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author jjohnson
date Fri, 07 Feb 2014 15:05:20 -0500
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1 <?xml version="1.0"?>
2 <tool id="snpeff_to_peptides" name="SnpEff to Peptide fasta" version="0.0.1">
3 <description> to create a Search DB fasta for variant SAP peptides</description>
4 <command interpreter="python">snpeff_to_peptides.py --input "$snpeff_vcf" --protein_fasta "$all_pep_fasta" --output "$peptide_variant_fasta"
5 #if $leading_aa_num:
6 --leading_aa_num $leading_aa_num
7 #end if
8 #if $trailing_aa_num:
9 --trailing_aa_num $trailing_aa_num
10 #end if
11 </command>
12 <inputs>
13 <param name="snpeff_vcf" type="data" format="vcf" label="SnpEff generated VCF file with NON_SYNONYMOUS_CODING annotations"/>
14 <param name="all_pep_fasta" type="data" format="fasta,tabular" label="Ensembl all_pep.fa"
15 help="An Ensembl all_pep.fa file corresponding to the genome build used for SnpEff (May be converted to tabular fasta format)"/>
16 <param name="leading_aa_num" type="integer" value="30" min="0" optional="true" label="Preceeding AAs"
17 help="The number of Amino Acids to include before the variant position (leave blank to include all)"/>
18 <param name="trailing_aa_num" type="integer" value="30" min="0" optional="true" label="Following AAs"
19 help="The number of Amino Acids to include after the variant position (leave blank to include all)"/>
20 </inputs>
21 <stdio>
22 <exit_code range="1:" level="fatal" description="Error" />
23 </stdio>
24 <outputs>
25 <data name="peptide_variant_fasta" metadata_source="all_pep_fasta" format="fasta"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="snpeff_vcf" value="snpeff.vcf" ftype="vcf" dbkey="hg19"/>
30 <param name="all_pep_fasta" value="all_pep.fa" ftype="fasta" dbkey="hg19"/>
31 <param name="leading_aa_num" value="10"/>
32 <param name="trailing_aa_num" value="10"/>
33 <output name="peptide_variant_fasta" file="peptides_10_10.fa"/>
34 </test>
35 <test>
36 <param name="snpeff_vcf" value="snpeff.vcf" ftype="vcf" dbkey="hg19"/>
37 <param name="all_pep_fasta" value="all_pep.tabular" ftype="tabular" dbkey="hg19"/>
38 <param name="leading_aa_num" value="10"/>
39 <param name="trailing_aa_num" value="10"/>
40 <output name="peptide_variant_fasta" file="peptides_10_10.fa"/>
41 </test>
42 </tests>
43 <help>
44 **SnpEff to Peptide Fasta**
45
46 This generates a fasta file of peptide sequences with SAPs ( Single Amino acid Polymorphisms )
47 from the NON_SYNONYMOUS_CODING EFF annnotations from the SnpEff_ application.
48 The SnpEff VCF may be filtered or annotated using SnpSift.
49
50 The following is appended to the fasta ID line: snp_location:chr:position codon_change:nnn/nnn sap:AposA
51
52 For VCF entry::
53
54 chr1 22846709 . G A 9.31 . DP=2;VDB=0.0174;AF1=1;AC1=2;DP4=0,0,1,1;MQ=20;FQ=-33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V885M|1127|ZBTB40|protein_coding|CODING|ENST00000374651|12|1) PL 40,6,0
55
56 The peptide fasta entry that matches transcript ID: ENST00000374651 would be::
57
58 >ENSP00000363782 pep:known chromosome:GRCh37:1:22778472:22853855:1 gene:ENSG00000184677 transcript:ENST00000374651 gene_biotype:protein_coding transcript_biotype:protein_coding
59
60 The ID of the output peptide fasta ID would be::
61
62 >ENSP00000363782 pep:sap chromosome:GRCh37:1:22778472:22853855:1 gene:ENSG00000184677 transcript:ENST00000374651 gene_biotype:protein_coding transcript_biotype:protein_coding snp_location:chr1:22846709 codon_change:Gtg/Atg sap:V885M
63
64
65 .. _SnpEff: http://snpeff.sourceforge.net/index.html
66
67 **Citation**
68
69 SnpEff citation:
70 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
71
72 SnpSift citation:
73 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
74
75 </help>
76 </tool>