# HG changeset patch
# User bgruening
# Date 1399278206 14400
# Node ID 20f12e7c279b690b362b7a4ffa6f500c2c04a80b

Imported from capsule None

diff -r 000000000000 -r 20f12e7c279b minced.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minced.xml	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,119 @@
+<tool id="crispr_recognition_tool" name="detect CRISPR sequences" version="0.1.5">
+    <description>(minced)</description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="50" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
+    <requirements>
+        <requirement type="package" version="0.1.5">minced</requirement>
+        <requirement type="set_environment">MINCED_SCRIPT_PATH</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" />
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    <command>
+        temp_output=\$(mktemp);
+        minced
+            -minNR $minNR
+            -minRL $minRL
+            -maxRL $maxRL
+            -minSL $minSL
+            -maxSL $maxSL
+            #if str($searchWL) != 'none':
+                -searchWL $searchWL
+            #end if
+            $input
+            \$temp_output
+            #if '-spacers' in str($outputs).split():
+                -spacers
+            #end if 
+            #if '-gffFull' in str($outputs).split():
+                -gffFull
+            #end if
+            #if '-gff' in str($outputs).split():
+                -gff
+            #end if
+            ;
+
+            python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab;
+            #if '-spacers' in str($outputs).split():
+                mv \$temp_output'_spacers.fa' $output_fasta;
+            #end if
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
+
+        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
+        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
+        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
+        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
+        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
+            <option value="none" selected="true">default</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+        </param>
+
+        <param name="outputs" type="select" multiple="True" label="Additional output format" help="Please select a output format.">
+            <option value="-gff">summary results in gff format</option>
+            <option value="BED" selected="true">summary results in BED format</option>
+            <option value="-gffFull">detailed results in gff format</option>
+            <option value="TABULAR" selected="true">detailed results in tabular format</option>
+            <option value="-spacers">fasta formatted file containing the spacers</option>
+            <validator type="no_options" message="Please select at least one output file." />
+        </param>
+
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" from_work_dir="results.tab" label="${tool.name} on ${on_string}">
+            <filter>'TABULAR' in outputs</filter>
+        </data>
+        <data format="bed" name="output_region" from_work_dir="results.bed" label="${tool.name} on ${on_string} - BED file">
+            <filter>'BED' in outputs</filter>
+        </data>
+        <data format="gff3" name="output_ggf_full" from_work_dir="results_full.gff" label="${tool.name} on ${on_string} - GFF file extended">
+            <filter>'-gffFull' in outputs</filter>
+        </data>
+        <data format="gff3" name="output_gff" from_work_dir="results.gff" label="${tool.name} on ${on_string} - GFF file">
+            <filter>'-gff' in outputs</filter>
+        </data>
+        <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string} - GFF file">
+            <filter>'-spacers' in outputs</filter>
+        </data>
+    </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="minced.tabular" ftype="tabular" />
+            <output name="output_region" file="minced.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+MinCED - Mining CRISPRs in Environmental Datasets
+
+
+MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
+Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
+in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
+command-line and was derived from CRT (http://www.room220.com/crt/).
+
+https://github.com/ctSkennerton/minced
+
+**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`
+
+If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools
+
+    </help>
+</tool>
+
diff -r 000000000000 -r 20f12e7c279b readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,51 @@
+Galaxy wrapper for minced
+=========================
+
+This wrapper is copyright 2014 by Björn Grüning and Omer Alkhnbashi
+
+MinCED - Mining CRISPRs in Environmental Datasets
+
+MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
+Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
+in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
+command-line and was derived from CRT (http://www.room220.com/crt/):
+  Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic
+  detection of clustered regularly interspaced palindromic repeats, BMC
+  Bioinformatics 8, no. 1 (2007): 209.
+
+https://github.com/ctSkennerton/minced
+
+
+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.
+
diff -r 000000000000 -r 20f12e7c279b reformat.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat.py	Mon May 05 04:23:26 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]):
+    # Sequence 'CRISPRs' (10798 bp)
+    if line.startswith('Sequence '):
+        organism = line.split("'")[1]
+    # 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]))
diff -r 000000000000 -r 20f12e7c279b test-data/minced.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minced.bed	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,3 @@
+CRISPRs	1	3592
+CRISPRs	3725	7933
+CRISPRs	7945	10797
diff -r 000000000000 -r 20f12e7c279b test-data/minced.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/minced.tabular	Mon May 05 04:23:26 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
diff -r 000000000000 -r 20f12e7c279b test-data/sequence.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sequence.fasta	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,2 @@
+>CRISPRs
+CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACAGATTTTGCTTCAGCTAGTACCAAAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATAATTGCTGATTAATCGTGGTGGTGGTGGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATATATGGCTAAATATTGCTCAAAAGATTTTAATACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCGGACAGACTCGATTAAGTCAATAACAGCTTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGAGGTTAAATTGTTGTCGATTCAAGAAGACTTGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATAGACACGAATTCCGGTTCCAGACCCAGCCCGTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCAGCTTCCGGCGTTGCCATTTGGATTCAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGTGAGGGGGCCAGATCCCTGCCAGATCCCCCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATCTTTGGCATAAGGCAACCGAAACTGATCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTATCGTGCTTCCTTCGATGCTAACTTTGCTCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCATAATGATTCTGCCTCGTTTCTACTTGGTTTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGGGTTTCCCTCCTGGGTAATGACGCCTACGGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGCTGGCACGGAAGCCCTTAAGGATATCCTCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATGCAGAGATTCCACCACCAAAGGAGAATCCGATAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGTTGGAACGAAAGCTAACGACAAAAACTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAACCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCCATTAATGATTCTTCAAAAATCACTCGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTGTTACTAGCCACCGCCCAACTCCTTTAATACTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTTTTCCAGTGATGGTGCATACCTAGCCGTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAGTCCCTCCCACACTGCCAATATTTCTTCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCGTCTGTATGACTTATACTCGCAAGGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACNNNNNNNNATAGCCAAAAATAAGGCTTTTATTGTTATGTTTTCAGTACGTAACAAATCGTTAAACGTCTACCTCTTGTTTGGCGGATTGGCACCTCGAAAACCGCATACAGACTGTTTTTCAGTGTGATAGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTTGGTATTTGTAGTTCTCGATGAGTGTTTTAGGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGATAACGGGATGCCAGCCCTAAAGGTGATGAGCGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTATTAAGGCTATTTTCGCCACTTCTGTTTGAAAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTCACACCTCTTCACGAATCCTCACATCATGAATAAGCTGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCGGGTCGAGATGTCGCTGGACACGCTGGTGCCGGACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTGGGCGGACTGGAGTTGCCACCTGCCGATGGCCTGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGAGCCAAAGTCAACTAGCACAGGCACGGCAAGCCATCCTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCGTGCATCTGCGCATAGGAAGAGGTTAATTCCTCAACGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACGGGCAGCCCGAGTGGTGGGCATCGAGGTGGTGCTCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCCGCCACATTTTCGGATTAGAGGATTTGAATCGGCCGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAGTTTCTCAAACTTTTCGGCGATCGCCGTCCAGGTGAGTTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTAGCGAAAAGTTATAGTTACCTTTGACCGGAGCTACCAACTCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCCGCTGCCACGAGGGCAGCTGTAGACGCACCCCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTAAATATACCCATCCCTAATAAAGGATAGAGATCTTGCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGCTCTATTCTAATAACCCAAGCTTTTTTCAATTCTAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCGCTTGGTAGGATTGACCACCAAAGCTAGAAACAGGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAGGGCGGTTAATCACTAGCGGCGATCTAGATATTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTAGACTTCTATTTCCCCTCTTGCCGAGGGATGATACTGCAATTGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGCGCTCTCTTATCAAACGCCGCAACGCCATCAAGGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACACGAGCGGAATCTTCTATGGATCGGATCACATCCTTAATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTGGTGTCGGGGTTGTAGTATTCGTCTCGGTACAACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACACTATAGGGAGCGTTACCCTAGCTAGACATTGCCTAATCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAAGAAGCAGAATAATGCGATTGAGTGGACAAAAATAAGAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGTTACGTATCGGCGTAACCGCCACTCCTTAGAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCCTCCTGCGCCCTGGAGGGGTGATCCTACACCTCGCGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGATTCTGGTATACGTTTATCCCACCACTCCTTAGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTCGTAAGCTAGGCAACGGCCTTGCTCGATGCACAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGTGCAGCTGCGCCTAAGGAGATGGCTGTACAAGCTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCACCTAGAGGGTACCTCCCGGTTAGACCGGGGCTCTTATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACATGGCCACAACAACCTTCCCGGAGCAAGGGATGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACAACATGGCCACAACAACCTTCCCGGAGCAAGGGATGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCTAGCCTTTGTGGCTAACCCTCCTGCGCTTTGACATATAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACNNNNNNNNNNNGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATCGATATACTTTTTAGCATCAGCTAAATGATAAAAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGGGATTCATGAACATGTTGATGGTGAATTATACCTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACAATTGCAAGGTTTATAAGTAAATGAACAACAACGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAACGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCGATGTAGCTCATAGCGACCTCGATAATTAATTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTTGTCTCCACTCGCAGGAGAAATTAATTGATTGGAAACAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAAC
diff -r 000000000000 -r 20f12e7c279b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon May 05 04:23:26 2014 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <set_environment version="1.0">
+      <environment_variable action="set_to" name="MINCED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="minced" version="0.1.5">
+      <repository changeset_revision="00b3a01c21bc" name="package_minced_0_1_5" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>