splitting lines with " from an infile in python

Question

I have a series of input files such as:

chr1    hg19_refFlat    exon    44160380    44160565    0.000000    +   .   gene_id "KDM4A"; transcript_id "KDM4A";
chr1    hg19_refFlat    exon    19563636    19563732    0.000000    -   .   gene_id "EMC1"; transcript_id "EMC1";
chr1    hg19_refFlat    exon    52870219    52870551    0.000000    +   .   gene_id "PRPF38A"; transcript_id "PRPF38A";
chr1    hg19_refFlat    exon    53373540    53373626    0.000000    -   .   gene_id "ECHDC2"; transcript_id "ECHDC2_dup2";
chr1    hg19_refFlat    exon    11839859    11840067    0.000000    +   .   gene_id "C1orf167"; transcript_id "C1orf167";
chr1    hg19_refFlat    exon    29037032    29037154    0.000000    +   .   gene_id "GMEB1"; transcript_id "GMEB1";
chr1    hg19_refFlat    exon    103356007   103356060   0.000000    -   .   gene_id "COL11A1"; transcript_id "COL11A1";

in my code I am trying to capture 2 elements from each line, the first is the number after where it says exon, the second is the gene (the number and letter combo surrounded by "", e.g. "KDM4A". Here is my code:

    with open(infile,'r') as r:
        start = set([line.strip().split()[3] for line in r])
        genes = set([line.split('"')[1] for line in r])
        print len(start)
        print len(genes)

for some reason start works fine but genes is not capturing anything. Here is the output:

 48050
 0

I figure this is something to do with the "" surrounding the gene name but if I enter this on the terminal it works fine:

>>> x = 'A b P "G" m'
>>> x
'A b P "G" m'
>>> x.split('"')[1]
'G'
>>> 

Any solutions would be much appreciated? If even if its a completely different way of capturing the 2 items of data from each line. Thanks

Answer 1

It is because your file object is exhausted when you loop over it once here start = set([line.strip().split()[3] for line in r]) again you are trying to loop here genes = set([line.split('"')[1] for line in r]) over the exhausted file object

Solution:

You could seek to the start of the file (this is one of the solutions)

Modification to your code:

with open(infile,'r') as r:
    start = set([line.strip().split()[3] for line in r])
    r.seek(0, 0)
    genes = set([line.split('"')[1] for line in r])
    print len(start)
    print len(genes)