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Include locus name and snp position in snp_table.txt #34

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Include locus name and snp position in snp_table.txt #34

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fa8a7bf
Add LocusName to SNP table
moorembioinfo Jun 27, 2022
88b8f70
Update README.md
moorembioinfo Jun 28, 2022
eb5856e
Dummy value for inclusion of ref startbp attempt
moorembioinfo Jul 10, 2022
6ed8afe
output snp position but of final genome in order
moorembioinfo Jul 11, 2022
284a3fb
LocusName and snp_position from reference now output to snp_table.txt…
moorembioinfo Jul 11, 2022
45ffd65
Cleanup
moorembioinfo Jul 11, 2022
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1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
[![Master branch build status](https://travis-ci.org/chadlaing/Panseq.svg?branch=master "Master Build Status")](https://travis-ci.org/chadlaing/Panseq)
# Panseq-LC: fork of Panseq, with output modified to include LocusName in SNP table

## OVERVIEW

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19 changes: 15 additions & 4 deletions lib/Modules/PanGenome/PanGenome.pm
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Expand Up @@ -714,7 +714,7 @@ sub _printResults{

foreach my $snpId(sort keys %{$finalResult->{genomeResults}->{$genome}->{snp}}){
$snpStringHash{$snpId}->{$genomeCounter} = $finalResult->{genomeResults}->{$genome}->{snp}->{$snpId}->{value};

$snpStringHash{$snpId}->{'loci'} = $finalResult->{locusInformation}->{name};
$self->_printCoreSnpData(
snpId=>$snpId
,locusName=>$finalResult->{locusInformation}->{name}
Expand All @@ -723,6 +723,10 @@ sub _printResults{
,startBp=>$finalResult->{genomeResults}->{$genome}->{snp}->{$snpId}->{start_bp}
,contigId=>$finalResult->{genomeResults}->{$genome}->{binary}->[0]->{contig_id}
);
my $lname = "" . $snpStringHash{$snpId}->{'loci'};
my @refgenome = (split(/[|]/, $lname));
my $refgenome_ = $refgenome[1];
$snpStringHash{$snpId}->{'snp_position'} = $finalResult->{genomeResults}->{$refgenome_}->{snp}->{$snpId}->{start_bp}; #if $refgenome==$genome;
}

#if there are SNPs in a region, add dashes to the snp string
Expand Down Expand Up @@ -841,14 +845,20 @@ sub _printCoreSnpData{
sub _printSnpTable{
my $self=shift;
my $snpStringHash = shift;

#my $finalResult = shift;
my @output;
foreach my $id(sort keys %{$snpStringHash}){
my $printLine = "\n";
my $startbp = ''; #get ref start ID

foreach my $genome(1..scalar(@{$self->settings->orderedGenomeNames})){
$printLine .= ("\t" . $snpStringHash->{$id}->{$genome})
$printLine .= ("\t" . $snpStringHash->{$id}->{$genome});
my $lociname = $snpStringHash->{$id}->{'loci'};
my $refgenome = (split /|/, $lociname)[1];
$startbp = $snpStringHash->{$id}->{'snp_position'};
}
push @output, $printLine;
my $snploci = $printLine . "\t" . $snpStringHash->{$id}->{'loci'} . "\t" . $startbp;
push @output, $snploci;
}
$self->_printFH->{snpTableFH}->print(@output);
}
Expand Down Expand Up @@ -1158,6 +1168,7 @@ sub _getCoreResult {
return $snpDataArrayRef;
}


1;


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10 changes: 10 additions & 0 deletions t/genomes.batch
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queryDirectory t/data/genomes/
percentIdentityCutoff 90
coreGenomeThreshold 3
minimumNovelRegionSize 1000
fragmentationSize 1000
overwrite 1
nameOrId name
baseDirectory t/genomes/
numberOfCores 1
runMode pan
14 changes: 14 additions & 0 deletions t/plasmids.batch
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percentIdentityCutoff 90
queryDirectory t/data/plasmids/
coreGenomeThreshold 2
cdhitDirectory /mnt/gvl/apps/linuxbrew/bin/
minimumNovelRegionSize 500
fragmentationSize 500
allelesToKeep 2
nameOrId name
overwrite 1
runMode pan
storeAlleles 1
numberOfCores 1
cdhit 1
baseDirectory t/plasmids/
12 changes: 12 additions & 0 deletions t/query.batch
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storeAlleles 1
runMode pan
queryFile t/data/testfragments.fasta
baseDirectory t/query/
numberOfCores 1
overwrite 1
nameOrId name
minimumNovelRegionSize 1
fragmentationSize 0
coreGenomeThreshold 2
percentIdentityCutoff 90
queryDirectory t/data/genomes/