Created
September 19, 2013 07:18
-
-
Save maasha/6620031 to your computer and use it in GitHub Desktop.
Ruby script for the reconstruction of deteriorated index in paired end Illumina reads. maasha/seq and maasha/fastq are from www.biopieces.org
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/env ruby | |
require 'pp' | |
require 'maasha/fastq' | |
require 'maasha/seq' | |
map_file = "/home/maasha/Data/KimMagnussen/20130904_hiseq2a_rescue/sample_table.txt" | |
barcode_hash = {} | |
barcode1_hash = {} | |
barcode2_hash = {} | |
File.open(map_file) do |ios| | |
ios.each do |line| | |
next if line[0] == '#' | |
fields = line.chomp.split("\t") | |
sample_name = fields[1] | |
barcode = fields[5] | |
barcode1, barcode2 = barcode.split('_') | |
barcode_hash[barcode1 + barcode2] = sample_name | |
barcode1_hash[barcode1] = sample_name | |
barcode2_hash[barcode2] = sample_name | |
end | |
end | |
files = Dir.glob("/home/maasha/data/KimMagnussen/20130904_hiseq2a_rescue/20130904_hiseq2a/Undetermined_indices/**/*fastq.gz") | |
fh_hash = {} | |
files.each do |file| | |
STDERR.puts "Processing file: #{File.basename(file)}" | |
lane_info = File.basename(file, ".fastq.gz").split('_')[2 .. -2].join('_') | |
Fastq.open(file) do |ios| | |
ios.each do |entry| | |
barcode = entry.seq_name.split(':').last | |
barcode1 = barcode[0 .. 7] | |
barcode2 = barcode[8 .. 15] | |
if barcode1_hash[barcode1] | |
if barcode2_hash[barcode2] | |
# STDERR.puts "OK: barcode2: #{barcode2} found in #{entry.seq_name}" | |
else | |
barcode2_regex = /^#{barcode2.tr('N', '.')}$/ | |
hits_hash = {} | |
barcode2_hash.each_key do |barcode2| | |
if barcode2.match barcode2_regex | |
hits_hash["#{barcode1}_#{barcode2}"] = barcode_hash[barcode1 + barcode2] | |
end | |
end | |
if hits_hash.size == 0 | |
# STDERR.puts "Warning: empty hits hash" | |
elsif hits_hash.size > 1 | |
# STDERR.puts "Warning: multiple hits: #{hits_hash.size}" | |
else | |
sample = hits_hash.first.last | |
if sample | |
outfile = "#{sample}_#{lane_info}.fastq" | |
unless fh_hash[outfile] | |
fh = File.open(outfile, 'w') | |
fh_hash[outfile] = fh | |
end | |
fh = fh_hash[outfile] | |
fh.puts entry.to_fastq | |
else | |
# STDERR.puts "Warning: no sample for barcode: #{hits_hash.first}" | |
end | |
end | |
end | |
else | |
# STDERR.puts "Warning: barcode1: #{barcode1} not in #{entry.seq_name}" | |
end | |
end | |
end | |
end |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment