Mercurial > repos > nml > mauve_contig_mover
diff mauve_contig_mover.pl @ 0:b8bc1922226a draft default tip
"planemo upload for repository https://github.com/phac-nml/mauve_contig_mover commit 2d8300acc533f8b9ec95ff24ad2f529e92e8da69"
| author | nml |
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| date | Thu, 21 Nov 2019 12:37:56 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mauve_contig_mover.pl Thu Nov 21 12:37:56 2019 -0500 @@ -0,0 +1,285 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use Data::Dumper; +use Getopt::Long; +use Pod::Usage; +use File::Copy; +use File::Basename; + + +my ($output, $reference_gbk, $reference_dat, $draft_fasta, $draft_dat, $alignment_file, $fasta_file, $html_file, $help, $best_alignment, + @files, @sorted_files, $num_of_alignments, $mauve_cmd, $out, $best_alignment_file, $best_fasta_file); + +Getopt::Long::Configure('bundling'); +GetOptions( + 'r|reference=s' => \$reference_dat, + 'd|draft=s' => \$draft_dat, + 'o|output=s' => \$output, + 'a|alignment=s' => \$alignment_file, + 'f|fasta=s' => \$fasta_file, + 'l|html=s' => \$html_file, + 'h|help' => \$help +); +pod2usage(1) if $help; + +#Format the fasta file. Some fastas were not working, so we're going to format all incoming fastas +my $draft_temp = "temporary.fasta"; + +open my $in, '<', $draft_dat or die "Could not open draft file: $?"; +open my $out, '>', $draft_temp or die "Could not open file for writing: $?"; + +my $first_header = <$in>; +chomp $first_header; +print $out "$first_header\n"; +while (my $line = <$in>) +{ + chomp $line; + + if ($line =~ />/) + { + print $out "\n$line\n"; + } + else + { + print $out $line; + } +} + + + +#progressiveMauve checks the file extension of inputs, and did not like .dat files passed in. + +#First get the file format for the extention. +my $format = get_format($reference_dat); +die "Input reference file isn't a properly formatted fasta or genbank file!\n" if $format eq "na"; + +#So here we create symbolic links to the .dat files using the proper file extensions. +$reference_gbk = "reference.".$format; +$draft_fasta = "draft.fasta"; + +system("ln -s $reference_dat $reference_gbk"); +system("ln -s $draft_temp $draft_fasta"); + +#First, run mauve with the given inputs +$mauve_cmd = "java -Djava.awt.headless=true -Xmx500m -cp \$path2jar org.gel.mauve.contigs.ContigOrderer -output ".$output." -ref ".$reference_gbk." -draft ".$draft_fasta; + +$out = system("$mauve_cmd"); + + +#Get all of the alignmentX folders and pick the latest one +opendir(DIR, $output) or die "Can't opendir $output"; +@files = readdir(DIR); +@sorted_files = sort @files; +$best_alignment = $sorted_files[@sorted_files -1]; +$num_of_alignments = $best_alignment; +$num_of_alignments =~ s/[^\d.]//g; + + +#Now let's give galaxy the right outputs. Is there a better way to do this? +#First extract the names from the paths +my ($a_name, $a_path, $a_suffix) = fileparse($best_alignment); +my ($d_name, $d_path, $d_suffix) = fileparse($draft_fasta, ".fasta"); + + +#Now we want some files (alignment and the final fasta file) to show up +#in the history. So we copy these files to send them to galaxy. +$best_alignment_file = $output."/".$best_alignment."/".$a_name; +$best_fasta_file = $output."/".$best_alignment."/".$d_name.".fasta"; + +#Now copy them to the galaxy locations +copy($best_alignment_file, $alignment_file) or die "$best_alignment_file Copying alignment failed: $!"; +copy($best_fasta_file, $fasta_file) or die "Copying fasta file failed: $!"; + + +#Let us write the html file! +open my $html_out, ">", $html_file; +printf $html_out "<!DOCTYPE html> +<html> +<style type=\"text/css\"> + +body { + font-family: sans-serif; + color: #000; + } + +table { + margin-left: 3em; + text-align: center; + } +th { + text-align:center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } +td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } +h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear: left; + } +</style></head> + + <body> + + + <h2 id=\"M0\">Mauve Output Summary</h2><br> + <ul><li>Number of alignments performed: $num_of_alignments (last alignment is usually the best)</li><li>The fasta and alignment files from the last alignment are shown in the history</li><li>To download the complete Mauve output, download the contents of this file</li><li>The contig orders of each alignment are shown below: </li></ul><br>"; + + +my %summary; +my $contig_count; + +#generate data html +foreach my $folder (@sorted_files) +{ + my $start = "Ordered Contigs"; + my $stop = "Contigs with conflicting ordering information"; + my $header = "type label contig strand left_end right_end"; + my $in_section = 0; + $contig_count = 0; + my @alignment_info; + next if ($folder =~ m/^\./); + my $file_path = $output."/".$folder."/".$d_name."_contigs.tab"; + open my $curr_file, "<", $file_path; + + #Go through the lines + while(<$curr_file>) + { + #find correct section. Note flip flop operators didn't work here for me + if(/$start/) {$in_section=1;} + elsif(/$stop/) {$in_section=0;} + + next if(/$start/ || /$stop/ || /$header/); + + #Store the line content + if ($in_section and /\S/) + { + $contig_count++; + my @tmp = split('\t', $_); + my @columns = ($tmp[1], $tmp[3]); + push(@alignment_info, [@columns]); + } + } + close $curr_file; + $summary{$folder} = [@alignment_info]; +} + + +#print out the headers + +printf $html_out "<table border=\"1\"><tbody><tr><th>Alignment</th>\n"; + +for my $a (sort keys %summary) +{ + my $tmp = $a; + $tmp =~ s/[^\d.]//g; + printf $html_out "<th colspan=\"2\">$tmp</th>\n"; +} + +printf $html_out "</tr>"; + +#print out the data +for my $i (0 .. $contig_count-1) +{ + printf $html_out "<tr><td></td>\n"; + for my $alignment (sort keys %summary) + { + printf $html_out "<td>". $summary{$alignment}[$i][0]."</td>\n<td>".$summary{$alignment}[$i][1]. "</td>\n"; + } + printf $html_out "</tr>\n"; +} + +printf $html_out "</tbody></table></body></html>"; + +#close all the things +closedir(DIR); +close $html_out; + +exit($out); + + +sub get_format +{ + my $file = shift; + my $format; + + open my $in, '<', $file or die "Could not open file for reading. $!"; + + my $line = <$in>; + + if ($line =~ /LOCUS/) + { + $format = "gbk"; + } + elsif ($line =~ /^>/) + { + $format = "fasta"; + } + else + { + $format = "na"; + } + close $in; + + return $format; +} + +__END__ + +=head1 NAME + + mauve_contig_mover.pl - A wrapper for galaxy to run Mauve Contig Mover + +=head1 SYNOPSIS + + mauve_contig_mover.pl -r <reference> -d <draft> -o <output> -a <alignment file output> -f <fasta file output> -l <html file output> -h <help> + +=head1 OPTIONS + +=over 8 + +=item B<-r> B<--reference> + +The input reference strain in either a fasta or genbank format + +=item B<-d> B<--draft> + +The input draft genome in fasta format + +=item B<-o> B<--output> + +The output folder created by Mauve + +=item B<-a> B<--alignment> + +The best output alignment produced by Mauve + +=item B<-f> B<--fasta> + +The best output fasta file produced by Mauve + +=item B<-l> B<--html> + +The html file containing all of the output files produced by Mauve + +=item B<-h> B<--help> + +Print a help message and exits + +=back + +=head1 DESCRIPTION + +B<mauve_contig_mover> is a galaxy wrapper for Mauve Contig Mover. This script runs the command line version of the Mauve Contig Mover + +=cut