I used defaultdic to store some variables but the output is blank
claire morandin
claire.morandin at gmail.com
Sun Jun 9 06:12:28 EDT 2013
I have the following script which does not return anything, no apparent mistake but my output file is empty.I am just trying to extract some decimal number from a file according to their names which are in another file. from collections import defaultdict import numpy as np
[code]ercc_contigs= {}
for line in open ('Faq_ERCC_contigs_name.txt'):
gene = line.strip().split()
ercc_rpkm = defaultdict(lambda: np.zeros(1, dtype=float))
output_file = open('out.txt','w')
rpkm_file = open('RSEM_Faq_Q1.genes.results.txt')
rpkm_file.readline()
for line in rpkm_file:
line = line.strip()
columns = line.strip().split()
gene = columns[0].strip()
rpkm_value = float(columns[6].strip())
if gene in ercc_contigs:
ercc_rpkm[gene] += rpkm_value
ercc_fh = open ('out.txt','w')
for gene, rpkm_value in ercc_rpkm.iteritems():
ercc = '{0}\t{1}\n'.format(gene, rpkm_value)
ercc_fh.write (ercc)[/code]
If someone could help me spot what's wrong it would be much appreciate cheers
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