Add minnumtx for test_file in both .fa and .gtf input test

tderrien · Jul 13, 2022 · b25be4d · b25be4d
1 parent 1fadb02
commit b25be4d
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/scripts/FEELnc_codpot.pl b/scripts/FEELnc_codpot.pl
@@ -348,6 +348,7 @@
 
 
 
+my $minnumtxtest = 1 ;
 ##########################################################
 # test file
 #######
@@ -356,13 +357,13 @@
 {
     print STDERR "> Extract ORFs/cDNAs for candidates RNAs from a GTF file\n";
     # Use undef for $nbtx/$numtx to get all sequences and ORFs
-    ExtractCdnaOrf::CreateORFcDNAFromGTF($infile, $testFile, $testOrfFile, undef, 1, $genome, 'exon,CDS,stop_codon,start_codon', undef, $orfTypeTest, $verbosity, $kmerMax);
+    ExtractCdnaOrf::CreateORFcDNAFromGTF($infile, $testFile, $testOrfFile, undef, $minnumtxtest, $genome, 'exon,CDS,stop_codon,start_codon', undef, $orfTypeTest, $verbosity, $kmerMax);
 }
 elsif(Utils::guess_format($infile) eq "fasta") # -- if FASTA
 {
     print STDERR "> Extract ORFs/cDNAs for candidates RNAs from a FASTA file\n";
     # Use undef for $nbtx/$numtx to get all sequences and ORFs
-    ExtractCdnaOrf::CreateORFcDNAFromFASTA($infile, $testFile, $testOrfFile, undef, 1, $orfTypeTest, $verbosity, $kmerMax);
+    ExtractCdnaOrf::CreateORFcDNAFromFASTA($infile, $testFile, $testOrfFile, undef, $minnumtxtest, $orfTypeTest, $verbosity, $kmerMax);
 }
 else
 {