Parsing tables in python and list strings

Question

I'm totally novice in the field and I am trying to parse items in a specific column of a table and list them. I used to do this in awk which was very straight forward, but I don't know how to do it python. Here is the piece of code I've written:

for line in file('Stable7.txt','r'): genefun=line.split('\t') gene= genefun[2].rstrip() gene.split("\n\r\t") vdr=[gene] print vdr.

this put element in a separate list, while I want all items to be listed in a same list.

I'd be also grateful if someone could advise me with regard to set operations in python. If I wanna compare this list with another list how can I do it. I am looking for some command like "intersect(a,b)" in R.

score 0 · Answer 1 · edited May 23 '17 at 11:58

0

Append to vdr instead of setting it each time:

vdr = []
for line in file('Stable7.txt','r'):
    genefun=line.split('\t')
    gene= genefun[2].rstrip()
    gene.split("\n\r\t")
    vdr.append(gene)
print vdr

For python list intersections, look at this SO question

edited May 23 '17 at 11:58

Community

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answered Aug 13 '15 at 15:46

Ryan

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Thanks very much Ryan – RJF Aug 13 '15 at 15:53
No problem. If I answered your question, can you accept my answer? – Ryan Aug 13 '15 at 16:38

Parsing tables in python and list strings

1 Answers1