Mercurial > repos > jjohnson > snpeff_cds_report
comparison 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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| 5:85b933b7d231 | 6:a64ef0611117 |
|---|---|
| 286 """ | 286 """ |
| 287 Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] ) | 287 Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] ) |
| 288 FRAME_SHIFT(HIGH||||745|CHUK|protein_coding|CODING|ENST00000370397|exon_10_101964263_101964414) | 288 FRAME_SHIFT(HIGH||||745|CHUK|protein_coding|CODING|ENST00000370397|exon_10_101964263_101964414) |
| 289 """ | 289 """ |
| 290 class SnpEffect( object ): | 290 class SnpEffect( object ): |
| 291 report_headings = ['Gene','Variant Position','Reference','Variation','Penetrance','Sequencing Depth','Transcript','AA Position','AA change','AA Length','Stop Codon','Stop Region','AA Variation'] | 291 report_headings = ['Gene','Variant Position','Reference','Variation','Prevalence','Sequencing Depth','Transcript','AA Position','AA change','AA Length','Stop Codon','Stop Region','AA Variation'] |
| 292 def __init__(self,chrom,pos,ref,alt,freq,depth,effect = None, snpEffVersion = None, biomart_host = None, filter_ccds = False): | 292 def __init__(self,chrom,pos,ref,alt,freq,depth,effect = None, snpEffVersion = None, biomart_host = None, filter_ccds = False): |
| 293 self.chrom = chrom | 293 self.chrom = chrom |
| 294 self.pos = int(pos) | 294 self.pos = int(pos) |
| 295 self.ref = ref | 295 self.ref = ref |
| 296 self.alt = alt | 296 self.alt = alt |
| 499 """ | 499 """ |
| 500 def printReportHtml(output_file, detail_dir, snpEffects): | 500 def printReportHtml(output_file, detail_dir, snpEffects): |
| 501 if output_file: | 501 if output_file: |
| 502 print >> output_file, '<HTML><BODY>\n' | 502 print >> output_file, '<HTML><BODY>\n' |
| 503 print >> output_file, '<TABLE BORDER="1">\n' | 503 print >> output_file, '<TABLE BORDER="1">\n' |
| 504 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' | 504 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' |
| 505 for snpEffect in snpEffects: | 505 for snpEffect in snpEffects: |
| 506 (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() | 506 (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() |
| 507 refname = '_'.join([snpEffect.transcript,str(snpEffect.pos),snpEffect.ref,snpEffect.alt]) + '.html' | 507 refname = '_'.join([snpEffect.transcript,str(snpEffect.pos),snpEffect.ref,snpEffect.alt]) + '.html' |
| 508 aa_ref = '#'.join([refname,aa_anchor]) | 508 aa_ref = '#'.join([refname,aa_anchor]) |
| 509 refpath = os.path.join(detail_dir,refname) | 509 refpath = os.path.join(detail_dir,refname) |