cutseq 0.0.4__tar.gz → 0.0.6__tar.gz

{cutseq-0.0.4 → cutseq-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cutseq
-Version: 0.0.4
+Version: 0.0.6
 Summary: Automatically cut adapter / barcode / UMI from NGS data
 Home-page: https://github.com/y9c/cutseq
 License: MIT

{cutseq-0.0.4 → cutseq-0.0.6}/cutseq/run.py

@@ -7,6 +7,7 @@
 # Created: 2024-04-19 18:57
 
 import argparse
+import importlib.metadata
 import logging
 import re
 import subprocess
@@ -18,6 +19,7 @@ from cutadapt.adapters import (
     NonInternalFrontAdapter,
     PrefixAdapter,
     RightmostFrontAdapter,
+    SuffixAdapter,
 )
 from cutadapt.files import InputPaths, OutputFiles
 from cutadapt.modifiers import (
@@ -29,18 +31,33 @@ from cutadapt.modifiers import (
     UnconditionalCutter,
 )
 from cutadapt.pipeline import PairedEndPipeline, SingleEndPipeline
-from cutadapt.predicates import IsUntrimmed, TooShort
+from cutadapt.predicates import Predicate, TooShort
+from cutadapt.report import Statistics
 from cutadapt.runners import make_runner
 from cutadapt.steps import (
-    InfoFileWriter,
     PairedEndFilter,
     PairedEndSink,
-    PairedSingleEndStep,
     SingleEndFilter,
     SingleEndSink,
 )
 from cutadapt.utils import Progress
 
+#  monkey patching ....
+original_method = Statistics._collect_modifier
+
+
+def patched_problematic_method(self, *args, **kwargs):
+    try:
+        return original_method(self, *args, **kwargs)
+    except AssertionError:
+        pass
+
+
+Statistics._collect_modifier = patched_problematic_method
+
+
+__version__ = importlib.metadata.version(__package__ or __name__)
+
 logging.basicConfig(
     level=logging.INFO,
     format="%(asctime)s -  %(levelname)s - %(message)s",
@@ -118,7 +135,7 @@ class BarcodeConfig:
 class CutadaptConfig:
     def __init__(self):
         self.rname_suffix = False
-        self.discarded_untrimmed = False
+        self.ensure_inline_barcode = False
         self.trim_polyA = False
         self.min_length = 20
         self.min_quality = 20
@@ -126,6 +143,25 @@ class CutadaptConfig:
         self.threads = 1
 
 
+class IsUntrimmedAny(Predicate):
+    """
+    Select reads for which no adapter match was found
+    """
+
+    def __init__(self, ref_adapters):
+        self.ref_adapters = ref_adapters
+
+    def __repr__(self):
+        return "IsUntrimmedAny()"
+
+    def test(self, read, info):
+        # check not all adapters with ref_adapters are exist in the matches
+        match_adapters = [match.adapter for match in info.matches]
+        if any([adapter not in match_adapters for adapter in self.ref_adapters]):
+            return True
+        return False
+
+
 def run_steps(steps, dry_run=False):
     if dry_run:
         print(
@@ -138,7 +174,7 @@ def run_steps(steps, dry_run=False):
     return process.stdout.decode(), process.stderr.decode()
 
 
-def pipeline_single(input1, output1, short1, untrimed1, barcode, settings):
+def pipeline_single(input1, output1, short1, untrimmed1, barcode, settings):
     modifiers = []
     # step 1: remove suffix in the read name
     modifiers.extend([SuffixRemover(".1"), SuffixRemover("/1")])
@@ -162,14 +198,11 @@ def pipeline_single(input1, output1, short1, untrimed1, barcode, settings):
     )
     # step 4: trim inline barcode
     if barcode.inline5.len > 0:
-        modifiers.append(
-            AdapterCutter(
-                [PrefixAdapter(sequence=barcode.inline5.fw, max_errors=0.2)],
-                times=1,
-            )
-        )
+        adapter_inline5 = PrefixAdapter(sequence=barcode.inline5.fw, max_errors=0.2)
+        modifiers.append(AdapterCutter([adapter_inline5], times=1))
     if barcode.inline3.len > 0:
-        modifiers.append(UnconditionalCutter(-barcode.inline3.len))
+        adapter_inline3 = SuffixAdapter(sequence=barcode.inline3.fw, max_errors=0.2)
+        modifiers.append(AdapterCutter([adapter_inline3], times=1))
 
     # step 5: extract UMI
     if barcode.umi5.len > 0:
@@ -215,19 +248,35 @@ def pipeline_single(input1, output1, short1, untrimed1, barcode, settings):
             qualities=runner.input_file_format().has_qualities(),
             interleaved=False,
         )
-        steps = [
+        steps = []
+        steps.append(
             # --info-file=info.txt
             # PairedSingleEndStep(InfoFileWriter(outfiles.open_text("info.txt"))),
             # -m 10
             SingleEndFilter(
                 TooShort(settings.min_length), outfiles.open_record_writer(short1)
             ),
-            # TODO: --max-n=0 support
-            # --discard-untrimmed
-            # SingleEndFilter( IsUntrimmed(), IsUntrimmed(), pair_filter_mode="any"),
+        )
+        if (
+            settings.ensure_inline_barcode
+            and barcode.inline5.len + barcode.inline3.len > 0
+        ):
+            ref_adapters = []
+            if barcode.inline5.len > 0:
+                ref_adapters.append(adapter_inline5)
+            if barcode.inline3.len > 0:
+                ref_adapters.append(adapter_inline3)
+            steps.append(
+                # TODO: --max-n=0 support
+                SingleEndFilter(
+                    IsUntrimmedAny(ref_adapters),
+                    outfiles.open_record_writer(untrimmed1, interleaved=False),
+                ),
+            )
+        steps.append(
             # -o
             SingleEndSink(outfiles.open_record_writer(output1, interleaved=False)),
-        ]
+        )
         pipeline = SingleEndPipeline(modifiers, steps)
         _stats = runner.run(pipeline, Progress(), outfiles)
         # _ = stats.as_json()
@@ -241,7 +290,7 @@ def pipeline_paired(
     output2,
     short1,
     short2,
-    untrimed1,
+    untrimmed1,
     untrimmed2,
     barcode,
     settings,
@@ -290,23 +339,19 @@ def pipeline_paired(
     )
     # step 4: trim inline barcode
     if barcode.inline5.len > 0:
+        adapter_inline5 = PrefixAdapter(sequence=barcode.inline5.fw, max_errors=0.2)
         modifiers.append(
             (
-                AdapterCutter(
-                    [PrefixAdapter(sequence=barcode.inline5.fw, max_errors=0.2)],
-                    times=1,
-                ),
+                AdapterCutter([adapter_inline5], times=1),
                 UnconditionalCutter(-barcode.inline5.len),
             )
         )
     if barcode.inline3.len > 0:
+        adapter_inline3 = PrefixAdapter(sequence=barcode.inline3.rc, max_errors=0.2)
         modifiers.append(
             (
                 UnconditionalCutter(-barcode.inline3.len),
-                AdapterCutter(
-                    [BackAdapter(sequence=barcode.inline3.rc, max_errors=0.2)],
-                    times=1,
-                ),
+                AdapterCutter([adapter_inline3], times=1),
             )
         )
 
@@ -387,21 +432,40 @@ def pipeline_paired(
             qualities=runner.input_file_format().has_qualities(),
             interleaved=False,
         )
-        steps = [
-            # --info-file=info.txt
-            # PairedSingleEndStep(InfoFileWriter(outfiles.open_text("info.txt"))),
-            # -m 10:10
+        steps = []
+        # --info-file=info.txt
+        # PairedSingleEndStep(InfoFileWriter(outfiles.open_text("info.txt"))),
+        # -m 10:10
+        steps.append(
             PairedEndFilter(
                 TooShort(settings.min_length),
                 TooShort(settings.min_length),
                 outfiles.open_record_writer(short1, short2, interleaved=False),
-            ),
-            # TODO: --max-n=0 support
-            # --discard-untrimmed
-            # PairedEndFilter( IsUntrimmed(), IsUntrimmed(), pair_filter_mode="any"),
+            )
+        )
+        if (
+            settings.ensure_inline_barcode
+            and barcode.inline5.len + barcode.inline3.len > 0
+        ):
+            steps.append(
+                # TODO: --max-n=0 support
+                PairedEndFilter(
+                    IsUntrimmedAny([adapter_inline5])
+                    if barcode.inline5.len > 0
+                    else None,
+                    IsUntrimmedAny([adapter_inline3])
+                    if barcode.inline3.len > 0
+                    else None,
+                    outfiles.open_record_writer(
+                        untrimmed1, untrimmed2, interleaved=False
+                    ),
+                    pair_filter_mode="any",
+                )
+            )
+        steps.append(
             # -o ... -p ...
-            PairedEndSink(outfiles.open_record_writer(output1, output2)),
-        ]
+            PairedEndSink(outfiles.open_record_writer(output1, output2))
+        )
         pipeline = PairedEndPipeline(modifiers, steps)
         _stats = runner.run(pipeline, Progress(), outfiles)
         # _ = stats.as_json()
@@ -411,12 +475,9 @@ def pipeline_paired(
 def run_cutseq(args):
     barcode_config = BarcodeConfig(args.adapter_scheme.upper())
     settings = CutadaptConfig()
-    if args.with_rname_suffix:
-        settings.rname_suffix = True
-    if args.untrimmed_file is None:
-        settings.discarded_untrimmed = True
-    if args.trim_polyA:
-        settings.trim_polyA = True
+    settings.rname_suffix = args.with_rname_suffix
+    settings.ensure_inline_barcode = args.ensure_inline_barcode
+    settings.trim_polyA = args.trim_polyA
     settings.threads = args.threads
     settings.min_length = args.min_length
     settings.dry_run = args.dry_run
@@ -506,6 +567,12 @@ def main():
         action="store_true",
         help="R1 and R2 suffix cotains suffix. MGI platform.",
     )
+
+    parser.add_argument(
+        "--ensure-inline-barcode",
+        action="store_true",
+        help="Output discarded reads without inline barcode.",
+    )
     parser.add_argument(
         "-U",
         "--untrimmed-file",
@@ -529,6 +596,11 @@ def main():
         action="store_true",
         help="Print command instead of running it.",
     )
+
+    parser.add_argument(
+        "-V", "--version", action="version", version=f"%(prog)s {__version__}"
+    )
+
     args = parser.parse_args()
 
     if args.adapter_name is not None:
@@ -584,12 +656,8 @@ def main():
     args.short_file = validate_output_file(
         args.short_file, args.input_file, args.output_prefix, "short"
     )
-    args.untrimmed_file = (
-        validate_output_file(
-            args.untrimmed_file, args.input_file, args.output_prefix, "untrimmed"
-        )
-        if args.untrimmed_file is not None
-        else [None] * len(args.input_file)
+    args.untrimmed_file = validate_output_file(
+        args.untrimmed_file, args.input_file, args.output_prefix, "untrimmed"
     )
 
     run_cutseq(args)

{cutseq-0.0.4 → cutseq-0.0.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cutseq"
-version = "0.0.4"
+version = "0.0.6"
 description = "Automatically cut adapter / barcode / UMI from NGS data"
 authors = ["Ye Chang <yech1990@gmail.com>"]
 license = "MIT"