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 3cad732c0b83bc5a21ca268c47f8680b0133047a..23eb0c67641bf667dbda2e34d711fc9412d4894c 100755 (executable)
--- 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 (file)
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'
+