pycmplot 0.2.3__py3-none-any.whl → 0.2.4__py3-none-any.whl

pycmplot/__init__.py

@@ -42,4 +42,4 @@ __all__ = [
     "ResourceConfig",
 ]
 
-__version__ = "0.2.3"
+__version__ = "0.2.4"

pycmplot/cli.py

@@ -328,12 +328,12 @@ def get_arguments(descmsg: str = DESCMSG) -> argparse.Namespace:
         help="File delimiter (autodetected if omitted)."
     )
     opt.add_argument(
-        "-bc",   "--build_column",  required=False, type=str, metavar="str",
+        "-bc",   "--build_column", default=None, required=False, type=str, metavar="str",
                      help=("Name of column containing genome build (hg18/hg19/hg38)." 
                          "Or use ``--build`` below to supply genome builds per summary stat file."
                     ))
     opt.add_argument(
-        "-b","--build", required=False, type=str, metavar='str',
+        "-b","--build", default=None, required=False, type=str, metavar='str',
         help=
         """Comma-sperated list of genome build of summary stats file(s) listed 
         in the same order as sumstats files. e.g. hg19,hg38,hg38,hg19 means:

pycmplot/io.py

@@ -564,15 +564,6 @@ def prep_pycmplot_input_info(
     snp_candidates = [c for c in snp_candidates if c]
     pvl_candidates = [c for c in pvl_candidates if c]
 
-    #if buildc:
-    bld_candidates = buildc
-    if not bld_candidates:
-        bld_candidates = ["BUILD", "Genome", "Genome_Build", "Genome-build"]
-        bld_candidates_l = [x.lower() for x in bld_candidates]
-        bld_candidates_u = [x.upper() for x in bld_candidates]
-        bld_candidates = [buildc] + bld_candidates + bld_candidates_l + bld_candidates_u
-        bld_candidates = [c for c in bld_candidates if c]
-
     # ------------------------------------------------------------------
     # Resolve column names per file
     # ------------------------------------------------------------------
@@ -612,21 +603,28 @@ def prep_pycmplot_input_info(
             pcol:      float,
         }
 
-    if not bld_candidates and isinstance(build, list):
+    # CHECK BUILD COLUMN
+    if buildc:
+        bld_candidates = buildc
+    else:
+        bld_candidates = ["BUILD", "Genome", "Genome_Build", "Genome-build"]
+        bld_candidates_l = [x.lower() for x in bld_candidates]
+        bld_candidates_u = [x.upper() for x in bld_candidates]
+        bld_candidates = [buildc] + bld_candidates + bld_candidates_l + bld_candidates_u
+        bld_candidates = [c for c in bld_candidates if c]
+
+    try:
+        bcol = next(c for c in hdr if c in set(bld_candidates))
+    except Exception:
+        bcol = False
+
+
+    if not bcol and isinstance(build, list):
         for name, fpath, build in zip(labels, sum_stats, build):
             sumstats_hdr_dic[name] = [old_cols, col_dtypes, new_cols, file_sep, build]
 
-    elif bld_candidates:
+    elif bcol:
         for name, fpath in zip(labels, sum_stats):
-            try:
-                bcol      = next(c for c in hdr if c in set(bld_candidates))
-            except StopIteration as exc:
-                sys.exit(
-                    f"Error: could not find build column in {fpath}.\n"
-                    f"  Header: {hdr}\n"
-                    f"  Details: {exc}"
-                )
-
             old_cols = [chrom_col, pos_col, snp_col, pcol, bcol]
             new_cols = {
                 chrom_col: "CHR",
@@ -645,7 +643,7 @@ def prep_pycmplot_input_info(
 
             sumstats_hdr_dic[name] = [old_cols, col_dtypes, new_cols, file_sep]
     else:
-        logger.warning("""No build column or builds specified. Summary stats will be
+        logger.warning("""No build column or builds detected. Summary stats will be
         plotted in their respective coordinate systems.
         If your data are in different coordinate systems, putting them in one plot
         is not advisable, especially if ``--annotate`` is set!""")
@@ -963,15 +961,14 @@ def get_sumstats_and_merged_sector_list(
             sub = assoc[assoc["CHR"] == chrom]
             lo_val = max(sub["POS"].min() - 1_000_000, 0)
             hi_val = sub["POS"].max()
-            chrom_max = hi_val
 
             # Ensure sector sizes are within chrom ranges if liftover
-            if liftover:
-                logger.info("Limiting sector sizes to chromosome ranges for liftover sumstats ...")
-                hg38_chr_lengths = {k.replace("chr",""): v for k, v in hg38_chr_lengths.items()}
-                chrom_max = hg38_chr_lengths[chrom]
+            #chrom_max = hi_val
+            #if liftover:
+            #    hg38_chr_lengths = {k.replace("chr",""): v for k, v in hg38_chr_lengths.items()}
+            #    chrom_max = hg38_chr_lengths[chrom]
+            #hi_val = min(hi_val, chrom_max)
 
-            hi_val = min(hi_val, chrom_max)
             assoc_dic[str(chrom)] = [lo_val, hi_val]
 
         min_dic_val = min(assoc_dic.values())

pycmplot/liftover.py

@@ -30,6 +30,7 @@ import numpy as np
 import pandas as pd
 
 from pycmplot.resources import ResourceConfig, default_resources
+from pycmplot.constants import hg38_chr_lengths
 
 logger = logging.getLogger(__name__)
 
@@ -136,6 +137,7 @@ def liftover_hg19_to_hg38(
 
 def liftover_position(
     df: pd.DataFrame,
+    hg38_chr_lengths = hg38_chr_lengths,
     resources: Optional[ResourceConfig] = None,
 ) -> pd.DataFrame:
     LIFTOVER_POSITION = """Liftover all hg19 rows in *df* from hg19 to hg38 coordinates.
@@ -190,6 +192,8 @@ def liftover_position(
     True
     """
 
+    hg38_chr_lengths = {k.replace("chr",""): v for k, v in hg38_chr_lengths.items()}
+
     if resources is None:
         resources = default_resources
 
@@ -208,4 +212,10 @@ def liftover_position(
     df["BUILD"] = "hg38"
     df["POS"] = new_positions
     df["POS"] = df["POS"].fillna(0).astype(int)
-    return df[df["POS"] != 0]
+    clean_df = []
+    for chrom in df["CHR"].unique():
+        chr_df = df[df["CHR"] == chrom]
+        chr_df = chr_df[chr_df["POS"] <= hg38_chr_lengths[chrom]]
+        clean_df = pd.concat([pd.DataFrame(clean_df), pd.DataFrame(chr_df)], axis = 0, ignore_index=True)
+
+    return clean_df[clean_df["POS"] != 0]

{pycmplot-0.2.3.dist-info → pycmplot-0.2.4.dist-info}/METADATA

@@ -1,10 +1,15 @@
 Metadata-Version: 2.4
 Name: pycmplot
-Version: 0.2.3
+Version: 0.2.4
 Summary: Multi-track circular and linear Manhattan plot generation for GWAS summary statistics
 Author: Kevin Esoh
 Author-email: Kevin Esoh <kesohku1@jh.edu>
 License-Expression: CC-BY-NC-SA-4.0
+Project-URL: Homepage, https://github.com/esohkevin/pycmplot
+Project-URL: Issues, https://github.com/esohkevin/pycmplot/issues
+Project-URL: Docs, https://pycmplot.readthedocs.io/en/latest/
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -101,6 +106,9 @@ pip install pycmplot
 ```bash
 git clone https://github.com/esohkevin/pycmplot.git
 
+# or with most recent updates from development branch
+# git clone -b dev https://github.com/esohkevin/pycmplot.git
+
 cd pycmplot
 
 pip install -e .
@@ -207,26 +215,12 @@ A demonstration of how to use the python API is provided in this notebook: https
 
 ---
 
-## Package structure
+## Contributing
+
+See how to contribute here https://github.com/esohkevin/pycmplot?tab=contributing-ov-file
+
+
+## Contributors
+
+- [Kevin Esoh](https://github.com/esohkevin)
 
-```
-pycmplot/
-├── pyproject.toml
-├── setup.py
-├── setup.cfg
-├── README.md
-└── pycmplot/
-      ├── __init__.py          # public API exports
-      ├── __main__.py          # python -m pycmplot
-      ├── _core.py             # main() orchestration
-      ├── cli.py               # argparse definitions
-      ├── constants.py         # chromosome lengths, biotype weights
-      ├── resources.py         # external resource path config
-      ├── io.py                # sumstat loading, delimiter detection
-      ├── stats.py             # get_lead_snps, get_highlight_snps
-      ├── liftover.py          # lazy hg19→hg38 liftover
-      ├── annotation.py        # nearest-gene annotation, hits table
-      └── plotting/
-          ├── __init__.py
-          ├── linear.py        # plot_linear
-          └── circular.py      # plot_circular, compute_track_radii_dict

{pycmplot-0.2.3.dist-info → pycmplot-0.2.4.dist-info}/RECORD

@@ -1,10 +1,10 @@
-pycmplot/__init__.py,sha256=XH0PANwq6BAlDe7qjz-77DsRzXk5qhmgMIyNd_83TaE,1288
+pycmplot/__init__.py,sha256=c87ZKZ-URgiW_M_LIlZF6jy1wkZ5fGByyO-o0kksTbM,1288
 pycmplot/_core.py,sha256=sA1kjavqEX9cLn98d8RU4YJSANCDtMbxbrgGFd8Trew,13046
 pycmplot/annotation.py,sha256=gMgDfnHmMYpkLuQIaJNHmtXVHHIeSUAcviLrisF2vmY,20886
-pycmplot/cli.py,sha256=k6uBR5V0Y89VSzq-GHZxfR0XmBGS6aEUt66fqYEmQ40,19430
+pycmplot/cli.py,sha256=1sb7Gx2qScFyLOe923NNTDeNVnl0c6DM-wxLIqKmmwE,19457
 pycmplot/constants.py,sha256=XaT3pTWM3dkawU1cA0HFpaNnUupSjv28wpPgmnVEjL0,3431
-pycmplot/io.py,sha256=mODcBGxOOH1s7hnJg9FdUgGAEdkM7b1tX5C-Z3ZWFhw,35905
-pycmplot/liftover.py,sha256=ZawfO9ZKZADFwyXZBnbrovh4TnV-ja1qHHnIgtxSCBM,6942
+pycmplot/io.py,sha256=drQ_3rnl8ZjC3HfYJd1FMZKPJ02vz8usy6bW8L2dFIg,35585
+pycmplot/liftover.py,sha256=zGuzpcEChFz-EEY7gHHVFAkc5VhV2uLCa_qxSWavoxE,7397
 pycmplot/resources.py,sha256=r0zHy_-9wu98lkqKENYrptX54uO6np_x94_ju3v2KYE,6414
 pycmplot/stats.py,sha256=8TXHxfGc4sUr3rE3cHnS2mXfIS1PPj0YgDk1C-z2Pqk,5813
 pycmplot/data/Homo_sapiens.GRCh37.geneinfo.tsv.gz,sha256=kLldtgT5-k4ZzU5jN--woFZEuOaWe9pQ4g4hhB3sdQI,840666
@@ -13,10 +13,10 @@ pycmplot/data/hg19ToHg38.over.chain,sha256=oHPYkUIztVQtKXYauOxLOBUFKxOWSRnBKh77L
 pycmplot/plotting/circular.py,sha256=Xa_2GDW7lLKb8PeN_IL3_hvfkQaqcbQ68Q5QrxjCKs4,27295
 pycmplot/plotting/linear.py,sha256=lrioORKyOaz34UAOhBWg3W2kLq6nBT7HNkPxy8hX340,37416
 pycmplot/plotting/qq.py,sha256=ylPJj9gMlDqTOR7JWnQ7wCfvEBUczqEUVMsFiXXEt3s,20883
-pycmplot-0.2.3.dist-info/licenses/LICENSE,sha256=7HtJWU-I9Tayt7xnvHU0D6oVqeTp3hMqCbTxbkYBTZQ,20904
+pycmplot-0.2.4.dist-info/licenses/LICENSE,sha256=7HtJWU-I9Tayt7xnvHU0D6oVqeTp3hMqCbTxbkYBTZQ,20904
 pycmplot_docs/docs/conf.py,sha256=gUt_OitflxpaOrIjeP2aYJ_LCWqTRRdmo_HIcVVf3hI,2992
-pycmplot-0.2.3.dist-info/METADATA,sha256=iAIL_nG9fv9JYJ9KA5n7jtqUzr8Cpe-XADv4oy1Asls,8108
-pycmplot-0.2.3.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-pycmplot-0.2.3.dist-info/entry_points.txt,sha256=cE8IAltA_Q-QQuWQ5DE3Lv-9ktYQ_jyWaD6I97QbeyU,49
-pycmplot-0.2.3.dist-info/top_level.txt,sha256=gxbPirasq6TczoykxC2gfk5_En7R65BN-J5ADiV5i3c,23
-pycmplot-0.2.3.dist-info/RECORD,,
+pycmplot-0.2.4.dist-info/METADATA,sha256=KHXVq9Q-SQ7mV7WzQAp5e4XaYyNAyqYsJDNKcPeDOpc,7683
+pycmplot-0.2.4.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+pycmplot-0.2.4.dist-info/entry_points.txt,sha256=cE8IAltA_Q-QQuWQ5DE3Lv-9ktYQ_jyWaD6I97QbeyU,49
+pycmplot-0.2.4.dist-info/top_level.txt,sha256=gxbPirasq6TczoykxC2gfk5_En7R65BN-J5ADiV5i3c,23
+pycmplot-0.2.4.dist-info/RECORD,,