# HG changeset patch
# User iuc
# Date 1533215490 14400
# Node ID f48ed38dfddf4cfc57c016deb9f24cfb44f6f2c3

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit e02d20338ee01ed58265d93e9cc5b0695a322d47

diff -r 000000000000 -r f48ed38dfddf exonerate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exonerate.xml	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,168 @@
+<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@">
+    <description>pairwise sequence comparison</description>
+    <macros>
+	<import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        exonerate
+
+        --query '$query'
+
+        #if str( $ref_seq.ref_seq_selector ) == "personal"
+            --target '${ref_seq.input_fasta}'
+        #else
+            --target '${ref_seq.input_fasta.fields.path}'
+        #end if
+
+        --score $score
+        --percent $percent
+        --bestn $bestn
+        --verbose 0
+
+        #if str($model) != "ungapped"
+            --model '${model}'
+        #end if
+
+        #if str($model) == "est2genome"
+            --querytype dna --targettype dna
+        #elif str($model) == "protein2genome"
+            --querytype protein --targettype dna
+        #elif str($model) == "coding2coding"
+            --querytype dna --targettype dna
+        #end if
+
+        #if str($outformat) == "alignment"
+            --showalignment yes --showvulgar no > '${output_ali}'
+        #elif str($outformat) == "targetgff"
+            --showalignment no --showvulgar no --showtargetgff yes --showquerygff no > '${output_gff}'
+        #elif str($outformat) == "querygff"
+            --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
+        #end if
+    ]]></command>
+
+    <inputs>
+        <param argument="--query" type="data" format="fasta" label="Select the query sequence(s) in fasta" />
+
+        <conditional name="ref_seq">
+            <param name="ref_seq_selector" type="select" label="Reference sequence(s)">
+                <option selected="True" value="database">Use a built-in genome</option>
+                <option value="personal">Use a genome from history</option>
+            </param>
+            <when value="database">
+                <param
+                  help="If your genome of interest is not listed, contact the Galaxy server administrators"
+                  label="Reference sequence(s)"
+                  name="input_fasta"
+                  type="select"
+                  >
+                    <options from_data_table="all_fasta">
+                        <filter column="2" type="sort_by" />
+                        <validator message="No sequences are available" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="personal">
+                <param name="input_fasta" type="data" format="fasta" label="Reference sequence(s)" />
+            </when>
+        </conditional>
+
+        <param name='model' type='select' label="Alignment method">
+            <option value="ungapped" selected="true">Simple ungapped alignment</option>
+            <option value="est2genome">est2genome: align cDNA to a genome</option>
+            <option value="protein2genome">protein2genome: align proteins to a genome</option>
+            <option value="coding2coding">coding2coding: 6-frame translated alignment of DNA sequences</option>
+        </param>
+        <param name='outformat' type='select' label="Output format">
+            <option value="targetgff" selected="true">GFF on target sequence(s)</option>
+            <option value="querygff">GFF on query sequence(s)</option>
+            <option value="alignment">Human readable alignment</option>
+        </param>
+        <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
+        <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/>
+        <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
+    </inputs>
+    <outputs>
+        <data name="output_gff" format="txt" label="${tool.name} on $on_string">
+            <filter>outformat != 'alignment'</filter>
+        </data>
+        <data name="output_ali" format="gff" label="${tool.name} on $on_string">
+            <filter>outformat == 'alignment'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="out_target.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="database"/>
+                <param name="input_fasta" value="merlin"/>
+            </conditional>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="out_target.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="querygff"/>
+            <output name="output_gff" file="out_query.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="outformat" value="alignment"/>
+            <output name="output_ali" file="out.txt"/>
+        </test>
+        <test>
+            <param name="query" value="transcriptome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="est2genome"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="est2genome.gff"/>
+        </test>
+        <test>
+            <param name="query" value="proteome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="protein2genome"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="protein2genome.gff"/>
+        </test>
+        <test>
+            <param name="query" value="genome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="coding2coding"/>
+            <param name="outformat" value="targetgff"/>
+            <output name="output_gff" file="coding2coding.gff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Exonerate is a generic tool for pairwise sequence comparison.
+        It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
+
+        .. _Exonerate website: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r f48ed38dfddf macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">exonerate</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <token name="@VERSION@">2.4.0</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-6-31</citation>
+        </citations>
+    </xml>
+
+</macros>
diff -r 000000000000 -r f48ed38dfddf test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+merlin	merlin	Merlin	${__HERE__}/genome.fa
diff -r 000000000000 -r f48ed38dfddf test-data/coding2coding.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coding2coding.gff	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,28 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:coding2coding 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:coding2coding	similarity	1	3536	6207	+	.	alignment_id 1 ; Query sample ; Align 1 1 2463 ; Align 2466 2464 3 ; Align 2469 2469 1068
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:coding2coding 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:coding2coding	similarity	2	3535	6151	-	.	alignment_id 1 ; Query sample ; Align 3536 3536 3534
+# --- END OF GFF DUMP ---
+#
diff -r 000000000000 -r f48ed38dfddf test-data/est2genome.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est2genome.gff	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,37 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:est2genome 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:est2genome	gene	2742	2819	102	-	.	gene_id 1 ; sequence sample ; gene_orientation . ; identity 58.97 ; similarity 58.97
+sample	exonerate:est2genome	exon	2742	2819	.	-	.	insertions 0 ; deletions 0 ; identity 58.97 ; similarity 58.97
+sample	exonerate:est2genome	similarity	2742	2819	102	-	.	alignment_id 1 ; Query sample ; Align 2820 1168 78
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:est2genome 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:est2genome	gene	758	3050	7309	+	.	gene_id 1 ; sequence sample ; gene_orientation + ; identity 99.93 ; similarity 99.93
+sample	exonerate:est2genome	utr5	758	1332	.	+	.	
+sample	exonerate:est2genome	exon	758	1332	.	+	.	insertions 0 ; deletions 2 ; identity 99.83 ; similarity 99.83
+sample	exonerate:est2genome	splice5	1333	1334	.	+	.	intron_id 1 ; splice_site "TT"
+sample	exonerate:est2genome	intron	1333	2151	.	+	.	intron_id 1
+sample	exonerate:est2genome	splice3	2150	2151	.	+	.	intron_id 0 ; splice_site "AT"
+sample	exonerate:est2genome	exon	2152	3050	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
+sample	exonerate:est2genome	similarity	758	3050	7309	+	.	alignment_id 1 ; Query sample ; Align 758 1 572 ; Align 1330 575 3 ; Align 2152 578 899
+# --- END OF GFF DUMP ---
+#
diff -r 000000000000 -r f48ed38dfddf test-data/genome.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fa	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,14 @@
+>sample
+TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG
+GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA
+GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG
+TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC
+AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC
+AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG
+TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC
+GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT
+GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA
+AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT
+ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT
+TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC
+AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG
diff -r 000000000000 -r f48ed38dfddf test-data/out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.txt	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,288 @@
+
+C4 Alignment:
+------------
+         Query: sample
+        Target: sample
+         Model: ungapped:dna2dna
+     Raw score: 17680
+   Query range: 0 -> 3536
+  Target range: 0 -> 3536
+
+    1 : TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACA :   62
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+    1 : TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACA :   62
+
+   63 : TTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATA :  124
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+   63 : TTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATA :  124
+
+  125 : GCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAA :  186
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  125 : GCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAA :  186
+
+  187 : TACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCC :  248
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  187 : TACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCC :  248
+
+  249 : AAGATGCAATTGCCATGATCAAGGGGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTC :  310
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  249 : AAGATGCAATTGCCATGATCAAGGGGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTC :  310
+
+  311 : GCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATT :  372
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  311 : GCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATT :  372
+
+  373 : GAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCC :  434
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  373 : GAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCC :  434
+
+  435 : CAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAAC :  496
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  435 : CAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAAC :  496
+
+  497 : GAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAAGTTGGCAACTCGAA :  558
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  497 : GAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAAGTTGGCAACTCGAA :  558
+
+  559 : ACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACC :  620
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  559 : ACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACC :  620
+
+  621 : TGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATG :  682
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  621 : TGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATG :  682
+
+  683 : CTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACC :  744
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  683 : CTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACC :  744
+
+  745 : CTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGC :  806
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  745 : CTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGC :  806
+
+  807 : CAGTCCGCAGTCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTG :  868
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  807 : CAGTCCGCAGTCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTG :  868
+
+  869 : TGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAA :  930
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  869 : TGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAA :  930
+
+  931 : CCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAG :  992
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  931 : CCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAG :  992
+
+  993 : AAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTG : 1054
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+  993 : AAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTG : 1054
+
+ 1055 : TAGTGCAATAAACTTGCCGTCCTGAATGGCTGGCAATCAAAGATCTGAATGCAAGATACGAT : 1116
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1055 : TAGTGCAATAAACTTGCCGTCCTGAATGGCTGGCAATCAAAGATCTGAATGCAAGATACGAT : 1116
+
+ 1117 : GACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTA : 1178
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1117 : GACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTA : 1178
+
+ 1179 : GTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATT : 1240
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1179 : GTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATT : 1240
+
+ 1241 : GACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTG : 1302
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1241 : GACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTG : 1302
+
+ 1303 : GCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACCAAAA : 1364
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1303 : GCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACCAAAA : 1364
+
+ 1365 : GGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTG : 1426
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1365 : GGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTG : 1426
+
+ 1427 : CGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTT : 1488
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1427 : CGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTT : 1488
+
+ 1489 : AAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGC : 1550
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1489 : AAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGC : 1550
+
+ 1551 : AGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAG : 1612
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1551 : AGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAG : 1612
+
+ 1613 : GCATCTCGAGATGTCTTGAGTCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTT : 1674
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1613 : GCATCTCGAGATGTCTTGAGTCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTT : 1674
+
+ 1675 : GGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGG : 1736
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1675 : GGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGG : 1736
+
+ 1737 : AGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATA : 1798
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1737 : AGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATA : 1798
+
+ 1799 : CGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATT : 1860
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1799 : CGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATT : 1860
+
+ 1861 : AATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGCGGGATATTTATTTATGGG : 1922
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1861 : AATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGCGGGATATTTATTTATGGG : 1922
+
+ 1923 : CTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTAT : 1984
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1923 : CTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTAT : 1984
+
+ 1985 : TATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCT : 2046
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 1985 : TATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCT : 2046
+
+ 2047 : GGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCAT : 2108
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2047 : GGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCAT : 2108
+
+ 2109 : AAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGT : 2170
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2109 : AAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGT : 2170
+
+ 2171 : CCGAGTGCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTG : 2232
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2171 : CCGAGTGCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTG : 2232
+
+ 2233 : CCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAG : 2294
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2233 : CCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAG : 2294
+
+ 2295 : CGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGC : 2356
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2295 : CGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGC : 2356
+
+ 2357 : AAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATG : 2418
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2357 : AAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATG : 2418
+
+ 2419 : CACTGGTAGCTCACAAACAGCCCACACAGAAACCAGTAATGAAATTGTGCGGCACTCGTCAT : 2480
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2419 : CACTGGTAGCTCACAAACAGCCCACACAGAAACCAGTAATGAAATTGTGCGGCACTCGTCAT : 2480
+
+ 2481 : TGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCG : 2542
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2481 : TGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCG : 2542
+
+ 2543 : GCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAA : 2604
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2543 : GCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAA : 2604
+
+ 2605 : ATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGA : 2666
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2605 : ATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGA : 2666
+
+ 2667 : GAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTTACGAGAGA : 2728
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2667 : GAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTTACGAGAGA : 2728
+
+ 2729 : CACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCC : 2790
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2729 : CACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCC : 2790
+
+ 2791 : CTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTC : 2852
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2791 : CTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTC : 2852
+
+ 2853 : CACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAA : 2914
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2853 : CACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAA : 2914
+
+ 2915 : GTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTG : 2976
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2915 : GTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTG : 2976
+
+ 2977 : GCATGAAATGGGGGCTTTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAA : 3038
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 2977 : GCATGAAATGGGGGCTTTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAA : 3038
+
+ 3039 : CTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGG : 3100
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3039 : CTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGG : 3100
+
+ 3101 : CGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGC : 3162
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3101 : CGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGC : 3162
+
+ 3163 : GAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCA : 3224
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3163 : GAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCA : 3224
+
+ 3225 : TTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGCAGGTTTTCGGTGCACATTTATT : 3286
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3225 : TTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGCAGGTTTTCGGTGCACATTTATT : 3286
+
+ 3287 : TCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAG : 3348
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3287 : TCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAG : 3348
+
+ 3349 : ATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCA : 3410
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3349 : ATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCA : 3410
+
+ 3411 : ACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAG : 3472
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3411 : ACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAG : 3472
+
+ 3473 : GCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAA : 3534
+        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ 3473 : GCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAA : 3534
+
+ 3535 : AG : 3536
+        ||
+ 3535 : AG : 3536
+
+
+C4 Alignment:
+------------
+         Query: sample
+        Target: sample
+         Model: ungapped:dna2dna
+     Raw score: 108
+   Query range: 607 -> 634
+  Target range: 595 -> 622
+
+ 608 : CTGAAGCTCAACCTGAAGCTCAACCGG : 634
+       || || ||||||||||||||||||| |
+ 596 : CTCAACCTCAACCTGAAGCTCAACCTG : 622
+
+
+C4 Alignment:
+------------
+         Query: sample
+        Target: sample
+         Model: ungapped:dna2dna
+     Raw score: 108
+   Query range: 595 -> 622
+  Target range: 607 -> 634
+
+ 596 : CTCAACCTCAACCTGAAGCTCAACCTG : 622
+       || || ||||||||||||||||||| |
+ 608 : CTGAAGCTCAACCTGAAGCTCAACCGG : 634
+
+
+C4 Alignment:
+------------
+         Query: sample
+        Target: sample [revcomp]
+         Model: ungapped:dna2dna
+     Raw score: 102
+   Query range: 2741 -> 2819
+  Target range: 2819 -> 2741
+
+ 2742 : ATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAA : 2803
+        ||||||| | ||   |   |  | || |    ||||||||||||||    | || |  |   
+ 2819 : ATACAAATTGCTGTTATTGTCATAAGCAGGGGAGAACTGCAGTTCTAGTTTACTGACTAGCT : 2758
+
+ 2804 : TAACAGCAATTTGTAT : 2819
+        |   || | |||||||
+ 2757 : TTCTAGAATTTTGTAT : 2742
+
diff -r 000000000000 -r f48ed38dfddf test-data/out_query.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_query.gff	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,56 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	1	3536	17680	+	.	alignment_id 1 ; Target sample ; Align 1 1 3536
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	608	634	108	+	.	alignment_id 2 ; Target sample ; Align 608 596 27
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	596	622	108	+	.	alignment_id 3 ; Target sample ; Align 596 608 27
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	2742	2819	102	+	.	alignment_id 1 ; Target sample ; Align 2742 2820 78
+# --- END OF GFF DUMP ---
+#
diff -r 000000000000 -r f48ed38dfddf test-data/out_target.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_target.gff	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,56 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	1	3536	17680	+	.	alignment_id 1 ; Query sample ; Align 1 1 3536
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	596	622	108	+	.	alignment_id 2 ; Query sample ; Align 596 608 27
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	608	634	108	+	.	alignment_id 3 ; Query sample ; Align 608 596 27
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:ungapped:dna2dna 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:ungapped:dna2dna	similarity	2742	2819	102	-	.	alignment_id 1 ; Query sample ; Align 2820 2742 78
+# --- END OF GFF DUMP ---
+#
diff -r 000000000000 -r f48ed38dfddf test-data/protein2genome.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/protein2genome.gff	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,22 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:protein2genome:local 2.4.0
+##date 2018-08-02
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:protein2genome:local	gene	1181	2291	456	+	.	gene_id 1 ; sequence sample ; gene_orientation + ; identity 98.97 ; similarity 100.00
+sample	exonerate:protein2genome:local	cds	1181	1326	.	+	.	
+sample	exonerate:protein2genome:local	exon	1181	1326	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
+sample	exonerate:protein2genome:local	splice5	1327	1328	.	+	.	intron_id 1 ; splice_site "CA"
+sample	exonerate:protein2genome:local	intron	1327	2143	.	+	.	intron_id 1
+sample	exonerate:protein2genome:local	splice3	2142	2143	.	+	.	intron_id 0 ; splice_site "AT"
+sample	exonerate:protein2genome:local	cds	2144	2291	.	+	.	
+sample	exonerate:protein2genome:local	exon	2144	2291	.	+	.	insertions 0 ; deletions 0 ; identity 97.96 ; similarity 100.00
+sample	exonerate:protein2genome:local	similarity	1181	2291	456	+	.	alignment_id 1 ; Query sample ; Align 1181 1 144 ; Align 2145 50 147
+# --- END OF GFF DUMP ---
+#
diff -r 000000000000 -r f48ed38dfddf test-data/proteome.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/proteome.fa	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,2 @@
+>sample
+PSSADSSPSGCHSFMSFRSIDIVKLALLHSEKMYLTSTQSWLFAAMTVSMPWIALNLVRVRRCCSFAVCCLLFLFALLAAGAQLFMWLLLVFRPESRR
diff -r 000000000000 -r f48ed38dfddf test-data/transcriptome.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptome.fa	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,8 @@
+>sample
+ATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG
+TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC
+AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATGCCATGGATTGCATTGAACTTAGTCCGAGT
+GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA
+AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT
+ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT
+TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCA
diff -r 000000000000 -r f48ed38dfddf tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r f48ed38dfddf tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r f48ed38dfddf tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Aug 02 09:11:30 2018 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>