Commit 5e62c05a authored by iquasere's avatar iquasere
Browse files

Preprocessing now considers "adapter content" module

closes #13
parent 71e2cd10
{% set name = "mosca" %}
{% set version = "1.3.0" %}
{% set version = "1.3.1" %}
{% set sha256 = "87cbca039ea9b9c85f417543f2426b2b2acffebe58179878ee6872a32ae949ba" %}
package:
......@@ -40,7 +40,7 @@ requirements:
- svn >=1.9.7
- reportlab >=3.5.45
- openpyxl >=3.0.3
- xlrd >=0.9.0
- xlrd =1.2
- r-rcolorbrewer >=1.1.2
- pandas >=1.1.4
- scikit-learn >=0.23.1
......
......@@ -6,7 +6,7 @@ import argparse
import multiprocessing
import sys
__version__ = '1.3.0'
__version__ = '1.3.1'
parser = argparse.ArgumentParser(description="MOSCA's main script")
parser.add_argument("-s", "--snakefile", type=str, default="{}/Snakefile".format(sys.path[0]), help="Snakefile file")
......
......@@ -58,8 +58,10 @@ class Preprocesser:
def has_adapters(self, fastqc_report):
data = parse_fastqc(fastqc_report)
terms_list = ['Adapter', 'Illumina',
'Primer'] # Terms that appear in FastQC chapter "overrepresented sequences"
if not data['Adapter Content'][0] == 'pass':
return True
terms_list = [
'Adapter', 'Illumina', 'Primer'] # Terms that appear in FastQC chapter "overrepresented sequences"
if not data['Overrepresented sequences'][0] == 'pass':
i = 0
while i < len(data['Overrepresented sequences'][1]['Possible Source']):
......
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