Updated manuals and added mview

README.txt

@@ -17,6 +17,7 @@ but includes code and binaries from other authors:
  Pfam (http://pfam.sanger.ac.uk , PubMed=19920124)
  PHYLIP 3.695 (http://evolution.genetics.washington.edu/phylip) 
  Transdecoder r20140704 (http://transdecoder.sf.net , PubMed=23845962)
+ MVIEW 1.60.1 (https://github.com/desmid/mview, PubMed=9632837)
 
 License
 ===============================================================================
@@ -64,6 +65,9 @@ by the author. Department of Genome Sciences, University of Washington, Seattle.
 reconstruction from RNA-seq using the Trinity platform for reference generation 
 and analysis. Nat Protoc. 8(8):1494-512.
 
+11) Brown NP, Leroy C, Sander C (1998) MView: A Web compatible database search or 
+multiple alignment viewer. Bioinformatics. 14 (4):380-381. 
+
 System requirements and installation:
 ================================================================================
 This software has been tested in Linux and MacOSX systems. It includes a 

compare_clusters.pl

@@ -272,23 +272,22 @@
 
     foreach $seq (0 .. $#{$cluster_ref})
     {
-
       # in case of missing nucleotide sequences, not retrieved from gbk files
       $cluster_ref->[$seq][SEQ] ||= '--unknown sequence--';
 
       # check for internal STOP codons if required
       next if($SKIPINTERNALSTOPS && $cluster_ref->[$seq][SEQ] =~ /\*[A-Z]/i);
 
-# fix header and remove possibly added bits: |intergenic199|,| aligned:1-296 (296)
+      # fix header and remove possibly added bits: |intergenic199|,| aligned:1-296 (296)
       $seqname = $cluster_ref->[$seq][NAME];
 
       next if($INP_include && !$included_input_files{$taxa{$file}{'sorted_taxa'}->[$seq]});
       push(@sorted_taxa,$taxa{$file}{'sorted_taxa'}->[$seq]);
 
-# store gi and/or neighbor (synteny) data if required
-# NOTE: assumes GI is first space-separated label in header
-# GI:15616631 |[B aphidicola (Acyrthosiphon pisum)]|APS|gidA|1887|NC_002528(640681):197-2083:1
-#^..^ ...|neighbours:start(),GI:15616(1)
+      # store gi and/or neighbor (synteny) data if required
+      # NOTE: assumes GI is first space-separated label in header
+      # GI:15616631 |[B aphidicola (Acyrthosiphon pisum)]|APS|gidA|1887|NC_002528(640681):197-2083:1
+      #^..^ ...|neighbours:start(),GI:15616(1)
       if($INP_synt || $INP_orthoxml)
       {
         $gi = (split(/\s/,$seqname))[0]; $gi =~ s/ //g;

get_homologues.pl

@@ -2355,7 +2355,7 @@
   else{ $names{$cluster_name}++ }
 
   if(!$saveRAM){ %aligned_coords = find_local_alignment_coords( $gene,@{$orthologues{$gene}} ); }
-  if($do_PFAM){ $pfam_annot = $pfam_hash{$gene} || '' }
+  if($do_PFAM){ $pfam_annot = $pfam_hash{$gene} || ''; }
 
   # 4.3.1) print reference gene/protein
   push(@taxon_names,$gindex2[$gene]); # global set in phyTools:constructAllFasta

lib/est/TransDecoder_r20140704/PerlLib/Fasta_reader.pm

@@ -91,8 +91,6 @@ sub retrieve_all_seqs_hash {
 	return(%acc_to_seq);
 }
 
-
-
 ##############################################
 package Sequence;
 use strict;

lib/est/TransDecoder_r20140704/PerlLib/GFF3_utils.pm

@@ -35,7 +35,7 @@ sub index_GFF3_gene_objs {
     my %cds_phases;
 
     my %gene_names;
-	my %loci;
+	  my %loci;
 
     open (my $fh, $gff_filename) or die $!;
 

lib/est/TransDecoder_r20140704/TransDecoder

@@ -62,7 +62,6 @@ use Longest_orf;
 my $UTIL_DIR = "$FindBin::RealBin/util";
 $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
 #$ENV{LD_LIBRARY_PATH} .= ":$FindBin::RealBin/util/lib64";# Bruno Dec2014
-
 #my ($cd_hit_est_exec) = &check_program('cd-hit-est');# Bruno Dec2014
 
 my ($transcripts_file,$train_file,$prepare_pfam_only);