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Polya trimming correction

Merged BIOPZ-Katsantoni Maria requested to merge polya_trimming_correction into master
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10 files
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@@ -228,9 +228,13 @@ def main():
snakemake_table.loc[index, 'soft_clip'] = options.soft_clip
snakemake_table.loc[index, 'pass_mode'] = options.pass_mode
snakemake_table.loc[index, 'libtype'] = options.libtype
if options.trim_polya is True:
snakemake_table.loc[index, 'fq1_polya'] = trim_polya(
fq1_polya_3p, fq1_polya_5p = trim_polya(
row[input_dict.loc['mate1_direction', 'labkey']])
snakemake_table.loc[index, 'fq1_polya_3p'] = fq1_polya_3p
snakemake_table.loc[index, 'fq1_polya_5p'] = fq1_polya_5p
snakemake_table.loc[index, 'kallisto_directionality'] = \
get_kallisto_directionality(
row[input_dict.loc['mate1_direction', 'labkey']])
@@ -247,8 +251,10 @@ def main():
input_dict.loc['fq2_5p', 'labkey']]
if options.trim_polya is True:
snakemake_table.loc[index, 'fq2_polya'] = trim_polya(
fq2_polya_3p, fq2_polya_5p = trim_polya(
row[input_dict.loc['mate2_direction', 'labkey']])
snakemake_table.loc[index, 'fq2_polya_3p'] = fq2_polya_3p
snakemake_table.loc[index, 'fq2_polya_5p'] = fq2_polya_5p
snakemake_table.fillna('XXXXXXXXXXXXX', inplace=True)
snakemake_table = snakemake_table.astype(
@@ -322,14 +328,15 @@ def get_kallisto_directionality(directionality):
def trim_polya(sense):
if sense == 'SENSE':
polya = 'AAAAAAAAAAAAAAAAA'
polya_3p = 'AAAAAAAAAAAAAAAAA'
polya_5p = 'XXXXXXXXXXXXXXXXX'
elif sense == 'ANTISENSE':
polya = 'TTTTTTTTTTTTTTTTT'
elif sense == 'RANDOM':
polya = 'AAAAAAAAAAAAAAAAA'
polya_3p = 'XXXXXXXXXXXXXXXXX'
polya_5p = 'TTTTTTTTTTTTTTTTT'
else:
polya = 'XXXXXXXXXXXXXXXXX'
return polya
polya_3p = 'XXXXXXXXXXXXXXXXX'
polya_5p = 'XXXXXXXXXXXXXXXXX'
return polya_3p, polya_5p
if __name__ == '__main__':
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