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update ngs module to address bug #93

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merged 1 commit into from
Sep 11, 2024
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update ngs module to address bug #93

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6 changes: 3 additions & 3 deletions screenpro/ngs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ def get_counts_matrix(self, fastq_dir, samples, get_recombinant=False, cas_type=
if get_recombinant:
raise ValueError("Recombinants are not applicable for single guide design!")
if protospacer_length == 'auto':
protospacer_length = self.library['protospacer'].str.lengths().unique().to_list()[0]
protospacer_length = self.library['protospacer'].str.len_bytes().unique().to_list()[0]
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@abearab abearab Sep 17, 2024

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@isabelleliuu – is this specific after an specific polars version? It would be helpful if we specify version (e.g. polars>=*.*)

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@isabelleliuu isabelleliuu Sep 17, 2024

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@abearab based on the polars github releases ([https://github.com/pola-rs/polars/releases/tag/py-0.19.8]) this change was made with the Python Polars 0.19.8 release


for sample_id in samples:
cnt = self._process_cas9_single_guide_sample(
Expand All @@ -218,8 +218,8 @@ def get_counts_matrix(self, fastq_dir, samples, get_recombinant=False, cas_type=
if get_recombinant: recombinants = {}

if protospacer_length == 'auto':
protospacer_A_length = self.library['protospacer_A'].str.lengths().unique().to_list()[0]
protospacer_B_length = self.library['protospacer_B'].str.lengths().unique().to_list()[0]
protospacer_A_length = self.library['protospacer_A'].str.len_bytes().unique().to_list()[0]
protospacer_B_length = self.library['protospacer_B'].str.len_bytes().unique().to_list()[0]
elif isinstance(protospacer_length, dict):
protospacer_A_length = protospacer_length['protospacer_A']
protospacer_B_length = protospacer_length['protospacer_B']
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