Commit b344449ca4a8587ff9bbc62f984498e32490d1d4
1 parent
00a435ae26
Exists in
master
Updated getDomainTopology to use extractTCDB.pl
Showing 1 changed file with 4 additions and 4 deletions Side-by-side Diff
getDomainTopology.pl
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b344449
| ... | ... | @@ -275,8 +275,8 @@ |
| 275 | 275 | |
| 276 | 276 | |
| 277 | 277 | #Extract sequences for reference family |
| 278 | - my $outFile = "$tcdbDir/family-${tcid}.faa"; | |
| 279 | - my $cmd2 = qq(extractFamily.pl -i $tcid -o $tcdbDir -d $tcdbSeqsFile); | |
| 278 | + my $outFile = "$tcdbDir/tcdb-${tcid}.faa"; | |
| 279 | + my $cmd2 = qq(extractTCDB.pl -i $tcid -o $tcdbDir -d $tcdbSeqsFile); | |
| 280 | 280 | system $cmd2 unless (-f $outFile); |
| 281 | 281 | die "Could not generate sequence file: $outFile" unless (-f $outFile); |
| 282 | 282 | |
| ... | ... | @@ -312,7 +312,7 @@ |
| 312 | 312 | |
| 313 | 313 | $blastdb = "$blastD/tcdb"; |
| 314 | 314 | |
| 315 | - my $cmd6 = qq(extractFamily.pl -i tcdb -o $blastD -f blast -d $new_tcdbSeqsFile); | |
| 315 | + my $cmd6 = qq(extractTCDB.pl -i tcdb -o $blastD -f blast -d $new_tcdbSeqsFile); | |
| 316 | 316 | system $cmd6 unless (-f "${blastdb}.pin"); |
| 317 | 317 | |
| 318 | 318 | |
| ... | ... | @@ -488,7 +488,7 @@ |
| 488 | 488 | |
| 489 | 489 | -s, --tcdb-seqs {file} (Optional; Default: $RESEARCH_DATA/pfam/download/tcdb.faa) |
| 490 | 490 | FASTA file with all sequences in TCDB (as generated by program |
| 491 | - extractFamily.pl). This file will be used to extract sequences | |
| 491 | + extractTCDB.pl). This file will be used to extract sequences | |
| 492 | 492 | and TCIDs for all members of the input family. This allows to |
| 493 | 493 | freeze TCDB contents at a specific date, for the purpose defining |
| 494 | 494 | a project. |