Mercurial > repos > jjohnson > snpeff_cds_report
diff snpEff_cds_report.py @ 6:a64ef0611117
Change field header from "Penetrance" to "Prevalence"
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 13 Jun 2013 11:37:34 -0500 |
| parents | 85b933b7d231 |
| children | fbb6510186df |
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--- a/snpEff_cds_report.py Fri May 24 08:50:03 2013 -0500 +++ b/snpEff_cds_report.py Thu Jun 13 11:37:34 2013 -0500 @@ -288,7 +288,7 @@ FRAME_SHIFT(HIGH||||745|CHUK|protein_coding|CODING|ENST00000370397|exon_10_101964263_101964414) """ class SnpEffect( object ): - report_headings = ['Gene','Variant Position','Reference','Variation','Penetrance','Sequencing Depth','Transcript','AA Position','AA change','AA Length','Stop Codon','Stop Region','AA Variation'] + report_headings = ['Gene','Variant Position','Reference','Variation','Prevalence','Sequencing Depth','Transcript','AA Position','AA change','AA Length','Stop Codon','Stop Region','AA Variation'] def __init__(self,chrom,pos,ref,alt,freq,depth,effect = None, snpEffVersion = None, biomart_host = None, filter_ccds = False): self.chrom = chrom self.pos = int(pos) @@ -501,7 +501,7 @@ if output_file: print >> output_file, '<HTML><BODY>\n' print >> output_file, '<TABLE BORDER="1">\n' - print >> output_file, '<TR align="LEFT"><TH>Gene</TH><TH>Variant Position</TH><TH>Reference</TH><TH>Variation</TH><TH>Penetrance</TH><TH>Sequencing Depth</TH><TH>Transcript Details</TH><TH>AA Position</TH><TH>AA Change</TH><TH>AA Length</TH> <TH>Stop Codon</TH><TH>AA Variation</TH></TR>\n' + print >> output_file, '<TR align="LEFT"><TH>Gene</TH><TH>Variant Position</TH><TH>Reference</TH><TH>Variation</TH><TH>Prevalence</TH><TH>Sequencing Depth</TH><TH>Transcript Details</TH><TH>AA Position</TH><TH>AA Change</TH><TH>AA Length</TH> <TH>Stop Codon</TH><TH>AA Variation</TH></TR>\n' for snpEffect in snpEffects: (gene_name,chrpos,cds_ref,cds_alt,freq,depth,transcript_name,alt_aa_pos,aa_change,aa_len,stop_codon,stop_region,novel_peptide) = snpEffect.getReportFields() refname = '_'.join([snpEffect.transcript,str(snpEffect.pos),snpEffect.ref,snpEffect.alt]) + '.html'