From 19bdc1ed4ad28032a9d3b8dbfc7e0519434b9b2d Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 5 May 2011 08:47:55 +0000
Subject: [PATCH] removed name option from asseble_seq_idba

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1372 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/assemble_seq_idba   | 16 ++++++++++------
 bp_bin/assemble_seq_velvet |  7 ++++---
 2 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index c1d72a2..31a1e68 100755
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -32,7 +32,6 @@ require 'biopieces'
 require 'fasta'
 
 casts = []
-casts << {:long=>'name',       :short=>'n', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'directory',  :short=>'d', :type=>'dir',    :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'scaffold',   :short=>'s', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>false, :default=>25,  :allowed=>nil, :disallowed=>nil}
@@ -49,7 +48,7 @@ options = bp.parse(ARGV, casts)
 
 Dir.mkdir(options[:directory]) unless Dir.exists?(options[:directory])
 
-file_fasta = [options[:directory], options[:name]].join(File::SEPARATOR) + ".fna"
+file_fasta = [options[:directory], "IDBA"].join(File::SEPARATOR) + ".fna"
 
 Fasta.open(file_fasta, mode="w") do |fasta_io|
   bp.each_record do |record|
@@ -58,7 +57,7 @@ Fasta.open(file_fasta, mode="w") do |fasta_io|
 end
 
 unless File.size(file_fasta) == 0
-  output = [options[:directory], options[:name]].join(File::SEPARATOR)
+  output = [options[:directory], "IDBA"].join(File::SEPARATOR)
 
   commands = []
   commands << "nice -n 19"
@@ -75,10 +74,15 @@ unless File.size(file_fasta) == 0
   commands << "> /dev/null 2>&1" unless options[:verbose]
 
   command = commands.join(" ")
-  system(command)
-  raise "Command failed: #{command}" unless $?.success?
 
-  file_contig = [options[:directory], options[:name] ].join(File::SEPARATOR) + "-contig.fa"
+  begin
+    system(command)
+    raise "Command failed: #{command}" unless $?.success?
+  rescue
+    $stderr.puts "Command failed: #{command}"
+  end
+
+  file_contig = [options[:directory], "IDBA"].join(File::SEPARATOR) + "-contig.fa"
 
   Fasta.open(file_contig, mode="r") do |fasta_io|
     fasta_io.each do |entry|
diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index cf6160f..557aa56 100755
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -46,7 +46,7 @@ class Velvet
     kmer = @kmer_min
 
     while kmer <= @kmer_max
-      dir_velveth = [@directory, "Velvet_#{kmer}"].join(File::SEPARATOR)
+      dir_velveth = [@directory, "Kmer_#{kmer}"].join(File::SEPARATOR)
 
       Dir.mkdir(dir_velveth)
 
@@ -65,7 +65,7 @@ class Velvet
   end
 
   def run_velvetg(cov_cutoffs, exp_cov)
-    Dir.glob("#{@directory}/Velvet_*").each do |dir_velveth|
+    Dir.glob("#{@directory}/Kmer_*").each do |dir_velveth|
       files_velveth = Dir.glob("#{dir_velveth}/*")
 
       cov_cutoffs.each do |cov_cutoff|
@@ -79,6 +79,7 @@ class Velvet
         commands << dir_velvetg
         commands << "-cov_cutoff #{cov_cutoff}"
         commands << "-exp_cov #{exp_cov}"
+        commands << "-clean yes"
 
         execute(commands)
       end
@@ -88,7 +89,7 @@ class Velvet
   def pick_best_assembly
     list = []
 
-    Dir.glob("#{@directory}/Velvet_*/Cov_cutoff_*/contigs.fa").each do |file|
+    Dir.glob("#{@directory}/Kmer_*/Cov_cutoff_*/contigs.fa").each do |file|
       n50 = fasta_n50(file)
       list << [file, n50]
     end
-- 
2.39.2