Sha256: e959f2323640413e45f545b5c78fb937c2b6672000c948886bcf024a434e9382
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Versions: 28
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Stored size: 1.48 KB
Contents
#!/usr/bin/env ruby
command_info="
#================================================
# Author: Almudena Bocinos Rioboo
#
#
# Usage: fasta2xml.rb <fasta_file> [> <out_file.xml>]
#
# Converts a fasta file to xml format (used for cabog)
#
# Prints to stdout, can be redirected to file with >
#
#================================================
\n";
#require "utils/fasta_utils"
require File.dirname(__FILE__) + "/utils/fasta_utils"
#receive one argument or fail
if ARGV.length != 1
puts command_info;
Process.exit(-1);
end
#get file name
file_name=ARGV[0];
#check if file exists
if !File.exist?(file_name)
puts "File #{file_name} not found.\n";
puts command_info;
Process.exit(-1);
end
######################################
# Define a subclass to override events
######################################
class FastaProcessor< FastaUtils::FastaReader
#override begin processing
def on_begin_process()
# print XML header
puts "<?xml version=\"1.0\"?>\n<trace_volume>\n";
end
#override sequence processing
def on_process_sequence(seq_name,seq_fasta)
# prints the xml tags
puts "<trace>\n\t<trace_name>#{seq_name}</trace_name>\n\t<clip_vector_left>1</clip_vector_left>\n\t<clip_vector_right>#{seq_fasta.length.to_s}</clip_vector_right>\n</trace>\n";
end
#override end processing
def on_end_process()
#print foot
puts "</trace_volume>\n";
end
end
#Create a new instance to process the file
f=FastaProcessor.new(file_name);
Version data entries
28 entries across 28 versions & 1 rubygems