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# Usage: python prepare_gene_file.py all-ath-gene-position.txt > gene_file.txt
# all-ath-gene-position contains all gene IDs in the genome, and their positions, orientation, etc, in BED format.
# See ../Data/information/all-ath-gene-position.txt
# Purpose: get gene name and gene annotation
# 2 JAN 2017 hui SLCU
import sys
import os
###################################################################################
GENE_DESCRIPTION = '../Data/information/gene_description_20140101.txt'
AGI_TO_GENE_NAMES = '../Data/information/AGI-to-gene-names.txt'
###################################################################################
def get_description(x, d):
result = ''
if x in d:
result = '\t' + d[x]
else:
result = '\tNot Found'
return result
def make_AGI_to_gene_name_dict(fname):
d = {}
f = open(fname)
for line in f:
line = line.strip()
lst = line.split()
agi = lst[0]
name = lst[1]
if not agi in d:
d[agi] = name
else:
d[agi] += ';' + name
f.close()
return d
## main
# make a dictionary of gene description
f0 = open(GENE_DESCRIPTION)
d = {}
for line in f0:
line = line.strip()
lst = line.split('\t')
id = lst[0]
id = id[0:9] # AGI id, omit .1, .2, .3, etc
s = '\t'.join(lst[1:])
if not id in d:
d[id] = s
else:
d[id] += '\t' + s
f0.close()
agi2genename_dict = make_AGI_to_gene_name_dict(AGI_TO_GENE_NAMES)
locus_file = sys.argv[1] # location of genes
f = open(locus_file) # see all-ath-gene-position.txt
for line in f:
line = line.strip()
lst = line.split('\t')
x = lst[3]
c = lst[0]
ss = lst[1]
ee = lst[2]
strand = lst[5]
result = [x]
if x in agi2genename_dict and not x == agi2genename_dict[x]:
result.append(agi2genename_dict[x])
else:
result.append(' ') # if no gene name, use a space
result.extend([c, ss, ee, strand, get_description(x, d)])
print('\t'.join(result))
f.close()
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