGGGAATAGGGGAGATTTTGGTCAGGAATAATTGATGtttgaccattataaaaattaaagatacacaaacataaactCCACATGTGCTTATCATAGGGAAATGGAAATCCCTGTATGACAAATGAATG-AGGGA----CCCTCCTTGA--CTGAAGAGTTTATGCAAACTGTGATGACAAAGACTAAAAAGGCAAGTGAGAACTCAGTGACAGTCACCAGCAGAAGGCTCACAGACACAGGCATACAGGTCACCTCTGTGTGCACCTGTGAGGGTGG-TTCCAGAGACGA-----TGGCATCATCAGGACCCGGAGCCAGTAAAAGGGTTACTCCACTGATCGACTCAAGATTAGAACAGATTACCAGGAAGTTTGAGAACCAGGGAAGATGGGACCAGATTGGAGACAGTGGTTCAGGGGGT-A-GGAGGGGCATGCCTAGGGGAAAAATCTGG----------TCAGGGATTCActctgcttcctacctatca-gatgtgaact----gctctatc--CT-----CCAGcctccttcatggact---------gaaaccat-gagcaaagtaaattctttctccct-------------cgagtttttcacagtgg---------ctg-tttt--atcacaAGTGCA
+s	Neotoma_floridana.CM113793.1	27922860	1142	-	95303938	ATCTTTTTAATATGAAAGTGATTTAAGACAACTGCAAAgctagct-----------------gctggggatgcagctcagtggtagagcacttgcctggcaagcatgaggccttgtGtttattccacaat-at----cacatatacacagacaacacacccacagcatacacaagac-----------------------------------------------------------------------acacaaaa-----------ggcatacaacagatatacataacatagATAACACAAAAACaacag-aaaaacagacatacataacagacatatatgtaacatgcacacaacacacaca--taa-catttacacaa-cacatacta-aagacatataatatacacagaacatctacaacaaacata--taat--a--g--atacacaac--agat--atatcac-atacaacacttgcaacagacac--atacaaAACtc---aaaacactcatacaacaatcacAGCTCTTACACAACATACAGCATacacataatataca--tgcacacacag--caaaaatta--ctttacattcatatgtacag-ataaaa-----ctcaaagtacaaagacacTAGGAGAATTATGAAGCTTTATAAATTAACATGGGAATAGGGGAGATTTTGGTCAGAGTTAATTGATGTTTGACCATTATAAAAATAAAACATCCACAAACATTAACTCCACATGAGGGTGTCATAGGCAAGTGGAAATCCCTGTATGACAAATGAAGATGGGAAA-CCCCCTCCCTGACTCTGAAGAGTTTACGGAAACTGTAATGACAGAGACTAACAAGGCAAGTGAAAACTCTGTGACAGTCACCAGCAGAAGGTTCACAGACACAGGCACACAGGCCACCTCTGTGTGCACCTGTGAGGGTGG-TTCCAGAGATGA-----AGACATCATCAGGACTCTGAGCCAGCAAAAGGTTTACACCACTGATTGACTCAT---TGGAATAGATTACCAGGAAGTGGGAGAGCTGGGGAGGATGGGATCAGATTGGAGGTAGTTCGTCAGGGGTTGAGGG-GGGGCACACCTAGAGGCACTATCTTG----------TTAGAGTTCCGctctccttcctgcctaccatgatgtgagct----gctctatctaCCTGATCCTTGcctccttcatggactcaaacctctgaaaccat-gagcaaagtaaatactttctccct-------------taagtttttcacattggCTATTTTGTcta-tttt--gtcacaggtGCa
+s	Onychomys_torridus.LR877198.1	72221593	1147	+	93020901	ATCTTTTTAATATGAAAGTGAttgaagacaacctcaaagctagat-----------------gctggggatgcagctcagtggtagagcacttgcccagcaagcctgaggccttatGtttattcttcaac-at----cacacatacacagataacacacccatagcatacataagacacata-----------atagacatattgtagacaacacatg--ACATGT----------------------acacaaca-----------ggcatacaacagttaaacacaacatagATACCAC-AAAACaactgaaataacagacatacataacagacatatatgtaacatgcacacaactcatgca--taa-cattcacacaa-cacacactaGaagacaaataatatacacagaacatacacaacaaacaca--tata--a--t--ata---------------------Aacacaacacctgcaacagacac--atacaaAACtc---aaa-cactcatacaacaatcacAGCTCTTATACAACATACAGCATacacataatataca--tgcatacacag--CAAAAATTA--CTTTGCATTCATATATAAAG-ATAAAATAAAACCCCAGGTACAAAGACACTAGGAGAATTATGAAGCTTTATATATTAACTTGGGAATAGGGGAGATTTTGGTCAAAGTTAATTGATGTTTGATCACTAGAAAAATGAAACATACACAAACATGAACTCCACAATAGGATGTCACAGACAAGTGGAAATCC-AGTGTGACAAAAGAAGA-AGGAAA-ACCCCTCCCTGACTCTGAAGAGTTTATGGAAACTGTAATGTCAAA-ACTGACAAGGCAAGTGAAAACTCTGTGACCGTCACCAGCAGAAGGTTCACAGACACAGGCCTAGAGGCCACCT--GTGTGCACCTGTGAGG--GG-TTCCAGAGATAA-----TGACATCATCAGGACTCTGAGCCAGTAACGAGTTTACTCCACTGATTGACTCAC---TGGAACAGATTACCAGGAAGTGGGAGAACTGGGCAAGATGGGACCAGATTGGAGGT-------CAGGGAGC-AGGG-GGAGCATGCCTACCAGCAATATCTTG----------TTAGGGTTCTGctctccttcctgcctatcatgatatgagctAGCTgctctagctaACTGACCCTCAcctccttcatggactcagacctctgaaactat-gagcaaattaaatactttctccct-------------tgaggttttcacagtgg---------cca-tctt--atcacaggcGCa
+s	Peromyscus_californicus.VALE03000237.1	12779675	1153	+	80346014	ATCTTTTTAATATGAAAATgatttaagacacccgcaaagctagct-----------------gctggggacgcagcccagtggtagagcacttgcccagcaagcacgaggccttgtGtttcttctacagtTat----cacacatacacagacaacacacccacagcatacataagacatgcg-----------atagacacattgtagacaacacatg--GCATGT----------------------acacagca-----------ggcatacaacagacatacacaacatagATACCACAGAAACaacagaaataacaga-------------catatatgtaacatgcacacaacacacaca--taa-cattcacacaa-cacatacta-gagatatataatatacacagaacatatacaacaaataca--tgta--aTAg--aaacacaac--agat--atataacAacacaacatttgcaacagacac--acaaaaAACtc---aaaacactcatacaacaatcacAGCTCTTACTCAACATACAGCATacacataatataca--tgcatacacag--GAAAAAATA--CTTCGCATTCATATATAAAG-ATAAAA-----CCCAAAGTACAAAGACACTGGGAGAATTATGAAGCTTGATACATTAACCTGGGAACAGGCGAGATTTCGGTCAGAGATAACTGATGTTTGAACATTATAAAAATGAAACATGCACAAACGTGAACTCCACATGAGGATGTCACAGGCAAGTGGAAATCCCAGTATGACAGAAGAAGA-AGGAAA-ACCCCTCCCTGACTCTGAAGAGTATATGGAAACTGTAATGACAAAGACTAACAAGGCAAGTGAAAACTCTGTGAACGTCATCAGCAG---GTTCACAGACACAGGCATCCAGGCCACCT--GTGAGCACCTGGGAGG--GGGTTCCAGAGATGA-----CGACATCATGAGGACTCTGAGCCAGTAACAGCTTTACTCCACTGATTGACTCAG---TGGAACAGAGTACCAGGAATTGGGAGAACTGGGCAAGATGGAACCAGATTGGAGGTAGTTGGTCAGGGGGC-AGAG-GGGA-ATGTCTACTGGCAATATCTTG----------TTAGGGTTCTGctctccttcctgcctatcatgatatgagct----gctctatctaCATGACCCTCAcctccttcacggactcaaacctctgaaactat-gagcaaattaaatactttcttcct-------------taaggttttcacattgg---------ctaCtttt--atcacaggtGCa
+s	Peromyscus_maniculatus_North.CM113205.1	35700359	1160	+	104458120	ATCTTTTTAATATGAAAGTGATTTAAGACACCCGCAAAGCTCGCt-----------------gctggggatgcagctcagtggtagagcacttgcccagcaagcacgaggccttgtGtttcttctacaatGat----cacacatacacagacaacacactcacagcatacataagacacgcg-----------atagacacattgtagacaacacatg--ACATGT----------------------acagagga-----------ggcatacaacagacatacacaacatagATACCACAAAAACaacagaaataacagagatatgtaacagacatatatgtaacatgcacacaacacacaca--taaAtattcacacaa-cacatacta-gaaatatataatatacacagaaca---------aacaca--taca--aTAg--aaacacaac--agat--atataacAacacaacatttgcaacagacac--ataaaaAACtc---aaaacactcatacaacaatcacAGCTCTTACACAACATACAGCATacacataatataca--tgcatacacCG--AAAAAAAAAACCTTCGCATTCATGTATAAAG-ATAAAA-----CCCAAAGTACAAAGACACTGGGAGAATTATGAAGCTTTATACATTAACTTGGGAATAGGGGAGATTTTGGTCAGAGTTAACTGATGTTTGACCATTATAAAAATGAAACATGCACAAACATGAACTCCACATGAGGATGTCATAGGCAAGTGGAAATCCCCGTGTGAGAAAAGAAGA-AGGAAA-ACCCCTCCCTGACTCTGAAGAGTTTGTGGAAACTGTAATGACAAAGACTAACAAGGTGAGTGAAAACTCTGTGACCGTCACCAGCAG---GCTCACAGACACAGGCATCCAGGCCACCT--GTGTGCACCTGTGGGG--GG-TTCCAGAGATGACGACATGACATCATCAGGACTCTGCGCCAGTAAC-AGGTTACTCCACTGATTGACTCAG---TGGAACAGGGTACCAGGAAGTGAGAGAACTGGGCAAGATGGGACCAGACTGGAGGTAGTTGGTCACGGGGC-AGGG-GGGGCGTGGCTATTGGCAATATCTTG----------TTAGGGTTCCGCTCTCCTTCCAGCCTAGCAT---ATGAGCT----GCTCTATCtaCTGGACTCTCAcctccttcatggactcaaacctctgaaaccat-gagcaaattaaatactttcttccc-------------taaggttttcacattgg---------ctg-tttt--atcacaggtGCa
+a
+s	Mus_musculus.CM000994.3	125891324	34	+	195154279	CACAGTCACCAAGTACTTCATGGTCTTGGATGAG
+s	Rattus_norvegicus.CM070403.1	39972568	30	+	109350286	CAAAATCACCAAG----TAATGGTCTTGGATAAA
+s	Phodopus_campbelli.chr12	18455457	34	-	32442325	CACAATAACCAAGTTCTGAATggtcctggatgac
+s	Phodopus_sungorus_new.chr12	17336886	34	-	31225933	CACAATAACCAAGTTCTGAATGgtcctggatgac
+s	Phodopus_roborovskii.JAEOAF010000031.1	16488072	34	+	29770300	CACAATGACCAAGTTCTGAATGGTCCTGGATGAC
+s	Cricetus_cricetus.OZ199631.1	140168521	34	-	205530201	CACAATCACCAAGTTCTTAATGATCCTGGATGAT
+s	Cricetulus_griseus.NC_048598.1	130956705	34	-	193770019	CACAATCACCAAGTTCTTAATGATCCTGGATGAT
+s	Dicrostonyx_torquatus.JAQHUG010000071.1	6040015	34	-	8539717	CACAAACATCAAGTTCTTAATGATcctgggtgac
+s	Arvicola_amphibius.NC_052058.2	72670208	31	-	166747489	cacaatca-caagttcttagtga-tccgggtga-
+s	Microtus_pennsylvanicus.CM073176.1	20977755	34	+	113485825	CACAACCATCAAGTTCTTAATGATTCTGGATGac
+s	Microtus_arvalis.JAHRII010002323.1	111062456	34	+	200229077	CACAACCATCAAGTTCTTAATGATTCTGGATGAC
+s	Neotoma_floridana.CM113793.1	27924014	34	-	95303938	CACAATCACCAAATTCTTAATggtcctggatgac
+s	Onychomys_torridus.LR877198.1	72222752	28	+	93020901	CACAATCACCAAGTTCTTAATGGTCCTG------
+s	Peromyscus_californicus.VALE03000237.1	12780840	34	+	80346014	cacaatcaccaagttcttaatggtcctggatgac
+s	Peromyscus_maniculatus_North.CM113205.1	35701531	34	+	104458120	cacaatcaccaagttcttcatggtcctgggtgac

mafutils-0.3.0/tests/real-excerpt.maf.block.idx ADDED Viewed

@@ -0,0 +1,9 @@
+# mafutils-index format=2 maf=real-excerpt.maf compression=none size=47241 mtime=1784644433.0 hash=md5:7146e0c45ac589e8998a3fe232ca5ad7
+CM000994.3	125888838	82	84	135	13	17	1874
+CM000994.3	125888920	187	223	275	9	1874	4416
+CM000994.3	125889107	10	31	82	9	4416	5221
+CM000994.3	125889117	440	487	539	14	5221	12879
+CM000994.3	125889557	280	356	408	15	12879	19122
+CM000994.3	125889837	333	336	388	15	19122	25065
+CM000994.3	125890170	1154	1324	1377	15	25065	45843
+CM000994.3	125891324	34	34	85	15	45843	47241

mafutils-0.3.0/tests/real-excerpt.maf.scaffold.idx ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ # mafutils-index format=2 maf=real-excerpt.maf compression=none size=47241 mtime=1784644433.0 hash=md5:7146e0c45ac589e8998a3fe232ca5ad7
2	+ CM000994.3 17 47241

{mafutils-0.2.1 → mafutils-0.3.0}/tests/test_fetch.py RENAMED Viewed

@@ -118,3 +118,64 @@ def test_maf_fetch_fasta_region(chrom, start, end, region_id, tmp_path):
     expected = expected.rstrip('\n')
     assert got == expected, f"FASTA output for region {region_id} does not match expected"
+def test_scaffold_subdirs_groups_output_by_scaffold(tmp_path):
+    """
+    --scaffold-subdirs groups per-region output files into
+    <outdir>/<scaffold>/<basename>.maf instead of a flat <outdir>/. Runs
+    with -p 2 (real multi-worker ProcessPoolExecutor dispatch, matching how
+    block-mode writes actually happen) across regions spanning multiple
+    scaffolds, including two scaffolds (chr1, chr4) with multiple regions
+    each, to confirm they land in the same subdirectory without any
+    cross-worker race (directories are pre-created upfront, see fetch.py).
+    """
+    out_dir = str(tmp_path)
+    cmd = [
+        sys.executable, "-m", "mafutils", "fetch",
+        MAF_FILE, BED_FILE,
+        "--index", INDEX_FILE,
+        "-b", "id",
+        "-o", out_dir,
+        "--scaffold-subdirs",
+        "-p", "2",
+    ]
+    result = subprocess.run(cmd, check=False, cwd=REPO_ROOT, capture_output=True, text=True)
+    assert result.returncode == 0, f"Unexpected non-zero exit: {result.stderr}"
+    # chr1 has 3 regions with real output (06-noalign has no overlap, so no
+    # file); chr4 has 2; chr2/chr3/chrX have 1 each. chrZ (09-missingchrom)
+    # never gets that far (unknown scaffold errors before any writes).
+    assert sorted(os.listdir(os.path.join(out_dir, "chr1"))) == [
+        "01-singleblock-gap.maf",
+        "02-truncatedblock.maf",
+        "03-crossblocks-missing.maf",
+    ]
+    assert os.listdir(os.path.join(out_dir, "chr2")) == ["04-singleblock.maf"]
+    assert os.listdir(os.path.join(out_dir, "chr3")) == ["05-crossblocks.maf"]
+    assert os.listdir(os.path.join(out_dir, "chrX")) == ["07-negstrand.maf"]
+    assert sorted(os.listdir(os.path.join(out_dir, "chr4"))) == [
+        "08-span-multiple-gaps.maf",
+        "10-crossblocks-missing-species.maf",
+    ]
+    # Content should be identical to the flat-layout output for the same region.
+    with open(os.path.join(out_dir, "chr2", "04-singleblock.maf")) as fp:
+        got = fp.read().rstrip("\n")
+    with open(os.path.join(EXPECTED_MAF_DIR, "04-singleblock.maf")) as fp:
+        expected = fp.read().rstrip("\n")
+    assert got == expected
+def test_scaffold_subdirs_rejected_with_single_output(tmp_path):
+    cmd = [
+        sys.executable, "-m", "mafutils", "fetch",
+        MAF_FILE, BED_FILE,
+        "--index", INDEX_FILE,
+        "--scaffold-subdirs",
+        "--single-output",
+        "-o", os.path.join(str(tmp_path), "out.maf"),
+    ]
+    result = subprocess.run(cmd, check=False, cwd=REPO_ROOT, capture_output=True, text=True)
+    assert result.returncode != 0
+    assert "--scaffold-subdirs cannot be used with --single-output" in result.stderr

mafutils-0.3.0/tests/test_real_data.py ADDED Viewed

@@ -0,0 +1,115 @@
+import csv
+import os
+import subprocess
+import sys
+TEST_DIR = os.path.dirname(__file__)
+REPO_ROOT = os.path.abspath(os.path.join(TEST_DIR, ".."))
+MAF_FILE = os.path.join(TEST_DIR, "real-excerpt.maf")
+INDEX_FILE = os.path.join(TEST_DIR, "real-excerpt.maf.block.idx")
+# 8 real, complete alignment blocks, extracted read-only from gwct's real
+# ~42GB production MAF (data/hamsters/uncompressed/...), a couple GB in to
+# skip past the initial all-N region. Unlike example.maf (hand-crafted, used
+# to independently verify exact output values in test_stats.py/test_gc.py),
+# this fixture exists to catch real-world-data surprises a hand-crafted
+# fixture wouldn't think to include (real species-naming conventions, real
+# gap patterns, real block-size distribution) -- so these tests check
+# plausibility/robustness/"does it run cleanly on real data", not exact
+# hand-computed values.
+EXPECTED_SPECIES = {
+    "Phodopus_sungorus_new",
+    "Phodopus_campbelli",
+    "Phodopus_roborovskii",
+    "Cricetulus_griseus",
+    "Cricetus_cricetus",
+    "Dicrostonyx_torquatus",
+    "Peromyscus_maniculatus_North",
+    "Microtus_arvalis",
+    "Microtus_pennsylvanicus",
+    "Arvicola_amphibius",
+    "Neotoma_floridana",
+    "Mus_musculus",
+    "Rattus_norvegicus",
+    "Peromyscus_californicus",
+    "Onychomys_torridus",
+}
+# All 8 blocks are on the same real reference scaffold/coordinate range.
+REAL_SCAFFOLD = "CM000994.3"
+REAL_START = 125888838
+REAL_END = 125891358  # last block's start (125891324) + size (34)
+def run(cmd_args):
+    cmd = [sys.executable, "-m", "mafutils"] + cmd_args
+    return subprocess.run(cmd, check=False, cwd=REPO_ROOT, capture_output=True, text=True)
+def read_overall(path):
+    with open(path, "r", encoding="utf-8") as fp:
+        lines = fp.readlines()[1:]
+    return dict(line.rstrip("\n").split("\t") for line in lines)
+def test_stats_runs_cleanly_on_real_data(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    result = run(["stats", MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert result.returncode == 0, result.stderr
+    overall = read_overall(out_prefix + ".overall.tsv")
+    assert int(overall["total_blocks"]) == 8
+    assert int(overall["total_species"]) == 15
+    assert int(overall["total_parse_errors"]) == 0
+    assert int(overall["blocks_with_zero_parsed_seq_lines_but_index_nonzero"]) == 0
+def test_stats_species_list_matches_known_species(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    result = run(["stats", MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert result.returncode == 0, result.stderr
+    with open(out_prefix + ".species.tsv", "r", encoding="utf-8") as fp:
+        reader = csv.DictReader(fp, delimiter="\t")
+        got_species = {row["species"] for row in reader}
+    assert got_species == EXPECTED_SPECIES
+def test_gc_runs_cleanly_and_plausibly_on_real_data(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    result = run(["gc", MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert result.returncode == 0, result.stderr
+    with open(out_prefix + ".gc.csv", "r", encoding="utf-8") as fp:
+        reader = csv.DictReader(fp)
+        gc_values = {row["species"]: float(row["gc"]) for row in reader}
+    assert gc_values.keys() == EXPECTED_SPECIES
+    for species, gc in gc_values.items():
+        # Real rodent genomic GC content clusters tightly around 0.40-0.45 in
+        # this fixture; 0.30-0.55 gives real margin without being so loose it
+        # would miss a genuine encoding/parsing bug (e.g. counting gaps as GC).
+        assert 0.30 <= gc <= 0.55, f"{species}: implausible GC content {gc}"
+def test_fetch_runs_cleanly_on_real_data(tmp_path):
+    bed_path = os.path.join(str(tmp_path), "region.bed")
+    with open(bed_path, "w", encoding="utf-8") as fp:
+        fp.write(f"{REAL_SCAFFOLD}\t{REAL_START}\t{REAL_END}\tregion1\n")
+    out_dir = str(tmp_path)
+    result = run([
+        "fetch", MAF_FILE, bed_path,
+        "--index", INDEX_FILE,
+        "-b", "id",
+        "-o", out_dir,
+    ])
+    assert result.returncode == 0, result.stderr
+    output_file = os.path.join(out_dir, "region1.maf")
+    assert os.path.isfile(output_file), "Expected fetch output file was not created"
+    with open(output_file, "r", encoding="utf-8") as fp:
+        content = fp.read()
+    assert content.count("\na") + content.startswith("a") >= 1, "Expected at least one alignment block in fetch output"
+    assert "Mus_musculus" in content

mafutils-0.3.0/tests/test_stats.py ADDED Viewed

@@ -0,0 +1,143 @@
+import csv
+import os
+import subprocess
+import sys
+import pytest
+TEST_DIR = os.path.dirname(__file__)
+REPO_ROOT = os.path.abspath(os.path.join(TEST_DIR, ".."))
+MAF_FILE = os.path.join(TEST_DIR, "example.maf")
+INDEX_FILE = os.path.join(TEST_DIR, "example.maf.block.idx")
+# Hand-verified directly against tests/example.maf's raw content (10 blocks;
+# human present in all 10, chimp in 8 [blocks 1,2,3,4,5,6,8,10], gorilla in 2
+# [blocks 7,9]). Every block has exactly 2 taxa, so parsimony-informative
+# sites (requiring >=2 states each seen >=2 times) are structurally
+# impossible; variable sites occur only in block 3 (6 columns) and block 4
+# (1 column), the only two blocks where both taxa have different non-gap
+# bases in the same column.
+EXPECTED_OVERALL = {
+    "total_blocks": 10,
+    "total_species": 3,
+    "total_alignment_columns": 61,
+    "total_sequence_lines": 20,
+    "all_gap_sites": 0,
+    "variable_sites": 7,
+    "invariant_sites": 54,
+    "parsimony_informative_sites": 0,
+    "total_parse_errors": 0,
+    "blocks_with_zero_parsed_seq_lines_but_index_nonzero": 0,
+}
+# blocks_present / gaps_total / nongaps_total per species, hand-counted
+# directly from each block's raw sequence strings.
+EXPECTED_SPECIES_RAW = {
+    "human": {"blocks_present": 10, "gaps_total": 3, "nongaps_total": 58},
+    "chimp": {"blocks_present": 8, "gaps_total": 11, "nongaps_total": 41},
+    "gorilla": {"blocks_present": 2, "gaps_total": 1, "nongaps_total": 8},
+}
+def run_stats(args):
+    cmd = [sys.executable, "-m", "mafutils", "stats"] + args
+    result = subprocess.run(cmd, check=False, cwd=REPO_ROOT, capture_output=True, text=True)
+    assert result.returncode == 0, f"stats failed (exit {result.returncode}):\n{result.stderr}"
+    return result
+def read_overall(path):
+    with open(path, "r", encoding="utf-8") as fp:
+        lines = fp.readlines()[1:]
+    return dict(line.rstrip("\n").split("\t") for line in lines)
+def read_species(path):
+    with open(path, "r", encoding="utf-8") as fp:
+        reader = csv.DictReader(fp, delimiter="\t")
+        return {row["species"]: row for row in reader}
+def assert_overall_matches(overall):
+    for key, expected in EXPECTED_OVERALL.items():
+        assert int(overall[key]) == expected, f"{key}: expected {expected}, got {overall[key]}"
+def assert_species_matches(species):
+    assert species.keys() == EXPECTED_SPECIES_RAW.keys()
+    for sp, expected in EXPECTED_SPECIES_RAW.items():
+        row = species[sp]
+        assert int(row["blocks_present"]) == expected["blocks_present"], sp
+        assert int(row["gaps_total"]) == expected["gaps_total"], sp
+        assert int(row["nongaps_total"]) == expected["nongaps_total"], sp
+        # Derived ratios computed from the hand-verified raw counts above,
+        # not hardcoded floats -- still an independent check of the formula
+        # application, without risking manual 8-decimal arithmetic errors.
+        blocks_present = expected["blocks_present"]
+        blocks_missing = 10 - blocks_present
+        total_cells = expected["gaps_total"] + expected["nongaps_total"]
+        assert int(row["blocks_missing"]) == blocks_missing, sp
+        assert float(row["presence_fraction"]) == pytest.approx(blocks_present / 10, abs=1e-6), sp
+        assert float(row["gap_fraction_cells"]) == pytest.approx(expected["gaps_total"] / total_cells, abs=1e-6), sp
+        assert float(row["avg_gaps_per_present_block"]) == pytest.approx(
+            expected["gaps_total"] / blocks_present, abs=1e-6
+        ), sp
+def test_overall_stats_match_hand_verified_values(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert_overall_matches(read_overall(out_prefix + ".overall.tsv"))
+def test_species_stats_match_hand_verified_values(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert_species_matches(read_species(out_prefix + ".species.tsv"))
+def test_no_block_table_omits_block_file(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", out_prefix, "--no-block-table"])
+    assert not os.path.exists(out_prefix + ".block.tsv")
+def test_block_table_present_by_default(tmp_path):
+    out_prefix = os.path.join(str(tmp_path), "out")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", out_prefix])
+    assert os.path.isfile(out_prefix + ".block.tsv")
+def test_sequential_and_parallel_paths_produce_identical_output(tmp_path):
+    """
+    Regression guard for the processes=1 ProcessPoolExecutor-skip fix: the
+    direct in-process call (-p 1) and the real multi-worker pool path
+    (-p 2, forced into multiple chunks via a small --chunk-size) must
+    produce identical overall/species output, not just "doesn't crash".
+    """
+    seq_prefix = os.path.join(str(tmp_path), "seq")
+    par_prefix = os.path.join(str(tmp_path), "par")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", seq_prefix, "-p", "1"])
+    run_stats([MAF_FILE, INDEX_FILE, "-o", par_prefix, "-p", "2", "--chunk-size", "3"])
+    assert read_overall(seq_prefix + ".overall.tsv") == read_overall(par_prefix + ".overall.tsv")
+    assert read_species(seq_prefix + ".species.tsv") == read_species(par_prefix + ".species.tsv")
+def test_expected_species_file_reports_missing_species(tmp_path):
+    species_file = os.path.join(str(tmp_path), "species.txt")
+    with open(species_file, "w", encoding="utf-8") as fp:
+        fp.write("human\nchimp\ngorilla\norangutan\n")
+    out_prefix = os.path.join(str(tmp_path), "out")
+    run_stats([MAF_FILE, INDEX_FILE, "-o", out_prefix, "--expected-species-file", species_file])
+    overall = read_overall(out_prefix + ".overall.tsv")
+    assert int(overall["total_species"]) == 4  # 3 observed + 1 expected-but-absent
+    species = read_species(out_prefix + ".species.tsv")
+    assert "orangutan" in species
+    assert int(species["orangutan"]["blocks_present"]) == 0
+    assert int(species["orangutan"]["blocks_missing"]) == 10