# HG changeset patch # User Jim Johnson # Date 1371141454 18000 # Node ID a64ef06111176118a4684d0698469b61c0dae273 # Parent 85b933b7d231e3e6e8419b7c1ba9d792048ea4ea Change field header from "Penetrance" to "Prevalence" diff -r 85b933b7d231 -r a64ef0611117 snpEff_cds_report.py --- 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, '\n' print >> output_file, '\n' - print >> output_file, '\n' + print >> output_file, '\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'

Gene	Variant Position	Reference	Variation	Penetrance	Sequencing Depth	Transcript Details	AA Position	AA Change	AA Length	Stop Codon	AA Variation
Gene	Variant Position	Reference	Variation	Prevalence	Sequencing Depth	Transcript Details	AA Position	AA Change	AA Length	Stop Codon	AA Variation