# HG changeset patch
# User iuc
# Date 1583056114 18000
# Node ID a03dead1bedee831db80eeee1de34e4c383ff9c2
# Parent  b03ae2ba8688026ebb5b3c67c460cb923a2d1933
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"

diff -r b03ae2ba8688 -r a03dead1bede exonerate.xml
--- a/exonerate.xml	Fri Jun 28 11:21:08 2019 -0400
+++ b/exonerate.xml	Sun Mar 01 04:48:34 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy1">
+<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy2">
     <description>pairwise sequence comparison</description>
     <macros>
 	<import>macros.xml</import>
@@ -32,6 +32,16 @@
             --querytype dna --targettype dna
         #end if
 
+        #if $minintron
+            --minintron ${minintron}
+        #end if
+
+        #if $maxintron
+            --maxintron ${maxintron}
+        #end if
+
+        --cores \${GALAXY_SLOTS:-1}
+
         #if str($outformat) == "alignment"
             --showalignment yes --showvulgar no > '${output_ali}'
         #elif str($outformat) == "targetgff"
@@ -40,7 +50,10 @@
             --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
         #end if
 
-        --cores \${GALAXY_SLOTS:-1}
+        ## Produce a more standard GFF3
+        #if str($outformat) in ["targetgff", "querygff"]
+            && python '$__tool_directory__/exonerategff_to_gff3.py' '${output_gff}' > '${output_gff3}'
+        #end if
     ]]></command>
 
     <inputs>
@@ -83,9 +96,14 @@
         <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)"/>
+        <param argument='--minintron' type='integer' optional="true" label="Minimum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
+        <param argument='--maxintron' type='integer' optional="true" label="Maximum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
     </inputs>
     <outputs>
-        <data name="output_gff" format="gff" label="${tool.name} on $on_string">
+        <data name="output_gff" format="gff" label="${tool.name} on $on_string - Raw GFF">
+            <filter>outformat != 'alignment'</filter>
+        </data>
+        <data name="output_gff3" format="gff3" label="${tool.name} on $on_string - GFF3">
             <filter>outformat != 'alignment'</filter>
         </data>
         <data name="output_ali" format="txt" label="${tool.name} on $on_string">
@@ -101,6 +119,7 @@
             </conditional>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="out_target.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -110,6 +129,7 @@
             </conditional>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="out_target.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -119,6 +139,7 @@
             </conditional>
             <param name="outformat" value="querygff"/>
             <output name="output_gff" file="out_query.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_query.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -138,6 +159,7 @@
             <param name="model" value="est2genome"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="est2genome.gff" lines_diff="4"/>
+            <output name="output_gff3" file="est2genome.gff3" lines_diff="4"/>
         </test>
         <test>
             <param name="query" value="proteome.fa"/>
@@ -148,6 +170,7 @@
             <param name="model" value="protein2genome"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="protein2genome.gff" lines_diff="2"/>
+            <output name="output_gff3" file="protein2genome.gff3" lines_diff="2"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -158,6 +181,20 @@
             <param name="model" value="coding2coding"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="coding2coding.gff" lines_diff="4"/>
+            <output name="output_gff3" file="coding2coding.gff3" lines_diff="4"/>
+        </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"/>
+            <param name="minintron" value="100"/>
+            <param name="maxintron" value="200"/>
+            <output name="output_gff" file="est2genome_introns.gff" lines_diff="6"/>
+            <output name="output_gff3" file="est2genome_introns.gff3" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r b03ae2ba8688 -r a03dead1bede exonerategff_to_gff3.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exonerategff_to_gff3.py	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+
+"""
+Converts a GFF produced by exonerate into a more standard GFF3 (e.g. usable in JBrowse)
+"""
+
+import argparse
+import sys
+
+from BCBio import GFF
+from Bio.SeqFeature import FeatureLocation, SeqFeature
+
+parser = argparse.ArgumentParser()
+parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
+parser.add_argument('outfile', nargs='?', type=argparse.FileType('a'), default=sys.stdout)
+args = parser.parse_args()
+
+
+scaffs = []
+gene_number = 0
+for scaff in GFF.parse(args.infile):
+    scaff.annotations = {}
+    scaff.seq = ""
+    kept_features = []
+    current_gene = None
+    exon_number = 0
+    last_utr = None
+
+    for feature in scaff.features:
+
+        if feature.type == "gene":
+            gene_number += 1
+            mrna_feature = SeqFeature(FeatureLocation(feature.location.start, feature.location.end), type="mRNA", strand=feature.location.strand)
+            mrna_feature.sub_features = []
+            mrna_feature.qualifiers['source'] = feature.qualifiers['source']
+            mrna_id = "mRNA_" + str(gene_number)
+            mrna_feature.qualifiers['ID'] = mrna_id
+            feature.sub_features = [mrna_feature]
+            feature.qualifiers['ID'] = "gene_" + str(gene_number)
+            if 'gene_orientation' in feature.qualifiers:
+                del feature.qualifiers['gene_orientation']
+            if current_gene:
+                kept_features.append(current_gene)
+
+            current_gene = feature
+            exon_number = 0
+            last_utr = None
+
+        elif feature.type == 'utr5':
+            feature.type = 'five_prime_UTR'
+            feature.qualifiers['ID'] = '%s_five_prime_UTR' % (mrna_id)
+            mrna_feature.sub_features.append(feature)
+            last_utr = {'start': feature.location.start, 'end': feature.location.end}
+
+        elif feature.type == 'utr3':
+            feature.type = 'three_prime_UTR'
+            feature.qualifiers['ID'] = '%s_three_prime_UTR' % (mrna_id)
+            mrna_feature.sub_features.append(feature)
+            last_utr = {'start': feature.location.start, 'end': feature.location.end}
+
+        elif feature.type == 'exon':
+            exon_number += 1
+            feature.qualifiers['ID'] = '%s_exon_%s' % (mrna_id, exon_number)
+            mrna_feature.sub_features.append(feature)
+
+            if last_utr is None:
+                cds_feature = SeqFeature(FeatureLocation(feature.location.start, feature.location.end), type="CDS", strand=feature.location.strand)
+                cds_feature.sub_features = []
+                cds_feature.qualifiers['source'] = feature.qualifiers['source']
+                cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
+                mrna_feature.sub_features.append(cds_feature)
+            elif feature.location.start != last_utr['start'] or feature.location.end != last_utr['end']:
+                if feature.location.start > last_utr['start']:
+                    cds_feature = SeqFeature(FeatureLocation(feature.location.start, last_utr['start']), type="CDS", strand=feature.location.strand)
+                    cds_feature.sub_features = []
+                    cds_feature.qualifiers['source'] = feature.qualifiers['source']
+                    cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
+                    mrna_feature.sub_features.append(cds_feature)
+                if feature.location.end < last_utr['end']:
+                    cds_feature = SeqFeature(FeatureLocation(feature.location.end, last_utr['end']), type="CDS", strand=feature.location.strand)
+                    cds_feature.sub_features = []
+                    cds_feature.qualifiers['source'] = feature.qualifiers['source']
+                    cds_feature.qualifiers['ID'] = mrna_id + "_CDS"
+                    mrna_feature.sub_features.append(cds_feature)
+
+            last_utr = None
+
+        elif feature.type == 'similarity':
+            if current_gene is None:
+                # We haven't seen any gene, just convert similarity to match
+                feature.type = 'match'
+                kept_features.append(feature)
+
+            last_utr = None
+
+        elif feature.type not in ['splice3', 'splice5', 'similarity', 'intron']:
+            mrna_feature.sub_features.append(feature)
+            last_utr = None
+
+    # For the last one
+    if current_gene:
+        kept_features.append(current_gene)
+
+    scaff.features = kept_features
+
+    if len(kept_features):
+        GFF.write([scaff], args.outfile)
diff -r b03ae2ba8688 -r a03dead1bede macros.xml
--- a/macros.xml	Fri Jun 28 11:21:08 2019 -0400
+++ b/macros.xml	Sun Mar 01 04:48:34 2020 -0500
@@ -3,6 +3,8 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">exonerate</requirement>
+            <requirement type="package" version="3.7">python</requirement>
+            <requirement type="package" version="0.6.6">bcbiogff</requirement>
             <yield />
         </requirements>
     </xml>
diff -r b03ae2ba8688 -r a03dead1bede test-data/coding2coding.gff
--- a/test-data/coding2coding.gff	Fri Jun 28 11:21:08 2019 -0400
+++ b/test-data/coding2coding.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -3,7 +3,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:coding2coding 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -17,7 +17,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:coding2coding 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
diff -r b03ae2ba8688 -r a03dead1bede test-data/coding2coding.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coding2coding.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,3 @@
+##gff-version 3
+sample	exonerate:coding2coding	match	1	3536	6207	+	.	Align=1 1 2463,2466 2464 3,2469 2469 1068;Query=sample;alignment_id=1
+sample	exonerate:coding2coding	match	2	3535	6151	-	.	Align=3536 3536 3534;Query=sample;alignment_id=1
diff -r b03ae2ba8688 -r a03dead1bede test-data/est2genome.gff
--- a/test-data/est2genome.gff	Fri Jun 28 11:21:08 2019 -0400
+++ b/test-data/est2genome.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -3,7 +3,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:est2genome 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -19,7 +19,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:est2genome 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
diff -r b03ae2ba8688 -r a03dead1bede test-data/est2genome.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est2genome.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,11 @@
+##gff-version 3
+sample	exonerate:est2genome	gene	2742	2819	102	-	.	ID=gene_1;gene_id=1;identity=58.97;sequence=sample;similarity=58.97
+sample	exonerate:est2genome	mRNA	2742	2819	.	-	.	ID=mRNA_1;Parent=gene_1
+sample	exonerate:est2genome	exon	2742	2819	.	-	.	ID=mRNA_1_exon_1;Parent=mRNA_1;deletions=0;identity=58.97;insertions=0;similarity=58.97
+sample	exonerate:est2genome	CDS	2742	2819	.	-	0	ID=mRNA_1_CDS;Parent=mRNA_1
+sample	exonerate:est2genome	gene	758	3050	7309	+	.	ID=gene_2;gene_id=1;identity=99.93;sequence=sample;similarity=99.93
+sample	exonerate:est2genome	mRNA	758	3050	.	+	.	ID=mRNA_2;Parent=gene_2
+sample	exonerate:est2genome	five_prime_UTR	758	1332	.	+	.	ID=mRNA_2_five_prime_UTR;Parent=mRNA_2
+sample	exonerate:est2genome	exon	758	1332	.	+	.	ID=mRNA_2_exon_1;Parent=mRNA_2;deletions=2;identity=99.83;insertions=0;similarity=99.83
+sample	exonerate:est2genome	exon	2152	3050	.	+	.	ID=mRNA_2_exon_2;Parent=mRNA_2;deletions=0;identity=100.00;insertions=0;similarity=100.00
+sample	exonerate:est2genome	CDS	2152	3050	.	+	0	ID=mRNA_2_CDS;Parent=mRNA_2
diff -r b03ae2ba8688 -r a03dead1bede test-data/est2genome_introns.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est2genome_introns.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,48 @@
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:est2genome 2.4.0
+##date 2020-02-26
+##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 2020-02-26
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:est2genome	gene	2146	3050	4525	+	.	gene_id 1 ; sequence sample ; gene_orientation . ; identity 100.00 ; similarity 100.00
+sample	exonerate:est2genome	exon	2146	3050	.	+	.	insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
+sample	exonerate:est2genome	similarity	2146	3050	4525	+	.	alignment_id 1 ; Query sample ; Align 2146 572 905
+# --- END OF GFF DUMP ---
+#
+# --- START OF GFF DUMP ---
+#
+#
+##gff-version 2
+##source-version exonerate:est2genome 2.4.0
+##date 2020-02-26
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+sample	exonerate:est2genome	gene	758	1357	2861	+	.	gene_id 2 ; sequence sample ; gene_orientation . ; identity 98.33 ; similarity 98.33
+sample	exonerate:est2genome	exon	758	1357	.	+	.	insertions 1 ; deletions 4 ; identity 98.33 ; similarity 98.33
+sample	exonerate:est2genome	similarity	758	1357	2861	+	.	alignment_id 2 ; Query sample ; Align 758 1 572 ; Align 1330 575 14 ; Align 1345 589 8 ; Align 1353 599 5
+# --- END OF GFF DUMP ---
+#
diff -r b03ae2ba8688 -r a03dead1bede test-data/est2genome_introns.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est2genome_introns.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,13 @@
+##gff-version 3
+sample	exonerate:est2genome	gene	2742	2819	102	-	.	ID=gene_1;gene_id=1;identity=58.97;sequence=sample;similarity=58.97
+sample	exonerate:est2genome	mRNA	2742	2819	.	-	.	ID=mRNA_1;Parent=gene_1
+sample	exonerate:est2genome	exon	2742	2819	.	-	.	ID=mRNA_1_exon_1;Parent=mRNA_1;deletions=0;identity=58.97;insertions=0;similarity=58.97
+sample	exonerate:est2genome	CDS	2742	2819	.	-	0	ID=mRNA_1_CDS;Parent=mRNA_1
+sample	exonerate:est2genome	gene	2146	3050	4525	+	.	ID=gene_2;gene_id=1;identity=100.00;sequence=sample;similarity=100.00
+sample	exonerate:est2genome	mRNA	2146	3050	.	+	.	ID=mRNA_2;Parent=gene_2
+sample	exonerate:est2genome	exon	2146	3050	.	+	.	ID=mRNA_2_exon_1;Parent=mRNA_2;deletions=0;identity=100.00;insertions=0;similarity=100.00
+sample	exonerate:est2genome	CDS	2146	3050	.	+	0	ID=mRNA_2_CDS;Parent=mRNA_2
+sample	exonerate:est2genome	gene	758	1357	2861	+	.	ID=gene_3;gene_id=2;identity=98.33;sequence=sample;similarity=98.33
+sample	exonerate:est2genome	mRNA	758	1357	.	+	.	ID=mRNA_3;Parent=gene_3
+sample	exonerate:est2genome	exon	758	1357	.	+	.	ID=mRNA_3_exon_1;Parent=mRNA_3;deletions=4;identity=98.33;insertions=1;similarity=98.33
+sample	exonerate:est2genome	CDS	758	1357	.	+	0	ID=mRNA_3_CDS;Parent=mRNA_3
diff -r b03ae2ba8688 -r a03dead1bede test-data/out_query.gff
--- a/test-data/out_query.gff	Fri Jun 28 11:21:08 2019 -0400
+++ b/test-data/out_query.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -3,7 +3,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -17,7 +17,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -31,7 +31,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -45,7 +45,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
diff -r b03ae2ba8688 -r a03dead1bede test-data/out_query.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_query.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,5 @@
+##gff-version 3
+sample	exonerate:ungapped:dna2dna	match	1	3536	17680	+	.	Align=1 1 3536;Target=sample;alignment_id=1
+sample	exonerate:ungapped:dna2dna	match	608	634	108	+	.	Align=608 596 27;Target=sample;alignment_id=2
+sample	exonerate:ungapped:dna2dna	match	596	622	108	+	.	Align=596 608 27;Target=sample;alignment_id=3
+sample	exonerate:ungapped:dna2dna	match	2742	2819	102	+	.	Align=2742 2820 78;Target=sample;alignment_id=1
diff -r b03ae2ba8688 -r a03dead1bede test-data/out_target.gff
--- a/test-data/out_target.gff	Fri Jun 28 11:21:08 2019 -0400
+++ b/test-data/out_target.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -3,7 +3,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -17,7 +17,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -31,7 +31,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
@@ -45,7 +45,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:ungapped:dna2dna 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
diff -r b03ae2ba8688 -r a03dead1bede test-data/out_target.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_target.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,5 @@
+##gff-version 3
+sample	exonerate:ungapped:dna2dna	match	1	3536	17680	+	.	Align=1 1 3536;Query=sample;alignment_id=1
+sample	exonerate:ungapped:dna2dna	match	596	622	108	+	.	Align=596 608 27;Query=sample;alignment_id=2
+sample	exonerate:ungapped:dna2dna	match	608	634	108	+	.	Align=608 596 27;Query=sample;alignment_id=3
+sample	exonerate:ungapped:dna2dna	match	2742	2819	102	-	.	Align=2820 2742 78;Query=sample;alignment_id=1
diff -r b03ae2ba8688 -r a03dead1bede test-data/protein2genome.gff
--- a/test-data/protein2genome.gff	Fri Jun 28 11:21:08 2019 -0400
+++ b/test-data/protein2genome.gff	Sun Mar 01 04:48:34 2020 -0500
@@ -3,7 +3,7 @@
 #
 ##gff-version 2
 ##source-version exonerate:protein2genome:local 2.4.0
-##date 2018-08-02
+##date 2020-02-26
 ##type DNA
 #
 #
diff -r b03ae2ba8688 -r a03dead1bede test-data/protein2genome.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/protein2genome.gff3	Sun Mar 01 04:48:34 2020 -0500
@@ -0,0 +1,9 @@
+##gff-version 3
+sample	exonerate:protein2genome:local	gene	1181	2291	456	+	.	ID=gene_1;gene_id=1;identity=98.97;sequence=sample;similarity=100.00
+sample	exonerate:protein2genome:local	mRNA	1181	2291	.	+	.	ID=mRNA_1;Parent=gene_1
+sample	exonerate:protein2genome:local	cds	1181	1326	.	+	.	Parent=mRNA_1
+sample	exonerate:protein2genome:local	exon	1181	1326	.	+	.	ID=mRNA_1_exon_1;Parent=mRNA_1;deletions=0;identity=100.00;insertions=0;similarity=100.00
+sample	exonerate:protein2genome:local	CDS	1181	1326	.	+	0	ID=mRNA_1_CDS;Parent=mRNA_1
+sample	exonerate:protein2genome:local	cds	2144	2291	.	+	.	Parent=mRNA_1
+sample	exonerate:protein2genome:local	exon	2144	2291	.	+	.	ID=mRNA_1_exon_2;Parent=mRNA_1;deletions=0;identity=97.96;insertions=0;similarity=100.00
+sample	exonerate:protein2genome:local	CDS	2144	2291	.	+	0	ID=mRNA_1_CDS;Parent=mRNA_1