jdoughertyii / pyvcf Goto Github PK

I see the --local-script command line argument, and how in vcf_filter.py's main method the classes defined in that local file are added as filters --- but I do not know enough modern :} python to know what to do with

see :doc:FILTERS for full description.

A sample local filter file would be a big help.

Thanks -- and kudos for the fine tool!

• Paul

I have a script that 'melts' a VCF file (melt is a ggplot term) from wide format to tab separated wide format - useful for grepping or loading into non-vcf aware applications.

see https://github.com/jamescasbon/PyVCF/blob/master/vcf_melt where I ported it over to use PyVCF.

Perhaps you can include it with PyVCF? add a scripts=['vcf_melt'] to setup.py to get it to install

"A Variant Cell Format reader for Python." should be "A Variant Call Format reader for Python."

Hi!

This is causing me problems:

alt = self._mapper(str, row[4].split(','))
@ line 396

There are times when one would want to put multicharacter strings in the ALT column but this:

<DEL:HOM>

Becomes this:

<,D,E,L,:,H,O,M,>

Thanks!

Hi,
The following code crashes with the error at the bottom:

Python 3.4.1 (default, Nov 11 2014, 09:06:26)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux
Type "help", "copyright", "credits" or "license" for more information.

import vcf
vcf_reader = vcf.Reader(filename='bar.vcf.gz',compress=True)
cr = vcf_reader.fetch(chrom='17')
cr
<vcf.parser.Reader object at 0x2ac5ddbd12b0>
x=next(cr)
Traceback (most recent call last):
File "", line 1, in
File "/usr//local/lib/python3.4/site-packages/vcf/parser.py", line 537, in next
line = next(self.reader)
File "pysam/ctabix.pyx", line 543, in pysam.ctabix.TabixIterator.next (pysam/ctabix.c:5906)
File "pysam/ctabix.pyx", line 69, in pysam.ctabix._charptr_to_str (pysam/ctabix.c:2311)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 5708: ordinal not in range(128)

It crashed at the record (line) in the vcf file (bar.vcf.gz) that contains several annotations as follows:
17 19559848 rs72547564 G A 0 . GENEINFO=ALDH3A2:224;OriginalChr=chr17;OriginalStart=19656535;RS=72547564;RSPOS=19656535;SAO=1;SSR=0;VC=SNV;VP=0x050260000a05000002110100;WGT=1;dbSNPBuildID=130;ASP;LSD;NSM;OM;PM;REF;S3D;ANN=A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000339618|protein_coding|4/11|c.641G>A|p.Cys214Tyr|862/3828|641/1527|214/508||,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000176643|protein_coding|4/10|c.641G>A|p.Cys214Tyr|1087/3928|641/1458|214/485||,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000581518|protein_coding|4/12|c.641G>A|p.Cys214Tyr|890/2785|641/1527|214/508||,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000395575|protein_coding|5/11|c.641G>A|p.Cys214Tyr|799/3640|641/1458|214/485||,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000579855|protein_coding|5/11|c.641G>A|p.Cys214Tyr|740/3583|641/1458|214/485||,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000571537|protein_coding|1/3|c.134G>A|p.Cys45Tyr|134/607|134/489|45/162||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ALDH3A2|ENSG00000072210|transcript|ENST00000578696|protein_coding|1/4|c.47G>A|p.Cys16Tyr|48/400|47/399|16/132||WARNING_TRANSCRIPT_NO_START_CODON,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|8/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|3/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|2/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|7/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|5/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|9/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|4/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|6/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000581518|protein_coding|1/12|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|9/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|4/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|3/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|8/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|6/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|10/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|5/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|2/11|c.641G>A||||||,A|sequence_feature|LOW|ALDH3A2|ENSG00000072210|topological_domain:Cytoplasmic|ENST00000579855|protein_coding|7/11|c.641G>A||||||,A|3_prime_UTR_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000472059|nonsense_mediated_decay|5/11|n._199G>A|||||1177|,A|upstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000574078|processed_transcript||n.-1G>A|||||3038|,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000446398|protein_coding||c._665G>A|||||143|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000467473|retained_intron||n._651G>A|||||3880|,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000580550|protein_coding||c._540G>A|||||3935|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000584332|protein_coding||c._573G>A|||||165|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000578614|nonsense_mediated_decay||n._359G>A|||||76|,A|downstream_gene_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000579403|retained_intron||n._582G>A|||||3838|,A|non_coding_exon_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000582991|nonsense_mediated_decay|4/10|n.641G>A||||||,A|non_coding_exon_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000472059|nonsense_mediated_decay|5/11|n._199G>A||||||,A|non_coding_exon_variant|MODIFIER|ALDH3A2|ENSG00000072210|transcript|ENST00000476965|retained_intron|1/7|n.391G>A||||||;dbNSFP_GERP++_RS=5.84;dbNSFP_MutationTaster_pred=D;dbNSFP_GERP++_RS_rankscore=0.93424;dbNSFP_phastCons46way_placental_rankscore=0.4774;dbNSFP_MutationTaster_score=1;dbNSFP_phastCons100way_vertebrate=1;dbNSFP_MetaSVM_pred=D;dbNSFP_VEST3_rankscore=0.99865;dbNSFP_fold-degenerate=0;dbNSFP_LRT_pred=D;dbNSFP_LRT_score=0;dbNSFP_SiPhy_29way_logOdds=19.1316;dbNSFP_phyloP100way_vertebrate=9.757;dbNSFP_cds_strand=+;dbNSFP_VEST3_score=0.996;dbNSFP_MetaSVM_score=0.6006;dbNSFP_MetaLR_pred=D;dbNSFP_phyloP100way_vertebrate_rankscore=0.98924;dbNSFP_rs_dbSNP141=rs72547564;dbNSFP_SIFT_pred=D,D,D;dbNSFP_clinvar_trait=Sjögren-Larsson_syndrome;dbNSFP_SiPhy_29way_pi=0.0:0.0:1.0:0.0;dbNSFP_LRT_converted_rankscore=0.85682;dbNSFP_aapos_FATHMM=ENSP00000176643:C214Y,ENSP00000378942:C214Y,ENSP00000345774:C214Y;dbNSFP_aapos=214;dbNSFP_SLR_test_statistic=-18.6067;dbNSFP_aapos_SIFT=ENSP00000176643:C214Y;dbNSFP_Reliability_index=10;dbNSFP_pos(1-coor)=19559848;dbNSFP_Ensembl_transcriptid=ENST00000176643,ENST00000395575,ENST00000339618;dbNSFP_MetaLR_rankscore=0.90604;dbNSFP_clinvar_rs=rs72547564;dbNSFP_Polyphen2_HVAR_score=1,0.997;dbNSFP_ref=G;dbNSFP_Polyphen2_HDIV_rankscore=0.89917;dbNSFP_Polyphen2_HVAR_rankscore=0.9711;dbNSFP_phyloP46way_placental_rankscore=0.95229;dbNSFP_phastCons46way_primate_rankscore=0.84299;dbNSFP_Ensembl_geneid=ENSG00000072210;dbNSFP_FATHMM_score=-0.96,-0.96,-0.96;dbNSFP_SiPhy_29way_logOdds_rankscore=0.9341;dbNSFP_FATHMM_pred=T,T,T;dbNSFP_MutationAssessor_score=3.55;dbNSFP_phyloP46way_primate_rankscore=0.77884;dbNSFP_phastCons100way_vertebrate_rankscore=0.71417;dbNSFP_LRT_Omega=0;dbNSFP_GERP++_NR=5.84;dbNSFP_PROVEAN_pred=D,D,D;dbNSFP_FATHMM_rankscore=0.75704;dbNSFP_Interpro_domain=Aldehydedehydrogenasedomain(1),Aldehydedehydrogenase,N-terminal(1),Aldehyde/histidinoldehydrogenase(1),;dbNSFP_MutationAssessor_pred=H;dbNSFP_PROVEAN_score=-10.53,-10.53,-10.53;dbNSFP_aaref=C;dbNSFP_MetaSVM_rankscore=0.92498;dbNSFP_hg18_pos(1-coor)=19500440;dbNSFP_genename=ALDH3A2;dbNSFP_phastCons46way_placental=0.991;dbNSFP_SIFT_converted_rankscore=0.90636;dbNSFP_MutationAssessor_rankscore=0.94542;dbNSFP_MetaLR_score=0.7054;dbNSFP_chr=17;dbNSFP_clinvar_clnsig=5;dbNSFP_Uniprot_acc=P51648,P51648-2;dbNSFP_codonpos=2;dbNSFP_Polyphen2_HDIV_score=1,1;dbNSFP_aaalt=Y;dbNSFP_refcodon=TGT;dbNSFP_alt=A;dbNSFP_Uniprot_aapos=214,214;dbNSFP_SIFT_score=0,0,0;dbNSFP_MutationTaster_converted_rankscore=0.70825;dbNSFP_hg38_pos=19656535;dbNSFP_Uniprot_id=AL3A2_HUMAN,.;dbNSFP_PROVEAN_converted_rankscore=0.99041;dbNSFP_phastCons46way_primate=0.994;dbNSFP_Ancestral_allele=G;dbNSFP_Polyphen2_HDIV_pred=D,D;dbNSFP_phyloP46way_primate=0.563;dbNSFP_phyloP46way_placental=2.769;dbNSFP_Polyphen2_HVAR_pred=D,D;dbSNP142=rs72547564;regulomeDB=2c;GERP=5.38;chainSelf=26.3

Can we get a setup.py and a pypi listing so that we can install from pip/easy_install and not have to manipulate python path?

A minimal setup.py that works:

from setuptools import setup

setup(
    name='PyVCF',
    py_modules=['vcf'],
)

You will need to add a bit more to list on pypi, but then see:
http://packages.python.org/an_example_pypi_project/setuptools.html#registering-your-project