cutseq 0.0.45__tar.gz → 0.0.47__tar.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.
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@@ -99,9 +99,8 @@ logging.basicConfig(
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def reverse_complement(b):
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-
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-
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-
)
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+
comp_map = dict(zip("ATGCatgc", "TACGtacg"))
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103
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return "".join([comp_map.get(x, x) for x in b[::-1]])
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def remove_fq_suffix(f):
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@@ -122,6 +121,11 @@ class BarcodeSeq:
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self.rc = reverse_complement(seq)
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self.len = len(seq)
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def __repr__(self):
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125
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if self.len == 0:
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126
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return ""
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127
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return f"{self.fw} ({self.rc})"
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class BarcodeConfig:
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"""
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@@ -640,8 +644,20 @@ def pipeline_paired(
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# dry run and exit code
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if settings.dry_run:
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647
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for b in [
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648
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"p5",
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"p7",
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"inline5",
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"inline3",
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"umi5",
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"umi3",
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654
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"mask5",
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655
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"mask3",
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"strand",
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]:
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print(f"{b}: {getattr(barcode, b)}")
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for i, m in enumerate(modifiers, 1):
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644
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-
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logging.info(f"Step {i}: {m}")
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return
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inpaths = InputPaths(input1, input2)
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File without changes
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File without changes
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