From ad1772aebdbd833813826c1e414d92e1da82c9a8 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 26 May 2011 15:04:58 +0000 Subject: [PATCH] added order_pairs git-svn-id: http://biopieces.googlecode.com/svn/trunk@1436 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/order_pairs | 80 +++++++++++++++++++++++++++++++++++ bp_test/in/order_pairs.in | 40 ++++++++++++++++++ bp_test/out/order_pairs.out.1 | 30 +++++++++++++ bp_test/test/test_order_pairs | 7 +++ 4 files changed, 157 insertions(+) create mode 100755 bp_bin/order_pairs create mode 100644 bp_test/in/order_pairs.in create mode 100644 bp_test/out/order_pairs.out.1 create mode 100755 bp_test/test/test_order_pairs diff --git a/bp_bin/order_pairs b/bp_bin/order_pairs new file mode 100755 index 0000000..8746548 --- /dev/null +++ b/bp_bin/order_pairs @@ -0,0 +1,80 @@ +#!/usr/bin/env ruby + +# Copyright (C) 2007-2011 Martin A. Hansen. + +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# http://www.gnu.org/copyleft/gpl.html + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# This program is part of the Biopieces framework (www.biopieces.org). + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Order records so SEQ_NAME/1 and SEQ_NAME/2 are in the order. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +require 'maasha/biopieces' +require 'pp' + +options = Biopieces.options_parse(ARGV) + +hash1 = {} +hash2 = {} + +Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| + input.each_record do |record| + if record[:SEQ_NAME] + name = record[:SEQ_NAME][0 ... -2].to_sym + pair = record[:SEQ_NAME][-1].to_i + + if pair == 1 + if hash2.has_key? name + output.puts record + output.puts hash2[name] + + hash2.delete(name) + else + hash1[name] = record + end + elsif pair == 2 + if hash1.has_key? name + output.puts hash1[name] + output.puts record + + hash1.delete(name) + else + hash2[name] = record + end + else + $stderr.puts "WARNING: Badly formatted name: #{record[:SEQ_NAME]}" if options[:verbose] + end + end + end +end + +if options[:verbose] + $stderr.puts "Unmatched names with /1: #{hash1.size}" + $stderr.puts "Unmatched names with /2: #{hash2.size}" +end + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ diff --git a/bp_test/in/order_pairs.in b/bp_test/in/order_pairs.in new file mode 100644 index 0000000..3e30de4 --- /dev/null +++ b/bp_test/in/order_pairs.in @@ -0,0 +1,40 @@ +SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB +SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NNNNNNNNGGNNCNANNANNNNGTNNNTNGNANNNNCNNANTTGNNNNNN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1041:14486#TTAGGC/2 +--- +SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB +SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1 +--- +SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2 +--- +SCORES: ffffcfffffded^eddddddbdcdeedcefecfefdffecabccBB`b` +SEQ: CCNAGGAGGAGNCAATAAGAGACCATTCGTATATGATCTCTCAGGAGAGC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1044:7943#TTAGGC/1 +--- +SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y +SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2 +--- diff --git a/bp_test/out/order_pairs.out.1 b/bp_test/out/order_pairs.out.1 new file mode 100644 index 0000000..b0906df --- /dev/null +++ b/bp_test/out/order_pairs.out.1 @@ -0,0 +1,30 @@ +SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB +SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2 +--- +SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB +SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1 +--- +SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2 +--- +SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y +SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2 +--- diff --git a/bp_test/test/test_order_pairs b/bp_test/test/test_order_pairs new file mode 100755 index 0000000..61c5709 --- /dev/null +++ b/bp_test/test/test_order_pairs @@ -0,0 +1,7 @@ +#!/bin/bash + +source "$BP_DIR/bp_test/lib/test.sh" + +run "$bp -I $in -O $tmp" +assert_no_diff $tmp $out.1 +clean -- 2.39.5