[gentoo-commits] proj/sci:master commit in: sci-biology/bambus/, sci-biology/bambus/files/

[Martin Mokrejs]

commit:     9aa415db19bd5661d638f9e0dcc7d1a2e51cb7a7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar  3 01:12:54 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar  3 01:12:54 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9aa415db

sci-biology/bambus: added goBambus.pl script and perl/python dependencies

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/bambus/bambus-2.33.ebuild |    6 +-
 sci-biology/bambus/files/goBambus.pl  |  244 +++++++++++++++++++++++++++++++++
 2 files changed, 249 insertions(+), 1 deletions(-)

diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 2a46d9c..045c267 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -18,6 +18,8 @@ IUSE=""
 
 DEPEND="sci-biology/tigr-foundation-libs"
 RDEPEND="${DEPEND}
+		dev-lang/perl
+		dev-lang/python
 		dev-perl/XML-Parser
 		dev-perl/Config-IniFiles
 		dev-perl/GraphViz"
@@ -95,6 +97,8 @@ src_install() {
 	mkdir -p "${D}"/usr/share/doc/"${P}" || die
 	mv "${D}"/usr/doc/* "${D}"/usr/share/doc/"${P}" || die
 	rmdir "${D}"/usr/doc || die
+
+	dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl"
 }
 
 pkg_postinst(){

diff --git a/sci-biology/bambus/files/goBambus.pl b/sci-biology/bambus/files/goBambus.pl
new file mode 100644
index 0000000..61f9ed3
--- /dev/null
+++ b/sci-biology/bambus/files/goBambus.pl
@@ -0,0 +1,244 @@
+#!/usr/bin/perl -w
+
+## Very simple perl script to drive the Bambus 2.0 pipeline (as I
+## currently understand it).
+## http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_2.0/goBambus-perl
+## as of 201103021123
+
+use strict;
+use Getopt::Long;
+
+
+
+## Configure defaults
+
+my $verbose = 1;
+
+my $contig_file = '';
+my $fasta_file  = '';
+my $mates_file  = '';
+
+my $output_prefix = 'out';
+
+## The threshold used to accept or reject a link between contigs
+my $link_redundancy = 1;
+
+## Weather or not to run the (crappy) 'repeat filter' code
+my $filter_repeats  = 0;
+
+## Not running dot saves time on 'big' runs
+my $run_dot = 1;
+
+
+
+## Process command line arguments
+
+GetOptions
+  ("contig_file=s"   => \$contig_file,
+   "fasta_file=s"    => \$fasta_file,
+   "mates_file=s"    => \$mates_file,
+   "output_prefix=s" => \$output_prefix,
+
+   "link_redundancy|r=i" => \$link_redundancy,
+   "repeat_filter|x"     => \$filter_repeats,
+   "dot|d!"              => \$run_dot,
+   "verbose+"            => \$verbose,
+  )
+  or die "failure to communicate\n";
+
+die "-c contig file plz!\n" unless -s $contig_file;
+die "-f fasta  file plz!\n" unless -s $fasta_file;
+die "-m mates  file plz!\n" unless -s $mates_file;
+
+die "are you crazy?\n"
+  if $output_prefix eq '';
+
+warn
+  join("\n",
+       "contig file     : $contig_file",
+       "fasta file      : $fasta_file",
+       "mates file      : $mates_file",
+       "output prefix   : $output_prefix",
+       "link redundancy : $link_redundancy",
+       "repeat filter   : $filter_repeats",
+       "run dot?        : $run_dot",
+       "verbose         : $verbose",
+      ), "\n"
+  if $verbose > 0;
+#exit;
+
+
+
+## Run the pipeline
+
+## Get data into bank format
+
+run(qq/
+ toAmos
+  -s $fasta_file
+  -c $contig_file
+  -m $mates_file
+  -o $output_prefix.afg
+/);
+
+## Debugging mates file
+#exit;
+
+run(qq/
+  bank-transact -cf
+    -m $output_prefix.afg
+    -b $output_prefix.bnk
+/);
+
+
+
+## Run the new Bambus pipeline
+
+run(qq/
+  clk
+    -b $output_prefix.bnk
+/);
+
+run(qq/
+  Bundler
+    -b $output_prefix.bnk
+/);
+
+## Repeat filtering?
+my $filter_repeats_option_string = '';
+if($filter_repeats){
+  run(qq/
+    MarkRepeats
+      -noCoverageRepeats
+      -b $output_prefix.bnk
+      -redundancy $link_redundancy
+       > $output_prefix.repeats
+  /);
+  
+  $filter_repeats_option_string =
+    "-repeats $output_prefix.repeats";
+}
+
+run(qq/
+  OrientContigs
+    -noreduce
+   $filter_repeats_option_string
+    -b $output_prefix.bnk
+    -redundancy $link_redundancy
+    -prefix $output_prefix
+/);
+
+
+
+## Generate some additional TEXT output
+
+## ouput a fasta sequence for the contigs from the bank (passed to
+## printScaff with -f)
+
+#run(qq/
+#  bank2fasta -iid
+#    -b $output_prefix.bnk
+#     > $output_prefix.contig.fasta
+#/);
+
+## Generates the useful .details, .oo, .sum and .stats files
+#    -f $output_prefix.contig.fasta
+run(qq/
+  printScaff -detail -oo -sum
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.xml
+    -l $output_prefix.library
+    -o $output_prefix
+/);
+
+run(qq/
+  mv -f
+    printScaff.error
+    $output_prefix.printScaff.error
+/)
+  if -s 'printScaff.error';
+
+
+
+
+
+## UNTANGLE
+
+run(qq/
+  untangle
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.xml
+    -o $output_prefix.out.untangle.xml
+/);
+
+run(qq/
+  mv -f
+    untangle.error
+    $output_prefix.untangle.error
+/)
+  if -s 'untangle.error';
+
+
+
+## Generates the useful .details, .oo, .sum and .stats files
+#    -f $output_prefix.contig.fasta
+run(qq/
+  printScaff -detail -oo -sum -dot
+    -e $output_prefix.evidence.xml
+    -s $output_prefix.out.untangle.xml
+    -l $output_prefix.library
+    -o $output_prefix.untangle
+/);
+
+run(qq/
+  mv -f
+    printScaff.error
+    $output_prefix.untangle.printScaff.error
+/)
+  if -s 'printScaff.error';
+
+
+
+
+
+## FINALLY, DOT
+
+if($run_dot){
+  # output before untangle
+  run(qq/
+    dot -Tps
+      $output_prefix.dot
+    > $output_prefix.ps
+  /);
+  
+  # output after untangle
+  run(qq/
+    dot -Tps
+      $output_prefix.untangle.dot
+    > $output_prefix.untangle.ps
+  /);
+}
+
+warn "OK\n";
+
+
+
+
+
+## Yup
+
+sub run{
+  my $cmd = shift;
+  
+  $cmd =~ s/\n/ /g;
+  
+  print "\n\n\nRUN: $cmd\n\n"
+    if $verbose > 0;
+  
+  `$cmd`;
+  
+  die if $? != 0;
+  
+  return 1;
+}
+