fixed parsing of filenames with -I in cases where input files are lik…

…e numbers.faa

CHANGES.txt

@@ -219,3 +219,4 @@
 28082017: fixed bug in compare_clusters.pl when .cluster_list file is not parsed, due to previous changes in find_taxa_FASTA_array_headers (thanks Audrey Bioteau)
 06092017: added options -x <regex>, -c <0|1> and -f <int> to hcluster_matrix.sh (thanks Marga Gomila)
 18092017: added oneliner to transpose matrix to compare_clusters.pl
+18092017: fixed parsing of filenames with -I in cases where input files are like numbers.faa (thanks cdeai)

get_homologues-est.pl

@@ -793,7 +793,7 @@
     $includedfull = "$included.nucl";
     foreach $taxon (@taxa)
     {
-      if($includedfull =~ /$taxon/)
+      if($taxon =~ /^$includedfull$/) #if($includedfull =~ /$taxon/) 
       {
         push(@Itaxa,$taxon);
         $n_of_sequences += $psize{$included};
@@ -806,7 +806,7 @@
   }
   print "\n";
 
-  if($n_of_matched_included < 3)
+  if($n_of_matched_included < scalar(keys(%included_input_files)))
   {
     die "# EXIT : failed to match taxa included in $include_file ($n_of_matched_included), ".
       "please make sure their names match those of input files\n";

get_homologues.pl

@@ -1059,8 +1059,8 @@
     $includedfull = $included;
     if($do_features){ $includedfull .= '_features'; }
     foreach $taxon (@taxa)
-    {
-      if($includedfull =~ /$taxon/)
+    { 
+      if($taxon =~ /^$includedfull$/) #if($includedfull =~ /$taxon/)
       {
         push(@Itaxa,$taxon);
         $n_of_sequences += $psize{$included};
@@ -1073,7 +1073,7 @@
   }
   print "\n";
 
-  if($n_of_matched_included < 3)
+  if($n_of_matched_included < scalar(keys(%included_input_files)))
   {
     die "# EXIT : failed to match taxa included in $include_file ($n_of_matched_included), ".
       "please make sure their names match those of input files\n";