removed name option from asseble_seq_idba

[biopieces.git] / bp_bin / assemble_seq_idba

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index c1d72a23f778a5aa7d4c54f1642ad0fccba2f294..31a1e686fb88404e3e2e41a2feea0cc311a25ab3 100755 (executable)
--- 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|