Mercurial > repos > bgruening > crispr_recognition_tool
changeset 0:db0f5c1cb227 draft
Imported from capsule None
| author | bgruening |
|---|---|
| date | Fri, 02 May 2014 06:15:38 -0400 |
| parents | |
| children | 222b7f7b8432 |
| files | crt.xml readme.rst reformat.py test-data/crt.bed test-data/crt.tab test-data/sequence.fasta tool_dependencies.xml |
| diffstat | 7 files changed, 318 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crt.xml Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,74 @@ +<tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0"> + <description>(CRT)</description> + <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" /> + <requirements> + <requirement type="package" version="1.2">crisper_recognition_tool</requirement> + <requirement type="set_environment">CRISPR_RECOGNITION_TOOL_SCRIPT_PATH</requirement> + </requirements> + <stdio> + <exit_code range=":-1" level="fatal" /> + <exit_code range="1:" level="fatal" /> + </stdio> + <command> + temp_output=\$(mktemp); + java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt + -minNR $minNR + -minRL $minRL + -maxRL $maxRL + -minSL $minSL + -maxSL $maxSL + #if str($searchWL) != 'none': + -searchWL $searchWL + #end if + $input + \$temp_output + ; + + python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/> + + <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/> + <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/> + <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/> + <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/> + <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/> + <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs"> + <option value="none" selected="true">default</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" /> + </outputs> + <tests> + <test> + <param name="input" value="sequence.fasta" ftype="fasta" /> + <param name="minNR" value="3" /> + <param name="minRL" value="29" /> + <param name="maxRL" value="38" /> + <param name="minSL" value="19" /> + <param name="maxSL" value="48" /> + <param name="searchWL" value="none" /> + <output name="output" file="crt.tabular" ftype="tabular" /> + <output name="output_region" file="crt.bed" ftype="bed" /> + </test> + </tests> + <help> +CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats + +http://www.room220.com/crt/ + +**Citation** + +For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: +CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209` + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,48 @@ +Galaxy wrapper for CRISPR RECOGNITION TOOL +========================================== + +This wrapper is copyright 2012-2013 by Björn Grüning and Omer Alkhnbashi + +This is a wrapper for the command line tool of CRT. + +CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats + +http://www.room220.com/crt/ + +For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: +CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209` + + +Installation +============ + +Galaxy should be able to automatically install the dependencies. + + +History +======= + +v0.1 - Initial public release + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformat.py Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +""" + Extract importent information from the standard output file and put it in some standard format, like BED and tabular. +""" + +import sys + +bed = open(sys.argv[2], 'w+') +tabular = open(sys.argv[3], 'w+') + +for line in open(sys.argv[1]): + # ORGANISM: gi|21226102|ref|NC_003901.1| Methanosarcina mazei Go1 chromosome, complete genome + if line.startswith('ORGANISM:'): + organism = line.lstrip('ORGANISM:').strip() + # CRISPR 1 Range: 679197 - 682529 + if line.startswith('CRISPR '): + start,end = line.split('Range:')[1].strip().split('-') + start = start.strip() + end = end.strip() + bed.write('%s\t%s\t%s\n' % (organism, start, end)) + if line.rstrip().endswith(']'): + cols = line.split() + tabular.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (organism, cols[0], cols[1], cols[2], cols[4].rstrip(','), cols[5]))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crt.bed Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,3 @@ +CRISPRs 1 3592 +CRISPRs 3725 7933 +CRISPRs 7945 10797
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crt.tab Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,142 @@ +CRISPRs 1 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCT 37 35 +CRISPRs 73 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCAT 37 37 +CRISPRs 147 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ACAGATTTTGCTTCAGCTAGTACCAAAGGCTAG 37 33 +CRISPRs 217 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGG 37 37 +CRISPRs 291 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAA 37 37 +CRISPRs 365 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAG 37 39 +CRISPRs 441 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TAATAATTGCTGATTAATCGTGGTGGTGGTGGTGG 37 35 +CRISPRs 513 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GATATATGGCTAAATATTGCTCAAAAGATTTTAATA 37 36 +CRISPRs 586 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGC 37 35 +CRISPRs 658 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG 37 35 +CRISPRs 730 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG 37 35 +CRISPRs 802 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTGCGGACAGACTCGATTAAGTCAATAACAGCTTGG 37 36 +CRISPRs 875 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCT 37 36 +CRISPRs 948 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAG 37 35 +CRISPRs 1020 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GAGGTTAAATTGTTGTCGATTCAAGAAGACTTGA 37 34 +CRISPRs 1091 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AATAGACACGAATTCCGGTTCCAGACCCAGCCCGTT 37 36 +CRISPRs 1164 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTA 37 35 +CRISPRs 1236 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTAT 37 35 +CRISPRs 1308 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGA 37 35 +CRISPRs 1380 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AATCAGCTTCCGGCGTTGCCATTTGGATTCAA 37 32 +CRISPRs 1449 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GTGAGGGGGCCAGATCCCTGCCAGATCCCCCAAT 37 34 +CRISPRs 1520 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATTAGATCTTTGGCATAAGGCAACCGAAACTGATC 37 35 +CRISPRs 1592 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GATTATCGTGCTTCCTTCGATGCTAACTTTGCTCT 37 35 +CRISPRs 1664 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCCATAATGATTCTGCCTCGTTTCTACTTGGTTTA 37 35 +CRISPRs 1736 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGG 37 37 +CRISPRs 1810 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAA 37 38 +CRISPRs 1885 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCGGGTTTCCCTCCTGGGTAATGACGCCTACGGG 37 34 +CRISPRs 1956 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CAAAGCTGGCACGGAAGCCCTTAAGGATATCCTC 37 34 +CRISPRs 2027 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GATGCAGAGATTCCACCACCAAAGGAGAATCCGATAA 37 37 +CRISPRs 2101 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG 37 37 +CRISPRs 2175 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG 37 41 +CRISPRs 2253 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG 37 37 +CRISPRs 2327 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG 37 41 +CRISPRs 2405 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCC 37 35 +CRISPRs 2477 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CAAAGTTGGAACGAAAGCTAACGACAAAAACTA 37 33 +CRISPRs 2547 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGG 37 38 +CRISPRs 2622 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC AATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGA 37 37 +CRISPRs 2696 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGT 37 36 +CRISPRs 2769 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGG 37 34 +CRISPRs 2840 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA 37 35 +CRISPRs 2912 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA 37 35 +CRISPRs 2984 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAAC 37 36 +CRISPRs 3057 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TTCCATTAATGATTCTTCAAAAATCACTCGATT 37 33 +CRISPRs 3127 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC ACTGTTACTAGCCACCGCCCAACTCCTTTAATACTT 37 36 +CRISPRs 3200 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAG 37 37 +CRISPRs 3274 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC CATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAAT 37 37 +CRISPRs 3348 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC GATTTTTCCAGTGATGGTGCATACCTAGCCGTAG 37 34 +CRISPRs 3419 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TAGTCCCTCCCACACTGCCAATATTTCTTCAT 37 32 +CRISPRs 3488 CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC TCCGTCTGTATGACTTATACTCGCAAGGATT 37 31 +CRISPRs 3725 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCG 37 36 +CRISPRs 3798 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGA 37 40 +CRISPRs 3875 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAA 37 42 +CRISPRs 3954 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTTGGTATTTGTAGTTCTCGATGAGTGTTTTAGGCA 37 36 +CRISPRs 4027 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGATAACGGGATGCCAGCCCTAAAGGTGATGAGCGG 37 36 +CRISPRs 4100 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA 37 39 +CRISPRs 4176 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC 37 39 +CRISPRs 4252 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA 37 39 +CRISPRs 4328 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC 37 39 +CRISPRs 4404 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTATTAAGGCTATTTTCGCCACTTCTGTTTGAAAG 37 35 +CRISPRs 4476 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GTCACACCTCTTCACGAATCCTCACATCATGAATAAGCTGCACA 37 44 +CRISPRs 4557 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGCGGGTCGAGATGTCGCTGGACACGCTGGTGCCGGACA 37 39 +CRISPRs 4633 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTGGGCGGACTGGAGTTGCCACCTGCCGATGGCCTGCA 37 38 +CRISPRs 4708 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GAGCCAAAGTCAACTAGCACAGGCACGGCAAGCCATCCTGA 37 41 +CRISPRs 4786 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TCGTGCATCTGCGCATAGGAAGAGGTTAATTCCTCAAC 37 38 +CRISPRs 4861 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AACGGGCAGCCCGAGTGGTGGGCATCGAGGTGGTGCTC 37 38 +CRISPRs 4936 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CCCCGCCACATTTTCGGATTAGAGGATTTGAATCGGCCGT 37 40 +CRISPRs 5013 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AGTTTCTCAAACTTTTCGGCGATCGCCGTCCAGGTGAGTTGA 37 42 +CRISPRs 5092 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TAGCGAAAAGTTATAGTTACCTTTGACCGGAGCTACCAACTCA 37 43 +CRISPRs 5172 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CCCCGCTGCCACGAGGGCAGCTGTAGACGCACCCC 37 35 +CRISPRs 5244 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TTAAATATACCCATCCCTAATAAAGGATAGAGATCTTGCA 37 40 +CRISPRs 5321 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GCTCTATTCTAATAACCCAAGCTTTTTTCAATTCTAA 37 37 +CRISPRs 5395 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CCGCTTGGTAGGATTGACCACCAAAGCTAGAAACAGGCACA 37 41 +CRISPRs 5473 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AGGGCGGTTAATCACTAGCGGCGATCTAGATATTG 37 35 +CRISPRs 5545 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TAGACTTCTATTTCCCCTCTTGCCGAGGGATGATACTGCAATTGA 37 45 +CRISPRs 5627 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TGCGCTCTCTTATCAAACGCCGCAACGCCATCAAGGCT 37 38 +CRISPRs 5702 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC ACGAGCGGAATCTTCTATGGATCGGATCACATCCTTAAT 37 39 +CRISPRs 5778 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTGGTGTCGGGGTTGTAGTATTCGTCTCGGTACAACA 37 37 +CRISPRs 5852 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC ACTATAGGGAGCGTTACCCTAGCTAGACATTGCCTAATCT 37 40 +CRISPRs 5929 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AAGAAGCAGAATAATGCGATTGAGTGGACAAAAATAAGAA 37 40 +CRISPRs 6006 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GGTTACGTATCGGCGTAACCGCCACTCCTTAGAG 37 34 +CRISPRs 6077 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGCCTCCTGCGCCCTGGAGGGGTGATCCTACACCTCGCG 37 39 +CRISPRs 6153 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GATTCTGGTATACGTTTATCCCACCACTCCTTAGCT 37 36 +CRISPRs 6226 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTCGTAAGCTAGGCAACGGCCTTGCTCGATGCACA 37 35 +CRISPRs 6298 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GGTGCAGCTGCGCCTAAGGAGATGGCTGTACAAGCT 37 36 +CRISPRs 6371 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CACCTAGAGGGTACCTCCCGGTTAGACCGGGGCTCTTAT 37 39 +CRISPRs 6447 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG 37 36 +CRISPRs 6520 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG 37 40 +CRISPRs 6597 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG 37 36 +CRISPRs 6670 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG 37 40 +CRISPRs 6747 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CTAGCCTTTGTGGCTAACCCTCCTGCGCTTTGACATATAG 37 40 +CRISPRs 6824 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAA 37 35 +CRISPRs 6896 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGT 37 36 +CRISPRs 6969 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC ATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGG 37 37 +CRISPRs 7043 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTC 37 40 +CRISPRs 7120 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTT 37 43 +CRISPRs 7200 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACC 37 37 +CRISPRs 7274 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGT 37 41 +CRISPRs 7352 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCA 37 35 +CRISPRs 7424 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGG 37 45 +CRISPRs 7506 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC ATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCA 37 41 +CRISPRs 7584 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC TCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTG 37 40 +CRISPRs 7661 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC ATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCC 37 45 +CRISPRs 7743 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC GTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGAT 37 34 +CRISPRs 7814 GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC CCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAG 37 46 +CRISPRs 7945 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGT 35 37 +CRISPRs 8017 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAA 35 37 +CRISPRs 8089 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGT 35 36 +CRISPRs 8160 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTA 35 37 +CRISPRs 8232 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACA 35 40 +CRISPRs 8307 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTT 35 37 +CRISPRs 8379 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCC 35 36 +CRISPRs 8450 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACA 35 38 +CRISPRs 8523 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGAT 35 38 +CRISPRs 8596 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCC 35 37 +CRISPRs 8668 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CATCGATATACTTTTTAGCATCAGCTAAATGATAAAAA 35 38 +CRISPRs 8741 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTT 35 36 +CRISPRs 8812 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATT 35 37 +CRISPRs 8884 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTGGGATTCATGAACATGTTGATGGTGAATTATACCT 35 37 +CRISPRs 8956 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTT 35 42 +CRISPRs 9033 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTA 35 36 +CRISPRs 9104 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGT 35 40 +CRISPRs 9179 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAACAATTGCAAGGTTTATAAGTAAATGAACAACAACG 35 38 +CRISPRs 9252 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTC 35 39 +CRISPRs 9326 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCG 35 41 +CRISPRs 9402 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGAT 35 40 +CRISPRs 9477 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAG 35 36 +CRISPRs 9548 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGA 35 38 +CRISPRs 9621 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGC 35 41 +CRISPRs 9697 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAG 35 40 +CRISPRs 9772 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGA 35 40 +CRISPRs 9847 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAG 35 47 +CRISPRs 9929 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAAC 35 40 +CRISPRs 10004 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CCGATGTAGCTCATAGCGACCTCGATAATTAATTGAT 35 37 +CRISPRs 10076 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGT 35 40 +CRISPRs 10151 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAG 35 43 +CRISPRs 10229 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGC 35 42 +CRISPRs 10306 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCA 35 36 +CRISPRs 10377 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTT 35 48 +CRISPRs 10460 GTCTCCACTCGCAGGAGAAATTAATTGATTGGAAA CAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTT 35 38 +CRISPRs 10533 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCA 35 40 +CRISPRs 10608 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAA 35 44 +CRISPRs 10687 GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA CATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTA 35 41
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.fasta Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,2 @@ +>CRISPRs +CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACAGATTTTGCTTCAGCTAGTACCAAAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATAATTGCTGATTAATCGTGGTGGTGGTGGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATATATGGCTAAATATTGCTCAAAAGATTTTAATACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCGGACAGACTCGATTAAGTCAATAACAGCTTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGAGGTTAAATTGTTGTCGATTCAAGAAGACTTGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATAGACACGAATTCCGGTTCCAGACCCAGCCCGTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCAGCTTCCGGCGTTGCCATTTGGATTCAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGTGAGGGGGCCAGATCCCTGCCAGATCCCCCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATCTTTGGCATAAGGCAACCGAAACTGATCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTATCGTGCTTCCTTCGATGCTAACTTTGCTCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCATAATGATTCTGCCTCGTTTCTACTTGGTTTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGGGTTTCCCTCCTGGGTAATGACGCCTACGGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGCTGGCACGGAAGCCCTTAAGGATATCCTCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATGCAGAGATTCCACCACCAAAGGAGAATCCGATAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGTTGGAACGAAAGCTAACGACAAAAACTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAACCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCCATTAATGATTCTTCAAAAATCACTCGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTGTTACTAGCCACCGCCCAACTCCTTTAATACTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTTTTCCAGTGATGGTGCATACCTAGCCGTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAGTCCCTCCCACACTGCCAATATTTCTTCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCGTCTGTATGACTTATACTCGCAAGGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACNNNNNNNNATAGCCAAAAATAAGGCTTTTATTGTTATGTTTTCAGTACGTAACAAATCGTTAAACGTCTACCTCTTGTTTGGCGGATTGGCACCTCGAAAACCGCATACAGACTGTTTTTCAGTGTGATAGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTTGGTATTTGTAGTTCTCGATGAGTGTTTTAGGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGATAACGGGATGCCAGCCCTAAAGGTGATGAGCGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTATTAAGGCTATTTTCGCCACTTCTGTTTGAAAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTCACACCTCTTCACGAATCCTCACATCATGAATAAGCTGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCGGGTCGAGATGTCGCTGGACACGCTGGTGCCGGACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTGGGCGGACTGGAGTTGCCACCTGCCGATGGCCTGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGAGCCAAAGTCAACTAGCACAGGCACGGCAAGCCATCCTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCGTGCATCTGCGCATAGGAAGAGGTTAATTCCTCAACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACGGGCAGCCCGAGTGGTGGGCATCGAGGTGGTGCTCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCCGCCACATTTTCGGATTAGAGGATTTGAATCGGCCGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAGTTTCTCAAACTTTTCGGCGATCGCCGTCCAGGTGAGTTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTAGCGAAAAGTTATAGTTACCTTTGACCGGAGCTACCAACTCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCCGCTGCCACGAGGGCAGCTGTAGACGCACCCCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTAAATATACCCATCCCTAATAAAGGATAGAGATCTTGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGCTCTATTCTAATAACCCAAGCTTTTTTCAATTCTAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCGCTTGGTAGGATTGACCACCAAAGCTAGAAACAGGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAGGGCGGTTAATCACTAGCGGCGATCTAGATATTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTAGACTTCTATTTCCCCTCTTGCCGAGGGATGATACTGCAATTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGCGCTCTCTTATCAAACGCCGCAACGCCATCAAGGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACACGAGCGGAATCTTCTATGGATCGGATCACATCCTTAATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTGGTGTCGGGGTTGTAGTATTCGTCTCGGTACAACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACACTATAGGGAGCGTTACCCTAGCTAGACATTGCCTAATCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAAGAAGCAGAATAATGCGATTGAGTGGACAAAAATAAGAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGTTACGTATCGGCGTAACCGCCACTCCTTAGAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCCTCCTGCGCCCTGGAGGGGTGATCCTACACCTCGCGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGATTCTGGTATACGTTTATCCCACCACTCCTTAGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTCGTAAGCTAGGCAACGGCCTTGCTCGATGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGTGCAGCTGCGCCTAAGGAGATGGCTGTACAAGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCACCTAGAGGGTACCTCCCGGTTAGACCGGGGCTCTTATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACATGGCCACAACAACCTTCCCGGAGCAAGGGATGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACATGGCCACAACAACCTTCCCGGAGCAAGGGATGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTAGCCTTTGTGGCTAACCCTCCTGCGCTTTGACATATAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACNNNNNNNNNNNGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATCGATATACTTTTTAGCATCAGCTAAATGATAAAAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGGGATTCATGAACATGTTGATGGTGAATTATACCTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACAATTGCAAGGTTTATAAGTAAATGAACAACAACGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAACGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCGATGTAGCTCATAGCGACCTCGATAATTAATTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTTGTCTCCACTCGCAGGAGAAATTAATTGATTGGAAACAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri May 02 06:15:38 2014 -0400 @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="CRISPR_RECOGNITION_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="crisper_recognition_tool" version="1.2"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.room220.com/crt/CRT1.2-CLI.jar.zip</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="CRISPR_RECOGNITION_TOOL_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency> + + +