fixed Pfam db check from _split_hmmscan.pl and updated manuals

CHANGES.txt

@@ -83,4 +83,7 @@
 11012016: added global $MINSEQLENGTH to filter out short oligomers
 13012016: fixed bug in get_homologues-est.pl -D
 13012016: EST manual updated
-
+13012016: fixed bug in compare_clusters.pl while parsing cluster list generated with -D
+19012016: fixed Pfam db check in _split_hmmscan.pl (thanks Jon Badalamenti)
+20012016: fixed src/Makefile error in mcl
+20012016: manuals updated

_split_hmmscan.pl

@@ -1,6 +1,6 @@
 #!/usr/bin/perl -w
 
-# May2013 Bruno Contreras, pablito
+# May2013 Bruno Contreras, Pablo Vinuesa, updated Jan2016
 # Script to take advantage of multicore machines when running hmmer3,
 # which seems to scale up to the number of physical cores in our tests.
 
@@ -53,7 +53,7 @@
   else{ die "# ERROR: hmmscan command must include database & input files \n" }
 
   if(!-s $input_seqfile){ die "# ERROR: cannot find input file $input_seqfile\n" }
-  elsif(!-s $db_file)
+  elsif(!-s $db_file.'.h3m')
   {
     die "# ERROR: cannot find database file $db_file\n"
   }

compare_clusters.pl

@@ -173,7 +173,8 @@
       # cluster 3491_1182 size=20 taxa=20 dnafile: 3491_1182.fna
       # cluster 76767_thrA size=20 taxa=20 Pfam=PF00696, file: 76767_thrA.faa dnafile: 76767_thrA.fna
       # cluster 1_Brdisv1ABR21035063m size=58 taxa=55 file: 1_Brdisv1ABR21035063m.fna aminofile: 1_Brdisv1ABR21035063m.faa
-
+      # cluster 1_TR20326-c1_g1_i1 size=12 taxa=12 Pfam=PF13920, file: 1_TR20326-c1_g1_i1.fna aminofile: 1_TR20326-c1_g1_i1.faa
+
       if(/^cluster \S+ size=\d+ taxa=\d+ .*?file: (\S+) dnafile: (\S+)/)
       {
         if($INP_prot){ $file = $1 }
@@ -186,7 +187,8 @@
         $file = $1;
         push(@files,$file);
       }
-      elsif(/^cluster \S+ size=\d+ taxa=\d+ file: (\S+) aminofile: (\S+)/)
+      elsif(/^cluster \S+ size=\d+ taxa=\d+ file: (\S+) aminofile: (\S+)/ || 
+        /^cluster \S+ size=\d+ taxa=\d+ .*?file: (\S+) aminofile: (\S+)/)
       {
         if($INP_prot){ $file = $2 }
         else{ $file = $1 }

install.pl

@@ -1,8 +1,8 @@
 #!/usr/bin/env perl
 
-# script that checks/compiles software required by get_homologues.pl and checks dependencies
+# script that checks/compiles software required by get_homologues[-est] and checks dependencies
 # for first-time users
-# last edited Dic2015
+# last checked Jan2016
 
 use strict;
 use Cwd;
@@ -78,7 +78,7 @@
   else{ print ">> OK\n"; }
 }
 
-# NCBI blast
+# NCBI blast+
 print "## Checking blast (lib/phyTools: \$ENV{'EXE_BLASTP'})\n";
 $output = `$ENV{'EXE_BLASTP'} 2>&1`;
 if(!$output || $output !~ /BLAST/)
@@ -101,7 +101,7 @@
 if($output =~ /Usage:/){ print ">> OK\n"; }
 else
 {
-  die "<< Cannot run shipped hmmscan, please download hmmer 3.1 from http://hmmer.janelia.org ,\n".
+  die "<< Cannot run shipped hmmscan, please download hmmer 3.1b2 from http://hmmer.janelia.org ,\n".
     "<< install it and edit variable EXE_HMMPFAM as explained in the manual\n".
     "<<(inside set_phyTools_env in file lib/phyTools.pm) .\n".
     "<< Then re-run\n";
@@ -255,7 +255,8 @@
 my (@missing_packages,@missing_perl_modules);
 
 print "## checking optional software R (lib/phyTools: \$ENV{'EXE_R'})\n";
-print "# required by compare_clusters.pl, parse_pangenome_matrix.pl -s, plot_pancore_matrix.pl\n";
+print "# required by compare_clusters.pl, parse_pangenome_matrix.pl -s, plot_pancore_matrix.pl and\n";
+print "# plot_matrix_heatmap.sh, hcluster_matrix.sh\n";
 $output = `$ENV{'EXE_R'} --version 2>&1`;
 if($output =~ /R version/){ print ">> OK\n"; }
 else