def read_genes(filename, chromosome=None, chromosome_map=None, rna=False):
genes = []
with open(filename, 'r') as f:
try:
# first two lines hold title and column headers:
title = f.next()
# figure out chromosome from title
if chromosome is None:
for key in chromosome_map:
if title.find(key) > -1:
chromosome = chromosome_map[key]
break
if chromosome is None:
raise Exception(
"Can't figure out chromosome for: %s\ntitle=%s", filename,
title)
# parse out column headers
columns = {}
i = 0
for column in f.next().strip().split("\t"):
columns[column] = i
i += 1
except Exception as e:
print "Error reading file: " + filename
print str(type(e)) + ": " + str(e)
return None
try:
# read line into objects
for line in f:
# strip leading and trailing whitespace
line = line.strip()
# skip blank lines
if (len(line) == 0): continue
fields = line.split("\t")
gene = OpenStruct()
gene.name = fields[columns['Locus_tag']] # locus tag
if (fields[columns['Locus']] != '-'):
gene.common_name = fields[columns['Locus']] # locus
if 'Gi' in columns:
gene.gi = int(fields[columns['Gi']])
gene.geneid = int(fields[columns['GeneID']])
gene.strand = fields[columns['Strand']] # '+' or '-'
gene.start = int(fields[columns['Start']])
gene.end = int(fields[columns['End']])
if (fields[columns['Product Name']] != '-'):
gene.description = fields[columns['Product Name']] # locus
gene.chromosome = chromosome
if rna:
gene.type = guess_rna_gene_type(gene.description)
else:
gene.type = 'CDS'
genes.append(gene)
except Exception as e:
print "Error reading line: " + line
print str(type(e)) + ": " + str(e)
return genes
