added roche mid module

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2245 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/roche/mids.rb b/code_ruby/lib/maasha/roche/mids.rb
new file mode 100644 (file)
index 0000000..7fac807
--- /dev/null
+++ b/code_ruby/lib/maasha/roche/mids.rb
@@ -0,0 +1,237 @@
+# Copyright (C) 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).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Module containing Roche's MID tags hashed according to name or barcode.
+module Roche
+  # 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"
+  }
+end

diff --git a/code_ruby/test/maasha/roche/test_mids.rb b/code_ruby/test/maasha/roche/test_mids.rb
new file mode 100755 (executable)
index 0000000..ad8c722
--- /dev/null
+++ b/code_ruby/test/maasha/roche/test_mids.rb
@@ -0,0 +1,42 @@
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# Copyright (C) 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 'test/unit'
+require 'test/helper'
+require 'maasha/roche'
+
+class RocheTest < Test::Unit::TestCase
+  test "Roche::GSMID_HASH returns correctly" do
+    assert_equal("MID1", Roche::GSMID_HASH[:ACGAGTGCGT])
+    assert_equal(nil,    Roche::GSMID_HASH[:FOO])
+  end
+
+  test "Roche::RLMID_HASH returns correctly" do
+    assert_equal("RL1", Roche::RLMID_HASH[:ACACGACGACT])
+    assert_equal(nil,   Roche::RLMID_HASH[:FOO])
+  end
+end