if col[x] == 'missense':
print col[withRefSeqID]
hth
________________________________
From: Anna Olofsson <olofsson_anna...@hotmail.com>
To: tutor@python.org
Sent: Friday, October 7, 2011 12:12 PM
Subject: [Tutor] vcf_files and strings
Hi,
I'm a beginner at Python and would really appreciate some help in how to
extract information from a vcf file.
The attached file consists of a lot of information on mutations, this one
though is just 2 rows and 10 columns (the real one has a lot more rows).
I want to extract the mRNA ID only if the mutation is missense. These two rows
(mutations) that I have attached happens to be missense but how do I say that
I'm not interested in the mutations that's not missense (they might be e.g.
synonymous). Also, how do I say that if a mutation starts with a # symbol I
don't want to include it (sometimes the chr starts with a hash).
vcf file: 2 rows, 10 columns.
col 0 col 1 col 2 col 3
col 4 col5 col6
col7 col8 col9
chromosome position . Reference
ALT position . some statistics and the ID:s not
important not important
The important column is 7 where the ID is, i.e.
refseq.functionalClass=missense. It's a missense mutation, so then I want to
extract refseq.name=NM_003137492, or I want to extract only the ID, which in
this case is NM_003137492.
Then I want to do exactly the same thing for all the other mutations, but only
for the missense mutations not the other ones. How do I accomplish that? Where
do I start?
Best,
Anna
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