Commit bbf0ef5765e6cc205108b61dd2dfbf0d0a0e6137
1 parent
68b41f16a3
Exists in
master
Added the ability to generate a tsv file as output for easy parsing
Showing 1 changed file with 13 additions and 3 deletions Side-by-side Diff
alignSeqsFiles.pl
View file @
bbf0ef5
| ... | ... | @@ -157,8 +157,10 @@ |
| 157 | 157 | |
| 158 | 158 | #Prepare output files |
| 159 | 159 | my $htmlFile = "$outdir/report.html"; |
| 160 | + my $tsvFile = "$outdir/report.tsv"; | |
| 160 | 161 | my $plotsFile = "$outdir/plots.html"; |
| 161 | 162 | |
| 163 | + my $tsvHeader = "#Query\tSubject\tQlen\tSlen\tE-value\tIdentity\tQstart\tQend\tQcov\tSstart\tSend\tScov\tQseq\tSseq\n"; | |
| 162 | 164 | |
| 163 | 165 | my $htmlHeader = <<HEADER; |
| 164 | 166 | <!DOCTYPE html> |
| ... | ... | @@ -231,6 +233,9 @@ |
| 231 | 233 | HEADER |
| 232 | 234 | |
| 233 | 235 | |
| 236 | + open (my $tsvh, ">", $tsvFile) || die $!; | |
| 237 | + print $tsvh $tsvHeader; | |
| 238 | + | |
| 234 | 239 | open (my $outh, ">", $htmlFile) || die $!; |
| 235 | 240 | print $outh $htmlHeader; |
| 236 | 241 | |
| ... | ... | @@ -299,6 +304,7 @@ |
| 299 | 304 | |
| 300 | 305 | print $outh $alnHit; |
| 301 | 306 | |
| 307 | + print $tsvh "$qacc\t$sacc\t$qlen\t$slen\t$eval\t$id\t$qstart\t$qend\t$qcov\t$sstart\t$send\t$scov\t$qseq\t$sseq\n"; | |
| 302 | 308 | |
| 303 | 309 | #Generate the hydropathy plots |
| 304 | 310 | my $good = run_quod($qacc, $sacc, $qstart, $qend, $sstart, $send, $qseq, $sseq); |
| ... | ... | @@ -355,6 +361,7 @@ |
| 355 | 361 | print $outh $closeRep; |
| 356 | 362 | |
| 357 | 363 | close $outh; |
| 364 | + close $tsvh; | |
| 358 | 365 | } |
| 359 | 366 | |
| 360 | 367 | |
| 361 | 368 | |
| 362 | 369 | |
| ... | ... | @@ -471,10 +478,13 @@ |
| 471 | 478 | print $sfh ">$s alignment\n$sseq\n"; |
| 472 | 479 | close $sfh; |
| 473 | 480 | |
| 481 | + my $labelsStr = "--axis-font 18.0 --tick-font 15.0 --title-font 20.0 --xlabel Residues --ylabel Hydropathy --width 15 --xticks 25"; | |
| 482 | + my $ylimStr = "--ylim -3 3"; | |
| 474 | 483 | |
| 484 | + | |
| 475 | 485 | #Note alnquod requires to add the extension to the image name |
| 476 | 486 | my $alnFig = "$plotsDir/${q}_vs_${s}_qs${qs}_qe${qe}_ss${ss}_se${se}.png"; |
| 477 | - my $cmd1 = qq(quod.py -q -l "$q (red) and $s (blue)" -o $alnFig --xticks 25 --width 15 --edgecolor +0:red +1:blue --facecolor +0:orange +1:cyan --multi frag -- $qalnFile $seqDir/${q}.faa $salnFile $seqDir/${s}.faa); | |
| 487 | + my $cmd1 = qq(quod.py -q $labelsStr -l "$q (red) and $s (blue)" -o $alnFig $ylimStr --edgecolor +0:red +1:blue --facecolor +0:orange +1:cyan --multi frag -- $qalnFile $seqDir/${q}.faa $salnFile $seqDir/${s}.faa); | |
| 478 | 488 | # print "$cmd1\n\n"; |
| 479 | 489 | # exit; |
| 480 | 490 | system $cmd1 unless (-f "${alnFig}"); |
| ... | ... | @@ -496,7 +506,7 @@ |
| 496 | 506 | #Plot query hydropathy |
| 497 | 507 | my $qPfam = get_pfam_coords_for_quod($q, "red"); |
| 498 | 508 | my $qName = "$plotsDir/${q}_vs_${s}_qaln_qs${qs}_qe${qe}.png"; |
| 499 | - my $cmd2 = qq(quod.py -q -l "$q" -o $qName --width 15 --edgecolor red --xticks 25 -w ${qs}-${qe}:+2.7:+:Alignment --no-tms +0 $qTMS $qPfam -- $seqDir/${q}.faa); | |
| 509 | + my $cmd2 = qq(quod.py -q $labelsStr -l "$q" -o $qName --edgecolor red $ylimStr -w ${qs}-${qe}:+2.7:+:Alignment --no-tms +0 $qTMS $qPfam -- $seqDir/${q}.faa); | |
| 500 | 510 | # print "$cmd2\n\n"; |
| 501 | 511 | # exit; |
| 502 | 512 | system $cmd2 unless (-f $qName); |
| ... | ... | @@ -514,7 +524,7 @@ |
| 514 | 524 | #Plot Subject hydropaty |
| 515 | 525 | my $sPfam = get_pfam_coords_for_quod($s, "blue"); |
| 516 | 526 | my $sName = "$plotsDir/${q}_vs_${s}_saln_ss${ss}_se${se}.png"; |
| 517 | - my $cmd3 = qq(quod.py -q -l "$s" -o $sName --width 15 --edgecolor blue --xticks 25 -w ${ss}-${se}:+2.7:+:Alignment --no-tms +0 $sTMS $sPfam -- $seqDir/${s}.faa); | |
| 527 | + my $cmd3 = qq(quod.py -q $labelsStr -l "$s" -o $sName --edgecolor blue $ylimStr -w ${ss}-${se}:+2.7:+:Alignment --no-tms +0 $sTMS $sPfam -- $seqDir/${s}.faa); | |
| 518 | 528 | # print "$cmd3\n\n"; |
| 519 | 529 | # exit; |
| 520 | 530 | system $cmd3 unless (-f $sName); |