| Previous changeset 0:c9a8ef2aa380 (2018-02-16) Next changeset 2:776ebd1239da (2019-03-18) |
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Commit message:
planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61 |
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modified:
snippy.xml test-data/fna_ref/snps.gff test-data/fna_ref/snps.txt test-data/gbk_ref/snps.gff test-data/gbk_ref/snps.txt test-data/map_qual/snps.gff test-data/map_qual/snps.txt test-data/min_cov/snps.gff test-data/min_cov/snps.txt test-data/min_frac/snps.gff test-data/min_frac/snps.txt |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 snippy.xml --- a/snippy.xml Fri Feb 16 13:40:16 2018 -0500 +++ b/snippy.xml Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="snippy" name="snippy" version="@VERSION@"> +<tool id="snippy" name="snippy" version="@VERSION@+galaxy1"> <description> Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. </description> @@ -40,14 +40,14 @@ --pe2 '$fastq_input.fastq_input2' #end if #if str( $fastq_input.fastq_input_selector ) == "paired_collection" - --pe1 '$fastq_input.fastq_input1.forward' - --pe2 '$fastq_input.fastq_input1.reverse' + --pe1 '$fastq_input.fastq_input.forward' + --pe2 '$fastq_input.fastq_input.reverse' #end if #if str( $fastq_input.fastq_input_selector ) == "single" - --se '$fastq_input.fastq_input1' + --se '$fastq_input.fastq_input' #end if #if str( $fastq_input.fastq_input_selector ) == "paired_iv" - --peil '$fastq_input.fastq_input1' + --peil '$fastq_input.fastq_input' #end if && @@ -57,9 +57,13 @@ && #import re - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) - mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ && + #if str( $fastq_input.fastq_input_selector ) == "paired" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) + #else + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) + #end if + mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ && tar -czf out.tgz ${dir_name} @@ -81,13 +85,13 @@ <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> </when> <when value="single"> - <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> + <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> </when> <when value="paired_collection"> - <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> </when> <when value="paired_iv"> - <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> </when> </conditional> @@ -204,6 +208,20 @@ <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" /> </test> + <test> <!-- test 6 - fasta ref default paired_collection --> + <param name="ref" value="wildtype.fna" ftype="fasta" /> + <param name="fastq_input_selector" value="paired_collection" /> + <param name="fastq_input"> + <collection type="paired"> + <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" /> + <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" /> + </collection> + </param> + <param name="outputs" value="outgff,outsum" /> + <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" /> + <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" /> + </test> + </tests> |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/fna_ref/snps.gff --- a/test-data/fna_ref/snps.gff Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/fna_ref/snps.gff Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,16 +1,17 @@ ##gff-version 3 Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 -Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 +Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 +Wildtype snippy:3.2-dev variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/fna_ref/snps.txt --- a/test-data/fna_ref/snps.txt Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/fna_ref/snps.txt Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,9 +1,10 @@ -DateTime 2017-07-12T04:51:24 -ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq -Reference /home/ubuntu/snippy/test-data/wildtype.fna +DateTime 2019-01-24T13:08:34 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.fna ReferenceSize 200694 Software snippy 3.2-dev -Variant-DEL 5 +Variant-DEL 4 +Variant-INS 1 Variant-MNP 1 -Variant-SNP 9 -VariantTotal 15 +Variant-SNP 10 +VariantTotal 16 |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/gbk_ref/snps.gff --- a/test-data/gbk_ref/snps.gff Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/gbk_ref/snps.gff Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,16 +1,17 @@ ##gff-version 3 Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/gbk_ref/snps.txt --- a/test-data/gbk_ref/snps.txt Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/gbk_ref/snps.txt Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,9 +1,10 @@ -DateTime 2017-07-12T04:52:49 -ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq -Reference /home/ubuntu/snippy/test-data/wildtype.gbk +DateTime 2019-01-24T13:29:29 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk ReferenceSize 200727 Software snippy 3.2-dev -Variant-DEL 5 +Variant-DEL 4 +Variant-INS 1 Variant-MNP 1 -Variant-SNP 9 -VariantTotal 15 +Variant-SNP 10 +VariantTotal 16 |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/map_qual/snps.gff --- a/test-data/map_qual/snps.gff Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/map_qual/snps.gff Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,16 +1,17 @@ ##gff-version 3 Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/map_qual/snps.txt --- a/test-data/map_qual/snps.txt Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/map_qual/snps.txt Sat Jan 26 14:36:48 2019 -0500 |
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| @@ -1,9 +1,10 @@ -DateTime 2017-07-13T05:37:56 -ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq -Reference /home/ubuntu/snippy/test-data/wildtype.gbk +DateTime 2019-01-24T14:57:31 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk ReferenceSize 200727 Software snippy 3.2-dev -Variant-DEL 5 +Variant-DEL 4 +Variant-INS 1 Variant-MNP 1 -Variant-SNP 9 -VariantTotal 15 +Variant-SNP 10 +VariantTotal 16 |
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| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_cov/snps.gff --- a/test-data/min_cov/snps.gff Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/min_cov/snps.gff Sat Jan 26 14:36:48 2019 -0500 |
| b |
| @@ -1,13 +1,12 @@ ##gff-version 3 Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_cov/snps.txt --- a/test-data/min_cov/snps.txt Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/min_cov/snps.txt Sat Jan 26 14:36:48 2019 -0500 |
| b |
| @@ -1,9 +1,9 @@ -DateTime 2017-07-12T04:54:55 -ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq -Reference /home/ubuntu/snippy/test-data/wildtype.gbk +DateTime 2019-01-24T15:21:35 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk ReferenceSize 200727 Software snippy 3.2-dev -Variant-DEL 4 +Variant-DEL 3 Variant-MNP 1 Variant-SNP 7 -VariantTotal 12 +VariantTotal 11 |
| b |
| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_frac/snps.gff --- a/test-data/min_frac/snps.gff Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/min_frac/snps.gff Sat Jan 26 14:36:48 2019 -0500 |
| b |
| @@ -1,17 +1,18 @@ ##gff-version 3 Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ -Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A -Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 -Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY -Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTA=>GTTTTTTA GTTTTTTA:11 GTTTTTA:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY -Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase -Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase -Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138954 138954 . . 0 note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125 hypothetical protein Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 -Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 -Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTATTA=>CATTA CATTA:18 CTATTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_frac/snps.txt --- a/test-data/min_frac/snps.txt Fri Feb 16 13:40:16 2018 -0500 +++ b/test-data/min_frac/snps.txt Sat Jan 26 14:36:48 2019 -0500 |
| b |
| @@ -1,10 +1,10 @@ -DateTime 2017-07-12T04:56:36 -ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq -Reference /home/ubuntu/snippy/test-data/wildtype.gbk +DateTime 2019-01-24T15:35:47 +ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq +Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk ReferenceSize 200727 Software snippy 3.2-dev Variant-DEL 5 Variant-INS 1 Variant-MNP 1 -Variant-SNP 9 -VariantTotal 16 +Variant-SNP 10 +VariantTotal 17 |