BOWTIE2:
' -x %(reference_genome)s -f -U %(input_file)s -S %(output_file)s',
SOAP:
' -D %(reference_genome)s.fa.index -o %(output_file)s -a %(input_file)s'
}[options.aligner]
logm('Aligner command: %s' % aligner_command)
# single end reads
if options.rrbs: # RRBS scan
bs_rrbs(options.infilename, options.rrbs_taginfo,
options.adapter_file, options.cutnumber1,
options.cutnumber2, options.no_split, indexname,
aligner_command, db_path, tmp_path, outfile, XS_pct,
XS_count)
else: # Normal single end scan
bs_single_end(options.infilename, asktag, options.adapter_file,
options.cutnumber1, options.cutnumber2,
options.no_split, indexname, aligner_command,
db_path, tmp_path, outfile, XS_pct, XS_count)
else:
logm('Pair end')
# pair end specific default options
aligner_options = dict({
BOWTIE: {
'--ff':
asktag == 'N',
'--fr':
asktag == 'Y',
'-X':
options.max_insert_size,
'-I':
options.min_insert_size
if options.min_insert_size > 0 else None
RMAP : ' -c %(reference_genome)s.fa -o %(output_file)s %(input_file)s'
}[options.aligner]
logm('Aligner command: %s' % aligner_command)
# single end reads
if options.rrbs: # RRBS scan
bs_rrbs(options.infilename, 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,
options.cut_format)
else: # Normal single end scan
bs_single_end(options.infilename, 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)
else:
logm('Pair end')
# pair end specific default options
aligner_options = dict(
{
BOWTIE: {
'--fr':
True,
'-X':
options.max_insert_size,
'-I':
options.min_insert_size
options.adapter_file,
options.cutnumber1,
options.cutnumber2,
options.no_split,
indexname,
aligner_command,
db_path,
tmp_path,
outfile)
else: # Normal single end scan
bs_single_end( options.infilename,
asktag,
options.adapter_file,
options.cutnumber1,
options.cutnumber2,
options.no_split,
indexname,
aligner_command,
db_path,
tmp_path,
outfile
)
else:
logm('Pair end')
# pair end specific default options
aligner_options = dict({BOWTIE: {'--ff' : asktag == 'N',
'--fr' : asktag == 'Y',
'-X' : options.max_insert_size,
'-I' : options.min_insert_size if options.min_insert_size > 0 else None
},
BOWTIE2 : {
'--ff' : asktag == 'N',
XS_count,
options.adapter_mismatch,
options.Output_multiple_hit,
options.Output_unmapped_hit,
options.cut_format
)
else: # Normal single end scan
bs_single_end( options.infilename,
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
)
else:
logm('Pair end')
# pair end specific default options
aligner_options = dict({BOWTIE: {'--fr' : True,
'-X' : options.max_insert_size,
'-I' : options.min_insert_size if options.min_insert_size > 0 else None,
'-a' : True # "-k 2" in bowtie would not report the best two
