for gene in gene_list:
# First row is ensembl_id, but we ignoreit.
output_writer.writerow(['did_not_read_ensembl_id', gene])
writecount += 1
print('%s rows written, no more genes to write.' %writecount)
print('File written to %s' %output_fullpath)
return None
if __name__ == '__main__':
if len(sys.argv) < 3:
print('List of comma-separated input filenames (partial paths relative to input folder)'\
' and output filename (relative to output folder) must be specified'\
' in command line.')
sys.exit()
comma_separated_input_partialpaths = sys.argv[1]
output_partialpath = sys.argv[2]
# Parse comma-separated inputs
input_partialpaths = comma_separated_input_partialpaths.split(',')
input_fullpaths = []
for i in input_partialpaths:
input_fullpaths.append(os.path.join(mydirs.inputdir, i))
output_fullpath = os.path.join(mydirs.inputdir, output_partialpath)
gene_list = []
for filepath in input_fullpaths:
gene_list += extract_gene_names_from_textfile(filepath, genename_colname)
write_gene_list_to_file(output_fullpath, gene_list, write_ensembl_id=False)
for i in col_indices:
influence_on_cgenes.append(current_row[i])
influence.writenext([current_gene] + influence_on_cgenes)
print("%s rows read, %s written." % (influence.readrowcount, influence.writerowcount))
if __name__ == "__main__":
if len(sys.argv) < 5:
print(
"4 files: influence matrix, aberrant, outlier, and outputfile "
"must be specified in command line. \nPaths relative to input folder."
)
sys.exit()
influence_partialpath = sys.argv[1]
aberrant_partialpath = sys.argv[2]
outlier_partialpath = sys.argv[3]
output_partialpath = sys.argv[4]
influence_fullpath = os.path.join(mydirs.outputdir, influence_partialpath)
aberrant_fullpath = os.path.join(mydirs.inputdir, aberrant_partialpath)
outlier_fullpath = os.path.join(mydirs.inputdir, outlier_partialpath)
output_fullpath = os.path.join(mydirs.outputdir, output_partialpath)
# Get list of aberrant and list of outlier genes.
aberrant_genes = extract_gene_names_from_textfile(aberrant_fullpath, genename_colname)
outlier_genes = extract_gene_names_from_textfile(outlier_fullpath, genename_colname)
# Get influence values between aberrant genes and outlier genes.
get_influence(influence_fullpath, aberrant_genes, outlier_genes, output_fullpath)
output_writer.writerow(['did_not_read_ensembl_id', gene])
writecount += 1
print('%s rows written, no more genes to write.' % writecount)
print('File written to %s' % output_fullpath)
return None
if __name__ == '__main__':
if len(sys.argv) < 3:
print('List of comma-separated input filenames (partial paths relative to input folder)'\
' and output filename (relative to output folder) must be specified'\
' in command line.')
sys.exit()
comma_separated_input_partialpaths = sys.argv[1]
output_partialpath = sys.argv[2]
# Parse comma-separated inputs
input_partialpaths = comma_separated_input_partialpaths.split(',')
input_fullpaths = []
for i in input_partialpaths:
input_fullpaths.append(os.path.join(mydirs.inputdir, i))
output_fullpath = os.path.join(mydirs.inputdir, output_partialpath)
gene_list = []
for filepath in input_fullpaths:
gene_list += extract_gene_names_from_textfile(filepath,
genename_colname)
write_gene_list_to_file(output_fullpath, gene_list, write_ensembl_id=False)
influence.writenext([current_gene] + influence_on_cgenes)
print('%s rows read, %s written.' %
(influence.readrowcount, influence.writerowcount))
if __name__ == '__main__':
if len(sys.argv) < 5:
print('4 files: influence matrix, aberrant, outlier, and outputfile '\
'must be specified in command line. \nPaths relative to input folder.')
sys.exit()
influence_partialpath = sys.argv[1]
aberrant_partialpath = sys.argv[2]
outlier_partialpath = sys.argv[3]
output_partialpath = sys.argv[4]
influence_fullpath = os.path.join(mydirs.outputdir, influence_partialpath)
aberrant_fullpath = os.path.join(mydirs.inputdir, aberrant_partialpath)
outlier_fullpath = os.path.join(mydirs.inputdir, outlier_partialpath)
output_fullpath = os.path.join(mydirs.outputdir, output_partialpath)
# Get list of aberrant and list of outlier genes.
aberrant_genes = extract_gene_names_from_textfile(aberrant_fullpath,
genename_colname)
outlier_genes = extract_gene_names_from_textfile(outlier_fullpath,
genename_colname)
# Get influence values between aberrant genes and outlier genes.
get_influence(influence_fullpath, aberrant_genes, outlier_genes,
output_fullpath)
