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| <div class="splash"> | ||
| <div class="middle"> | ||
| <h1>T6SS prediction finished</h1> | ||
| <p>Scroll down to see results</p> | ||
| <hr> | ||
| <p>Downloadable results:</p> | ||
| <ul style="list-style-type:none;"> | ||
| <li><a href="genome.fasta">Input genome (noramlized)</a></li> | ||
| <li><a href="nucleotides.fna">Nucleotide fasta</a></li> | ||
| <li><a href="proteins.faa">Protein fasta</a></li> | ||
| <li><a href="log.txt">Analysis log</a></li> | ||
| </ul> | ||
| <hr> | ||
| </div> | ||
| <div class="bottomleft"> | ||
| <p><a href="https://T6SS.Vibriocholera.com" target=_blank style="color: black; text-decoration: none;">T6SS.Vibriocholera.com</a></p> | ||
| </div> | ||
| </div> | ||
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| <style> | ||
| body, html { | ||
| height: 100% | ||
| } | ||
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| .splash { | ||
| height: 100%; | ||
| position: relative; | ||
| color: black; | ||
| /* Add a font */ | ||
| font-family: "Courier New", Courier, monospace; | ||
| /* Set the font-size to 25 pixels */ | ||
| font-size: 25px; | ||
| } | ||
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| /* Position text in the bottom-left corner */ | ||
| .bottomleft { | ||
| position: absolute; | ||
| bottom: 0; | ||
| left: 16px; | ||
| } | ||
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| /* Position text in the middle */ | ||
| .middle { | ||
| position: absolute; | ||
| top: 50%; | ||
| left: 50%; | ||
| transform: translate(-50%, -50%); | ||
| text-align: center; | ||
| } | ||
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| /* Style the <hr> element */ | ||
| hr { | ||
| margin: auto; | ||
| width: 40%; | ||
| } | ||
| </style> |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,79 @@ | ||
| #!/usr/bin/perl -w | ||
| # Aroon Chande | ||
| use strict; | ||
| use Getopt::Long; | ||
| use File::Basename; | ||
| use File::Temp; | ||
| my ($fasta,$gff,$outdir,$hmmFile,$protFile,$outfile,$prots,@prots,%prots,@gff,%gff,@hits,$predict); | ||
| $prots = ''; | ||
| GetOptions ('fasta=s' => \$fasta, 'gff=s' => \$gff, 'predict=s' => \$predict); | ||
| $outdir = dirname($fasta); | ||
| open PROT, "$outdir/predictions.faa" or die "Cannot open $outdir/predictions.faa $!\n"; | ||
| foreach (<PROT>){ | ||
| $prots .= $_; | ||
| } | ||
| close PROT; | ||
| @prots = split(/\>/,$prots); | ||
| shift @prots; | ||
| foreach (@prots){ | ||
| my($desc, undef) = split(/\r?\n/,$_,2); | ||
| my @desc = split(/\|/,$desc); | ||
| $prots{$desc[0]} = $desc[1]; | ||
| } | ||
| if (!(defined $gff)){$gff = "$outdir/prots.gff";} | ||
| open GFF, $gff or die "Cannot open $outdir/prots.gff $!\n"; | ||
| foreach(<GFF>){ | ||
| my @cols = split(/\t/,$_); | ||
| if ($cols[0] =~ /\#/){next;} | ||
| else{ | ||
| #print "$cols[0]\t$cols[8]\n"; | ||
| my $base = $cols[0]; | ||
| my $id = $cols[8]; | ||
| my @idcols = split(/;/,$id); | ||
| ($id) = $idcols[0] =~ m/(_\d*)/; | ||
| $id = join('',$cols[0],$id); | ||
| $gff{$id}{start} = $cols[3]; | ||
| $gff{$id}{stop} = $cols[4]; | ||
| $gff{$id}{strand} = $cols[6]; | ||
| if(defined $prots{$id}){$gff{$id}{gene} = $prots{$id};} | ||
| else{$gff{$id}{gene} = "-";} | ||
| } | ||
| } | ||
| #foreach (keys %gff){ print "$_\t$gff{$_}{start}\t$gff{$_}{stop}\t$gff{$_}{strand}\t$gff{$_}{gene}\n" } | ||
| no warnings 'uninitialized'; | ||
| my %files; | ||
| my $j = 1; | ||
| my $scale; | ||
| my $max; | ||
| foreach my $key(keys %prots){ | ||
| if ($prots{$key} =~ /vgrg/){ | ||
| my ($num) = $key =~ m/(\d*$)/; | ||
| $key =~ s/_\d*$//g; | ||
| open OUT, ">$outdir/$j.ptt"; | ||
| print OUT "Location\tStrand\tLength\tPID\tGene\tSynonym\tCode\tCOG\tProduct\n"; | ||
| for(my $i = -5; $i <6; $i++){ | ||
| if($num + $i < 1){next;} | ||
| else{ | ||
| my $gffkey = join("_",$key,$num+$i); | ||
| if ((defined $gff{$gffkey}) & !(defined $scale)){$scale = $gff{$gffkey}{start}-1;} | ||
| $max = $gff{$gffkey}{stop}-$scale if (defined $gff{$gffkey}); | ||
| print OUT $gff{$gffkey}{start}-$scale,"..",$gff{$gffkey}{stop}-$scale,"\t$gff{$gffkey}{strand}\t",abs($gff{$gffkey}{start}-$gff{$gffkey}{stop}),"\t-\t$gff{$gffkey}{gene}\t-\t-\t-\t-\n" if (defined $gff{$gffkey}); | ||
| } | ||
| } | ||
| close OUT; | ||
| $files{$j}{max}=$max; | ||
| undef $scale; | ||
| $j++; | ||
| } | ||
| } | ||
| foreach my $key (keys %files){ | ||
| print "$key\n"; | ||
| open IN, "$outdir/$key.ptt"; | ||
| my @temp = <IN>; | ||
| close IN; | ||
| open OUT, ">$outdir/$key.ptt"; | ||
| print OUT "Genome - 1..$files{$key}{max}\n",@temp-1," proteins\n"; | ||
| print OUT @temp; | ||
| close OUT; | ||
| } | ||
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