claire morandin wrote:
> 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()
You probably planned to use the loop above to populate the ercc_contigs
dict, but there's no code for that.
> 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())
Remember that ercc_contigs is empty; therefore the test
> if gene in ercc_contigs:
always fails and the following line is never executed.
> 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
By the way: it is unclear to my why you are using a numpy array here:
> ercc_rpkm = defaultdict(lambda: np.zeros(1, dtype=float))
I think
ercc_rpkm = defaultdict(float)
should suffice. Also:
> line = line.strip()
> columns = line.strip().split()
> gene = columns[0].strip()
> rpkm_value = float(columns[6].strip())
You can remove all strip() method calls here as line.split() implicitly
removes all whitespace.
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