def action(args):
book = Workbook()
filetype = args.type
(infiles, ) = args.infiles
if filetype == 'Analysis':
tabs = ['0_QC', '1_QC_Metrics', '2_QC_by_Gene', '3_QC_by_Exon',
'4_SV_Gridss', '5_SV_Breakdancer', '6_SV_Pindel',
'7_CNV_Gene', '8_CNV_Exon', '9_Clinically_Flagged',
'10_SNP','11_INDEL', '12_MSI', '13_Amplicons', '14_PolyHunter']
# for each tab, find its file and process.
for tab in tabs:
try:
#Find file in infiles
sheet_name, fname = process_files(infiles, tab, filetype)
print sheet_name, fname
write_workbook(sheet_name, book, fname)
except TypeError:
print "Tab %s not processed" % tab
elif filetype == 'Combined':
for fname in infiles:
(f_path, f_name) = os.path.split(fname)
if re.search(str(filetype), f_name):
(f_short_name, f_extension) = os.path.splitext(f_name)
sheet_name = f_short_name.split('Combined_')
sheet_name = '_'.join(sheet_name[1:30])
print sheet_name, fname
write_workbook(sheet_name, book, fname)
book.filename=args.outfile
book.close()
def action(args):
book = Workbook()
filetype = args.type
(infiles, ) = args.infiles
if filetype == 'Analysis':
tabs = [
'0_QC', '1_QC_Metrics', '2_QC_by_Gene', '3_QC_by_Exon',
'4_SV_Gridss', '5_SV_Breakdancer', '6_SV_Pindel', '7_CNV_Gene',
'8_CNV_Exon', '9_Clinically_Flagged', '10_SNP', '11_INDEL',
'12_MSI', '13_Amplicons', '14_PolyHunter', '15_Gene_Coverage',
'16_Exon_Coverage'
]
# for each tab, find its file and process.
for tab in tabs:
try:
#Find file in infiles
sheet_name, fname = process_files(infiles, tab, filetype)
print sheet_name, fname
write_workbook(sheet_name, book, fname)
except TypeError:
print "Tab %s not processed" % tab
elif filetype == 'Combined':
for fname in infiles:
(f_path, f_name) = os.path.split(fname)
if re.search(str(filetype), f_name):
(f_short_name, f_extension) = os.path.splitext(f_name)
sheet_name = f_short_name.split('Combined_')
sheet_name = '_'.join(sheet_name[1:30])
print sheet_name, fname
write_workbook(sheet_name, book, fname)
book.filename = args.outfile
book.close()
def action(args):
book = Workbook()
(infiles, ) = args.infiles
for fname in infiles:
(f_path, f_name) = os.path.split(fname)
(f_short_name, f_extension) = os.path.splitext(f_name)
print(fname)
write_workbook(f_short_name, book, fname)
book.filename = args.outfile
book.close()