fixed bug in get_homologues.pl -X which produced zero clusters when n…

…ew sequences files were added to previous results

CHANGES.txt

@@ -194,3 +194,4 @@
 16052017: added message to make_nr_pangenome_matrix.pl to warn users that BLAST files must be removed with different refs
 17052017: added option -r to annotate_cluster.pl so that external sequences can be used to drive cluster alignment
 30052017: updated lib/ForkManager.pm to v1.19 (http://search.cpan.org/perldoc?Parallel%3A%3AForkManager)
+09062017: fixed bug in get_homologues.pl -X which produced zero clusters when new sequences files were added to previous results

get_homologues.pl

@@ -1,6 +1,6 @@
 #!/usr/bin/env perl 
 
-# 2016 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
+# 2017 Bruno Contreras-Moreira (1) and Pablo Vinuesa (2):
 # 1: http://www.eead.csic.es/compbio (Estacion Experimental Aula Dei/CSIC/Fundacion ARAID, Spain)
 # 2: http://www.ccg.unam.mx/~vinuesa (Center for Genomic Sciences, UNAM, Mexico)
 
@@ -1295,14 +1295,14 @@
 
       # now concat the other accessions
       $blastDBfile = $newDIR ."/". $new_infile .".others";
-      if(!-s $blastDBfile.".dmnd")
+      if(!-s $blastDBfile.".dmnd" || $current_files ne $previous_files)
       {
         open(ALLOTHERS,">",$blastDBfile) || die "# EXIT: cannot create $blastDBfile\n";
         foreach my $other_infile (@newfiles)
         {
           next if($other_infile eq $new_infile);
           $infile = (split(/\.$FASTAEXTENSION/,$other_infile))[0];
-          next if($include_file && !$included_input_files{$infile});
+          next if($include_file && !$included_input_files{$infile}); 
 
           open(OTHER,"$newDIR/$other_infile") ||
             die "# EXIT: cannot read $newDIR/$other_infile\n";
@@ -1408,7 +1408,7 @@
       $clusteroutfile = $newDIR ."/_". $new_infile ."_others.queue";
       push(@to_be_deleted,$clusteroutfile);
 
-      if(-s $blastout) # check previous runs
+      if(-s $blastout && $current_files eq $previous_files) # check previous runs
       {
         if(!-s $blast_file){ push(@tmp_blast_output_files,$blastout); }
         next;