VCF - Variant Call Format
VCF files are nothing special but tab delim files describing the genetic
mutations, friquencies and other base information (bases here mean ATGC
pertaining to DNA).
These files are generated by variety of genome sequence data analysis
pipelines. MIT and Haplotype Mapping Project consortium developed this format.
Nothing special except that a genetics or any biologist will understand this -
nothing special!
hth
cheers
________________________________
From: Steven D'Aprano <st...@pearwood.info>
To: tutor@python.org
Sent: Sunday, October 9, 2011 10:04 PM
Subject: Re: [Tutor] vcf_files and strings
Anna Olofsson wrote:
> Hi,
>
> I'm a beginner at Python and would really like 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).
What do you mean by a VCF file? On my computer, a VCF file is an electronic
business card, which tries to open in an Address Book application (which
obviously fails).
I don't know how to interpret the contents of your VCF file. After opening it
in a hex editor, I can *guess* that it is a tab-separated file: each row takes
one line, with the columns separated by tab characters. Column 7 appears to be
a great big ugly blob with sub-fields separated by semi-colons. Am I right? Can
you link us to a description of the vcf file format?
> 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).
What chr? Where is the mutation? I'm afraid your questions are assuming
familiarity with your data that we don't have.
> 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.
This is what I *think* you want to do. Am I right?
* read each line of the file
* for each line, split on tabs
* extract the 7th column and split it on semi-colons
* inspect the refseq.functionalClass field
* if it matches, extract the ID from the refseq.name and store it in a list for
later
(I have completely ignored the part about the #, because I don't understand
what you mean by it.)
Here's some code to do it:
ids = []
f = open('vcf_file.vcf', 'r')
for row in f:
columns = row.split('\t') # Split on tabs
data = columns[7] # Huge ugly blob of data
values = data.split(';') # Split on semi-colons
if values[25] == "refseq.functionalClass=missense":
name_chunk = values[28] # looks like "refseq.name=..."
a, b = name_chunk.split("=")
if a != "refseq.name":
raise ValueError('expected refseq.name but got %s' % a)
ids.append(b)
f.close()
print(ids)
Does this help?
-- Steven
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