if options.min_insert_size > 0 else None,
'--no-discordant': True,
'--no-mixed': True
},
SOAP: {
'-x':
options.max_insert_size,
'-m':
options.min_insert_size if options.min_insert_size > 0 else 100
}
}[options.aligner], **aligner_options)
aligner_command = aligner_exec + aligner_options_string() + {
BOWTIE:
' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s',
BOWTIE2:
' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s',
SOAP:
' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired'
}[options.aligner]
logm('Aligner command: %s' % aligner_command)
bs_pair_end(options.infilename_1, options.infilename_2, asktag,
options.adapter_file, options.cutnumber1,
options.cutnumber2, options.no_split, indexname,
aligner_command, db_path, tmp_path, outfile, XS_pct,
XS_count)
outfile.close()
aligner_command = aligner_exec + aligner_options_string() + \
{ BOWTIE : ' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s',
BOWTIE2 : ' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s',
SOAP : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired' #,
# RMAP : # rmappe, also paste two inputs into one file.
}[options.aligner]
logm('Aligner command: %s' % aligner_command)
if '--end-to-end' not in aligner_options:
aligner_options_defaults[BOWTIE2].update({'-D': 50})
else:
aligner_options_defaults[BOWTIE2].update({
'-D':
50,
'-L':
15,
'--score-min':
'L,-0.6,-0.6'
})
bs_pair_end(options.infilename_1, options.infilename_2, asktag,
options.adapter_file, options.cutnumber1,
options.cutnumber2, options.no_split, str_no_mismatches,
aligner_command, db_path, tmp_path, outfile, XS_pct,
XS_count, options.adapter_mismatch,
options.Output_multiple_hit, options.Output_unmapped_hit)
outfile.close()
'--no-mixed' : True
},
SOAP: {
'-x' : options.max_insert_size,
'-m' : options.min_insert_size if options.min_insert_size > 0 else 100
}}[options.aligner],
**aligner_options)
aligner_command = aligner_exec + aligner_options_string() + { BOWTIE : ' %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s %(output_file)s',
BOWTIE2 : ' -x %(reference_genome)s -f -1 %(input_file_1)s -2 %(input_file_2)s -S %(output_file)s',
SOAP : ' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file_1)s -b %(input_file_2)s -2 %(output_file)s.unpaired'}[options.aligner]
logm('Aligner command: %s' % aligner_command)
bs_pair_end(options.infilename_1,
options.infilename_2,
asktag,
options.adapter_file,
options.cutnumber1,
options.cutnumber2,
options.no_split,
indexname,
aligner_command,
db_path,
tmp_path,
outfile
)
outfile.close()
}[options.aligner]
logm('Aligner command: %s' % aligner_command)
if '--end-to-end' not in aligner_options:
aligner_options_defaults[BOWTIE2].update({'-D' : 50})
else:
aligner_options_defaults[BOWTIE2].update({'-D' : 50, '-L': 15, '--score-min': 'L,-0.6,-0.6' })
bs_pair_end(options.infilename_1,
options.infilename_2,
asktag,
options.adapter_file,
int(options.cutnumber1),
int(options.cutnumber2),
options.no_split,
str_no_mismatches,
aligner_command,
db_path,
tmp_path,
outfile,
XS_pct,
XS_count,
options.adapter_mismatch,
options.Output_multiple_hit,
options.Output_unmapped_hit
)
outfile.close()
