cutseq 0.0.44__tar.gz → 0.0.45__tar.gz

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Files changed (5) hide show
  1. {cutseq-0.0.44 → cutseq-0.0.45}/PKG-INFO +1 -1
  2. {cutseq-0.0.44 → cutseq-0.0.45}/cutseq/run.py +8 -6
  3. {cutseq-0.0.44 → cutseq-0.0.45}/pyproject.toml +1 -1
  4. {cutseq-0.0.44 → cutseq-0.0.45}/README.md +0 -0
  5. {cutseq-0.0.44 → cutseq-0.0.45}/cutseq/run_cmd.py +0 -0
{cutseq-0.0.44 → cutseq-0.0.45}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: cutseq
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- Version: 0.0.44
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+ Version: 0.0.45
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  Summary: Automatically cut adapter / barcode / UMI from NGS data
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  Home-page: https://github.com/y9c/cutseq
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  License: MIT
{cutseq-0.0.44 → cutseq-0.0.45}/cutseq/run.py RENAMED
@@ -344,12 +344,13 @@ def pipeline_single(input1, output1, short1, untrimmed1, barcode, settings):
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  # step 7: trim polyA
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  if settings.trim_polyA:
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  pA_max_errors = 0.15
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+ pA_max_length = 100
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  if barcode.strand == "+":
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  modifiers.append(
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  AdapterCutter(
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  [
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  NonInternalBackAdapter(
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- sequence="A" * 100, max_errors=pA_max_errors
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+ sequence="A" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  )
@@ -359,7 +360,7 @@ def pipeline_single(input1, output1, short1, untrimmed1, barcode, settings):
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  AdapterCutter(
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  [
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  NonInternalFrontAdapter(
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- sequence="T" * 100, max_errors=pA_max_errors
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+ sequence="T" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  )
@@ -580,20 +581,21 @@ def pipeline_paired(
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  # step 7: trim polyA
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  if settings.trim_polyA:
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  pA_max_errors = 0.15
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+ pA_max_length = 100
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  if barcode.strand == "+":
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  modifiers.append(
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  (
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  AdapterCutter(
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  [
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  NonInternalBackAdapter(
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- sequence="A" * 100, max_errors=pA_max_errors
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+ sequence="A" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  ),
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  AdapterCutter(
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  [
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  NonInternalFrontAdapter(
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- sequence="T" * 100, max_errors=pA_max_errors
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+ sequence="T" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  ),
@@ -605,14 +607,14 @@ def pipeline_paired(
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  AdapterCutter(
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  [
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  NonInternalFrontAdapter(
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- sequence="T" * 100, max_errors=pA_max_errors
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+ sequence="T" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  ),
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  AdapterCutter(
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  [
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  NonInternalBackAdapter(
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- sequence="A" * 100, max_errors=pA_max_errors
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+ sequence="A" * pA_max_length, max_errors=pA_max_errors
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  )
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  ]
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  ),
{cutseq-0.0.44 → cutseq-0.0.45}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "cutseq"
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- version = "0.0.44"
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+ version = "0.0.45"
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  description = "Automatically cut adapter / barcode / UMI from NGS data"
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  authors = ["Ye Chang <yech1990@gmail.com>"]
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  license = "MIT"
{cutseq-0.0.44 → cutseq-0.0.45}/README.md RENAMED
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{cutseq-0.0.44 → cutseq-0.0.45}/cutseq/run_cmd.py RENAMED
File without changes