From: martinahansen Date: Thu, 24 Oct 2013 08:49:27 +0000 (+0000) Subject: now using roche mid module for find_barcodes X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=5b1df1b9a1948782de35eea563cfee49d6a542f0 now using roche mid module for find_barcodes git-svn-id: http://biopieces.googlecode.com/svn/trunk@2246 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/find_barcodes b/bp_bin/find_barcodes index 3cad732..23eb0c6 100755 --- a/bp_bin/find_barcodes +++ b/bp_bin/find_barcodes @@ -29,220 +29,10 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'maasha/biopieces' +require 'maasha/roche' require 'maasha/bits' require 'pp' -# Hard coded Roche Genome Sequencing MIDs -GSMID_HASH = { - ACGAGTGCGT: "MID1", - TCTCTATGCG: "MID10", - TAGACTGCAC: "MID100", - TAGCGCGCGC: "MID101", - TAGCTCTATC: "MID102", - TATAGACATC: "MID103", - TATGATACGC: "MID104", - TCACTCATAC: "MID105", - TCATCGAGTC: "MID106", - TCGAGCTCTC: "MID107", - TCGCAGACAC: "MID108", - TCTGTCTCGC: "MID109", - TGATACGTCT: "MID11", - TGAGTGACGC: "MID110", - TGATGTGTAC: "MID111", - TGCTATAGAC: "MID112", - TGCTCGCTAC: "MID113", - ACGTGCAGCG: "MID114", - ACTCACAGAG: "MID115", - AGACTCAGCG: "MID116", - AGAGAGTGTG: "MID117", - AGCTATCGCG: "MID118", - AGTCTGACTG: "MID119", - TACTGAGCTA: "MID12", - AGTGAGCTCG: "MID120", - ATAGCTCTCG: "MID121", - ATCACGTGCG: "MID122", - ATCGTAGCAG: "MID123", - ATCGTCTGTG: "MID124", - ATGTACGATG: "MID125", - ATGTGTCTAG: "MID126", - CACACGATAG: "MID127", - CACTCGCACG: "MID128", - CAGACGTCTG: "MID129", - CATAGTAGTG: "MID13", - CAGTACTGCG: "MID130", - CGACAGCGAG: "MID131", - CGATCTGTCG: "MID132", - CGCGTGCTAG: "MID133", - CGCTCGAGTG: "MID134", - CGTGATGACG: "MID135", - CTATGTACAG: "MID136", - CTCGATATAG: "MID137", - CTCGCACGCG: "MID138", - CTGCGTCACG: "MID139", - CGAGAGATAC: "MID14", - CTGTGCGTCG: "MID140", - TAGCATACTG: "MID141", - TATACATGTG: "MID142", - TATCACTCAG: "MID143", - TATCTGATAG: "MID144", - TCGTGACATG: "MID145", - TCTGATCGAG: "MID146", - TGACATCTCG: "MID147", - TGAGCTAGAG: "MID148", - TGATAGAGCG: "MID149", - ATACGACGTA: "MID15", - TGCGTGTGCG: "MID150", - TGCTAGTCAG: "MID151", - TGTATCACAG: "MID152", - TGTGCGCGTG: "MID153", - TCACGTACTA: "MID16", - CGTCTAGTAC: "MID17", - TCTACGTAGC: "MID18", - TGTACTACTC: "MID19", - ACGCTCGACA: "MID2", - ACGACTACAG: "MID20", - CGTAGACTAG: "MID21", - TACGAGTATG: "MID22", - TACTCTCGTG: "MID23", - TAGAGACGAG: "MID24", - TCGTCGCTCG: "MID25", - ACATACGCGT: "MID26", - ACGCGAGTAT: "MID27", - ACTACTATGT: "MID28", - ACTGTACAGT: "MID29", - AGACGCACTC: "MID3", - AGACTATACT: "MID30", - AGCGTCGTCT: "MID31", - AGTACGCTAT: "MID32", - ATAGAGTACT: "MID33", - CACGCTACGT: "MID34", - CAGTAGACGT: "MID35", - CGACGTGACT: "MID36", - TACACACACT: "MID37", - TACACGTGAT: "MID38", - TACAGATCGT: "MID39", - AGCACTGTAG: "MID4", - TACGCTGTCT: "MID40", - TAGTGTAGAT: "MID41", - TCGATCACGT: "MID42", - TCGCACTAGT: "MID43", - TCTAGCGACT: "MID44", - TCTATACTAT: "MID45", - TGACGTATGT: "MID46", - TGTGAGTAGT: "MID47", - ACAGTATATA: "MID48", - ACGCGATCGA: "MID49", - ATCAGACACG: "MID5", - ACTAGCAGTA: "MID50", - AGCTCACGTA: "MID51", - AGTATACATA: "MID52", - AGTCGAGAGA: "MID53", - AGTGCTACGA: "MID54", - CGATCGTATA: "MID55", - CGCAGTACGA: "MID56", - CGCGTATACA: "MID57", - CGTACAGTCA: "MID58", - CGTACTCAGA: "MID59", - ATATCGCGAG: "MID6", - CTACGCTCTA: "MID60", - CTATAGCGTA: "MID61", - TACGTCATCA: "MID62", - TAGTCGCATA: "MID63", - TATATATACA: "MID64", - TATGCTAGTA: "MID65", - TCACGCGAGA: "MID66", - TCGATAGTGA: "MID67", - TCGCTGCGTA: "MID68", - TCTGACGTCA: "MID69", - CGTGTCTCTA: "MID7", - TGAGTCAGTA: "MID70", - TGTAGTGTGA: "MID71", - TGTCACACGA: "MID72", - TGTCGTCGCA: "MID73", - ACACATACGC: "MID74", - ACAGTCGTGC: "MID75", - ACATGACGAC: "MID76", - ACGACAGCTC: "MID77", - ACGTCTCATC: "MID78", - ACTCATCTAC: "MID79", - CTCGCGTGTC: "MID8", - ACTCGCGCAC: "MID80", - AGAGCGTCAC: "MID81", - AGCGACTAGC: "MID82", - AGTAGTGATC: "MID83", - AGTGACACAC: "MID84", - AGTGTATGTC: "MID85", - ATAGATAGAC: "MID86", - ATATAGTCGC: "MID87", - ATCTACTGAC: "MID88", - CACGTAGATC: "MID89", - TAGTATCAGC: "MID9", - CACGTGTCGC: "MID90", - CATACTCTAC: "MID91", - CGACACTATC: "MID92", - CGAGACGCGC: "MID93", - CGTATGCGAC: "MID94", - CGTCGATCTC: "MID95", - CTACGACTGC: "MID96", - CTAGTCACTC: "MID97", - CTCTACGCTC: "MID98", - CTGTACATAC: "MID99" -} - -# Hard coded Roche Rapid Labrary MIDs -RLMID_HASH = { - ACACGACGACT: "RL1", - ACACGTAGTAT: "RL2", - ACACTACTCGT: "RL3", - ACGACACGTAT: "RL4", - ACGAGTAGACT: "RL5", - ACGCGTCTAGT: "RL6", - ACGTACACACT: "RL7", - ACGTACTGTGT: "RL8", - ACGTAGATCGT: "RL9", - ACTACGTCTCT: "RL10", - ACTATACGAGT: "RL11", - ACTCGCGTCGT: "RL12", - AGACTCGACGT: "RL13", - AGTACGAGAGT: "RL14", - AGTACTACTAT: "RL15", - AGTAGACGTCT: "RL16", - AGTCGTACACT: "RL17", - AGTGTAGTAGT: "RL18", - ATAGTATACGT: "RL19", - CAGTACGTACT: "RL20", - CGACGACGCGT: "RL21", - CGACGAGTACT: "RL22", - CGATACTACGT: "RL23", - CGTACGTCGAT: "RL24", - CTACTCGTAGT: "RL25", - GTACAGTACGT: "RL26", - GTCGTACGTAT: "RL27", - GTGTACGACGT: "RL28", - ACACAGTGAGT: "RL29", - ACACTCATACT: "RL30", - ACAGACAGCGT: "RL31", - ACAGACTATAT: "RL32", - ACAGAGACTCT: "RL33", - ACAGCTCGTGT: "RL34", - ACAGTGTCGAT: "RL35", - ACGAGCGCGCT: "RL36", - ACGATGAGTGT: "RL37", - ACGCGAGAGAT: "RL38", - ACGCTCTCTCT: "RL39", - ACGTCGCTGAT: "RL40", - ACGTCTAGCAT: "RL41", - ACTAGTGATAT: "RL42", - ACTCACACTGT: "RL43", - ACTCACTAGCT: "RL44", - ACTCTATATAT: "RL45", - ACTGATCTCGT: "RL46", - ACTGCTGTACT: "RL47", - ACTGTAGCGCT: "RL48", - AGACACTCACT: "RL49", - AGACATATAGT: "RL50" -} - class BarCodeFinderError < StandardError; end class BarCodeFinder @@ -347,8 +137,8 @@ options = Biopieces.options_parse(ARGV, casts) bc_finder = BarCodeFinder.new(options[:pos], options[:mismatches]) bc_finder.parse_barcodes(options[:barcodes_in]) if options[:barcodes_in] -bc_finder.load_barcodes(GSMID_HASH) if options[:gsmids] -bc_finder.load_barcodes(RLMID_HASH) if options[:rlmids] +bc_finder.load_barcodes(Roche::GSMID_HASH) if options[:gsmids] +bc_finder.load_barcodes(Roche::RLMID_HASH) if options[:rlmids] Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| input.each_record do |record| diff --git a/code_ruby/lib/maasha/roche.rb b/code_ruby/lib/maasha/roche.rb new file mode 100644 index 0000000..c69abff --- /dev/null +++ b/code_ruby/lib/maasha/roche.rb @@ -0,0 +1,26 @@ +# Copyright (C) 2007-2013 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 software is part of the Biopieces framework (www.biopieces.org). + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +require 'maasha/roche/mids' +