Re: [Tutor] vcf_files and strings
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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Re: [Tutor] vcf_files and strings
On 11/10/11 18:16, Hs Hs wrote: VCF - Variant Call Format ... Nothing special except that a genetics or any biologist will understand this - nothing special! The problem is that this list, being for beginners to Python, is a bit short on Geneticists and Biologists! :-) So you need to explain your problem in general terms, that the rest of us can make sense of, or else rely on the few who might understand being available/willing to respond. -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] vcf_files and strings
http://www.1000genomes.org/node/101 From: Alan Gauld alan.ga...@btinternet.com To: tutor@python.org Sent: Tuesday, October 11, 2011 1:52 PM Subject: Re: [Tutor] vcf_files and strings On 11/10/11 18:16, Hs Hs wrote: VCF - Variant Call Format ... Nothing special except that a genetics or any biologist will understand this - nothing special! The problem is that this list, being for beginners to Python, is a bit short on Geneticists and Biologists! :-) So you need to explain your problem in general terms, that the rest of us can make sense of, or else rely on the few who might understand being available/willing to respond. -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] vcf_files and strings
Hi, I still don't know how to make a loop that makes it work for all the mutations. Best, Anna Date: Fri, 7 Oct 2011 13:17:07 -0700 From: ilhs...@yahoo.com Subject: Re: [Tutor] vcf_files and strings To: olofsson_anna...@hotmail.com; tutor@python.org 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 1col 2 col 3 col 4 col5col6 col7 col8 col9 chromosome position . Reference ALT position . some statistics and the ID:s not importantnot 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 ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
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 1col 2
col 3 col 4 col5col6
col7 col8
col9 chromosome position .
Reference ALT position . some statistics
and the ID:s not importantnot 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
___
Tutor maillist - Tutor@python.org
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[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 1col 2 col 3 col 4 col5col6 col7 col8 col9 chromosome position . Reference ALT position . some statistics and the ID:s not importantnot 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 4 69345 . C T 32 . 1kg.AD=0;1kg.AF=0.8865;1kg.AN=345;AC=1;AF=0.50;AN=2;BaseQRankSum=-6.432;DP=327;DS;Dels=0.00;FS=6.435;HRun=0;HaplotypeScore=5.0380;MQ=54.34;MQ0=13;MQRankSum=-5.3457;QD=2.65;ReadPosRankSum=-0.321;SB=-321.04;dbsnp.ID=rs43032118;dbsnp.dbSNPBuildID=112;hgid.AF=0.6754;refseq.changesAA=true;refseq.codingCoordStr=c.345CT;refseq.codonCoord=234;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=321;refseq.name=NM_003137492;refseq.name2=PQ3D2;refseq.positionType=CFD;refseq.proteinCoordStr=p.C132T;refseq.referenceAA=BRT;refseq.referenceCodon=DGF;refseq.spliceDist=321;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA GT:AD:DP:GQ:PL 1/1:134,32:765:99:56,1,4576 4 87342 . A G 57.7 . 1kg.AD=0;1kg.AF=1.0;1kg.AN=345;AC=2;AF=0.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.;MQ=29.00;MQ0=0;QD=54.97;SB=-52.65;dbsnp.ID=rs6732096;dbsnp.dbSNPBuildID=136;hgid.AF=0.9567;refseq.changesAA=true;refseq.codingCoordStr=c.3207AG;refseq.codonCoord=349;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=4509;refseq.name=NM_132768;refseq.name2=PQR321;refseq.positionType=CDS;refseq.proteinCoordStr=p.O125R;refseq.referenceAA=Trp;refseq.referenceCodon=ATG;refseq.spliceDist=-45;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CTT GT:AD:DP:GQ:PL 0/1:0,5:5:2.02:67,9,1 ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] vcf_files and strings
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 ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] vcf_files and strings
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). 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 1col 2 col 3 col 4 col5col6 col7 col8 col9 chromosome position . Reference ALT position . some statistics and the ID:s not importantnot 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 4 69345 . C T 32 . 1kg.AD=0;1kg.AF=0.8865;1kg.AN=345;AC=1;AF=0.50;AN=2;BaseQRankSum=-6.432;DP=327;DS;Dels=0.00;FS=6.435;HRun=0;HaplotypeScore=5.0380;MQ=54.34;MQ0=13;MQRankSum=-5.3457;QD=2.65;ReadPosRankSum=-0.321;SB=-321.04;dbsnp.ID=rs43032118;dbsnp.dbSNPBuildID=112;hgid.AF=0.6754;refseq.changesAA=true;refseq.codingCoordStr=c.345CT;refseq.codonCoord=234;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=321;refseq.name=NM_003137492;refseq.name2=PQ3D2;refseq.positionType=CFD;refseq.proteinCoordStr=p.C132T;refseq.referenceAA=BRT;refseq.referenceCodon=DGF;refseq.spliceDist=321;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA GT:AD:DP:GQ:PL 1/1:134,32:765:99:56,1,4576 4 87342 . A G 57.7 . 1kg.AD=0;1kg.AF=1.0;1kg.AN=345;AC=2;AF=0.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.;MQ=29.00;MQ0=0;QD=54.97;SB=-52.65;dbsnp.ID=rs6732096;dbsnp.dbSNPBuildID=136;hgid.AF=0.9567;refseq.changesAA=true;refseq.codingCoordStr=c.3207AG;refseq.codonCoord=349;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=4509;refseq.name=NM_132768;refseq.name2=PQR321;refseq.positionType=CDS;refseq.proteinCoordStr=p.O125R;refseq.referenceAA=Trp;refseq.referenceCodon=ATG;refseq.spliceDist=-45;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CTT GT:AD:DP:GQ:PL 0/1:0,5:5:2.02:67,9,1 ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] vcf_files and strings
On 2011-10-05 21:29, Anna Olofsson wrote: vcf file: 2 rows, 10 columns. 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? I would split the rows into the columns (analyze your file to find the seperator), then look for missense in the 7th column in every row and if found regex for the name/ID. Are you able to code that yourself or do you need more hints? Bye, Andreas ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
