报错内容如下：
(env_name) [lhh@gpu RawData]$ python merge_deletions.py -f deletions.list
Traceback (most recent call last): File "merge_deletions.py", line 67, in <module> save_deletions(master_dictionary, options.filename+'.bed') NameError: name 'master_dictionary' is not defined
合并的文件为deletions_A.bed,deletions_B.bed...
内容为：
chr1 287 555 + ID1 0
chr1 676 789 +ID2 1
merge_deletions.py代码为
#! /usr/bin/env python
def create_master_dict(sample, fname):
with open(fname, 'r') as masterfile:
x = 0
master_dict = {}
for line in masterfile:
field = line.rsplit()
if line[0] == 'ins_chr':
pass
else:
coords = '\t'.join(field[:5])
master_dict[x] = {'coords': coords, 'accessions': [sample]}
x += 1
return master_dict
def merge_deletions(master, fname, sample):
with open(fname, 'r') as infile:
for line in infile:
field = line.rsplit()
coords = '\t'.join(field[:5])
i = len(master)-1
x = 0
while x <= i:
if master[x]['coords'] == coords:
master[x]['accessions'].append(sample)
break
elif x == i:
master[x+1] = {'coords': coords, 'accessions': [sample]}
break
else:
x += 1
def save_deletions(master, outf):
with open(outf, 'w+') as outfile:
for key, value in master.iteritems():
accessions = set(value['accessions'])
outfile.write('{c}\t{a}\n'.format(c=value['coords'], a=','.join(accessions)))
if __name__ == "__main__":
import os
from argparse import ArgumentParser
parser = ArgumentParser(description='Merge TE deletions calls')
parser.add_argument('-f', '--filename', help='filename prefix for merge files', required=True)
options = parser.parse_args()
for dirs in os.listdir('.'):
if os.path.isdir(dirs) is True:
os.chdir(dirs)
if os.path.isfile(options.filename+'_{d}.bed'.format(d=dirs)) is True:
print "Processing {d}".format(d=dirs)
try:
master_dictionary
except NameError:
master_dictionary = create_master_dict(dirs, options.filename+'_{d}.bed'.format(d=dirs))
else:
merge_deletions(master_dictionary, options.filename+'_{d}.bed'.format(d=dirs), dirs)
os.chdir('..')
else:
os.chdir('..')
else:
pass
save_deletions(master_dictionary, options.filename+'.bed')
不知道你这个问题是否已经解决, 如果还没有解决的话: