Mercurial > repos > earlhaminst > gstf_preparation

changeset 10:e8e75a79de59 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 9c8611fee927883f50bc6955771aa69df1ce8457"
author earlhaminst
date Thu, 31 Oct 2019 08:16:51 -0400
parents f4acbfe8d6fe
children dbe37a658cd2
files gstf_preparation.py gstf_preparation.xml test-data/MGP_PahariEiJ_G0008413.1.gff3 test-data/Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa test-data/test1.ns.fasta test-data/test4.ns.fasta test-data/test5.sqlite test-data/test6.fasta test-data/test6.sqlite
diffstat 7 files changed, 289 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/gstf_preparation.py	Wed Oct 17 07:31:29 2018 -0400
+++ b/gstf_preparation.py	Thu Oct 31 08:16:51 2019 -0400
@@ -2,6 +2,7 @@
 
 import json
 import optparse
+import os
 import sqlite3
 import sys
 
@@ -114,10 +115,7 @@
         # a 5' UTR can be split among multiple exons
         # a CDS can be part of multiple transcripts
         for parent in d['Parent'].split(','):
-            if parent not in parent_dict:
-                parent_dict[parent] = [d]
-            else:
-                parent_dict[parent].append(d)
+            parent_dict.setdefault(parent, []).append(d)
     return d
 
 
@@ -139,6 +137,8 @@
 
 def add_transcript_to_dict(cols, species, transcript_dict):
     transcript = feature_to_dict(cols)
+    if 'biotype' in transcript and transcript['biotype'] != 'protein_coding':
+        return
     transcript.update({
         'object_type': 'Transcript',
         'seq_region_name': cols[0],
@@ -302,7 +302,7 @@
     parser.add_option('--regions', default="", help='Comma-separated list of region IDs for which FASTA sequences should be filtered')
     parser.add_option('-o', '--output', help='Path of the output SQLite file')
     parser.add_option('--of', help='Path of the output FASTA file')
-    parser.add_option('--ff', help='Path of the filtered sequences output FASTA file')
+    parser.add_option('--ff', default=os.devnull, help='Path of the filtered sequences output FASTA file')
 
     options, args = parser.parse_args()
     if args:
@@ -403,10 +403,7 @@
             else:
                 break
 
-            if gene_id in gene_transcripts_dict:
-                gene_transcripts_dict[gene_id].append((transcript_id, len(entry.sequence)))
-            else:
-                gene_transcripts_dict[gene_id] = [(transcript_id, len(entry.sequence))]
+            gene_transcripts_dict.setdefault(gene_id, []).append((transcript_id, len(entry.sequence)))
 
     if options.longestCDS:
         # For each gene, select the transcript with the longest sequence.
--- a/gstf_preparation.xml	Wed Oct 17 07:31:29 2018 -0400
+++ b/gstf_preparation.xml	Thu Oct 31 08:16:51 2019 -0400
@@ -1,7 +1,6 @@
 <tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.1">
     <description>converts data for the workflow</description>
-    <command detect_errors="exit_code">
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/gstf_preparation.py'
 #for $q in $queries
     --gff3 '${q.genome}:${q.gff3_input}'
@@ -22,12 +21,11 @@
 #end if
 #if $regions
     --regions '$regions'
+    --ff '$filtered_fasta'
 #end if
 -o '$output_db'
 --of '$output_fasta'
---ff '$filtered_fasta'
-]]>
-    </command>
+    ]]></command>
 
     <inputs>
         <repeat name="queries" title="GFF3 dataset">
@@ -40,58 +38,56 @@
         <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
         <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
         <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
-        <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
+        <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered out" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter out chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
     </inputs>
 
     <outputs>
-         <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
-         <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
-         <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences" />
+        <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
+        <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
+        <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences">
+            <filter>regions</filter>
+        </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
             <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
             <param name="genome" value="caenorhabditis_elegans" />
             <param name="longestCDS" value="false" />
             <param name="headers" value="true" />
 
-            <output name="output_db" file="test1.sqlite" compare="sim_size" />
+            <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
             <output name="output_fasta" file="test1.fasta" />
-            <output name="filtered_fasta" file="test1.ns.fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
             <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
             <param name="genome" value="caenorhabditis_elegans" />
             <param name="longestCDS" value="true" />
             <param name="headers" value="true" />
 
-            <output name="output_db" file="test1.sqlite" compare="sim_size" />
+            <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
             <output name="output_fasta" file="test1_longest.fasta" />
-            <output name="filtered_fasta" file="test1.ns.fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
             <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
             <param name="genome" value="caenorhabditis_elegans" />
             <param name="longestCDS" value="false" />
             <param name="headers" value="false" />
 
-            <output name="output_db" file="test1.sqlite" compare="sim_size" />
+            <output name="output_db" file="test1.sqlite" compare="sim_size" delta="30000" />
             <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
-            <output name="filtered_fasta" file="test1.ns.fasta" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
             <param name="json" ftype="json" value="gene.json" />
             <param name="longestCDS" value="false" />
             <param name="headers" value="true" />
 
-            <output name="output_db" file="test4.sqlite" compare="sim_size" />
+            <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
             <output name="output_fasta" file="test4.fasta" />
-            <output name="filtered_fasta" file="test4.ns.fasta" />
         </test>
         <test>
             <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
@@ -100,13 +96,22 @@
             <param name="headers" value="true" />
             <param name="regions" value="X" />
 
-            <output name="output_db" file="test5.sqlite" compare="sim_size" />
+            <output name="output_db" file="test4.sqlite" compare="sim_size" delta="30000" />
             <output name="output_fasta" file="test5_filtered.fasta" />
             <output name="filtered_fasta" file="test5.ns.fasta" />
         </test>
+        <test expect_num_outputs="2">
+            <param name="fasta_inputs" ftype="fasta" value="Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa" />
+            <param name="gff3_input" ftype="gff3" value="MGP_PahariEiJ_G0008413.1.gff3" />
+            <param name="genome" value="mus_pahari" />
+            <param name="longestCDS" value="true" />
+            <param name="headers" value="true" />
+
+            <output name="output_db" file="test6.sqlite" compare="sim_size" delta="30000" />
+            <output name="output_fasta" file="test6.fasta" />
+        </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
@@ -140,8 +145,7 @@
 .. class:: warningmark
 
 If a value in the **ID** and **Parent** attribute contains a colon, everything up to the first colon will be discarded.
-]]>
-    </help>
+    ]]></help>
     <citations>
     </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MGP_PahariEiJ_G0008413.1.gff3	Thu Oct 31 08:16:51 2019 -0400
@@ -0,0 +1,139 @@
+##gff-version 3
+##sequence-region 13 1 96704406
+13	Ensembl	gene	62596741	62686932	.	+	.	ID=MGP_PahariEiJ_G0008413.1;Name=MGP_PahariEiJ_G0008413.1;biotype=polymorphic_pseudogene
+13	Ensembl	transcript	62596741	62626623	.	+	.	ID=MGP_PahariEiJ_T0009933.1;Name=MGP_PahariEiJ_T0009933.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=protein_coding
+13	Ensembl	transcript	62596741	62686932	.	+	.	ID=MGP_PahariEiJ_T0009934.1;Name=MGP_PahariEiJ_T0009934.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=polymorphic_pseudogene
+13	Ensembl	transcript	62596766	62625799	.	+	.	ID=MGP_PahariEiJ_T0009935.1;Name=MGP_PahariEiJ_T0009935.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=retained_intron
+13	Ensembl	transcript	62660839	62686932	.	+	.	ID=MGP_PahariEiJ_T0009936.1;Name=MGP_PahariEiJ_T0009936.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=processed_transcript
+13	Ensembl	transcript	62671962	62686919	.	+	.	ID=MGP_PahariEiJ_T0009937.1;Name=MGP_PahariEiJ_T0009937.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=processed_transcript
+13	Ensembl	transcript	62671962	62686918	.	+	.	ID=MGP_PahariEiJ_T0009938.1;Name=MGP_PahariEiJ_T0009938.1;Parent=MGP_PahariEiJ_G0008413.1;biotype=protein_coding
+13	Ensembl	intron	62596975	62624027	.	+	.	Name=intron00001;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	intron	62624355	62626424	.	+	.	Name=intron00002;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	intron	62596975	62624027	.	+	.	Name=intron00003;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62624355	62626424	.	+	.	Name=intron00004;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62626620	62637349	.	+	.	Name=intron00005;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62637436	62640660	.	+	.	Name=intron00006;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62640768	62641046	.	+	.	Name=intron00007;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62641179	62641725	.	+	.	Name=intron00008;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62641854	62641961	.	+	.	Name=intron00009;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62642215	62651556	.	+	.	Name=intron00010;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62651793	62657150	.	+	.	Name=intron00011;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62657340	62660197	.	+	.	Name=intron00012;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62660808	62662195	.	+	.	Name=intron00013;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62662303	62663623	.	+	.	Name=intron00014;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62663751	62665451	.	+	.	Name=intron00015;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62665637	62668991	.	+	.	Name=intron00016;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62669299	62671283	.	+	.	Name=intron00017;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62671361	62671958	.	+	.	Name=intron00018;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62672085	62673958	.	+	.	Name=intron00019;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62674160	62678497	.	+	.	Name=intron00020;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62678579	62679702	.	+	.	Name=intron00021;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62679808	62683727	.	+	.	Name=intron00022;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62683916	62685193	.	+	.	Name=intron00023;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	intron	62596975	62624027	.	+	.	Name=intron00024;Parent=MGP_PahariEiJ_T0009935.1
+13	Ensembl	intron	62660879	62662195	.	+	.	Name=intron00025;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62662389	62663623	.	+	.	Name=intron00026;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62663751	62665451	.	+	.	Name=intron00027;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62665637	62668991	.	+	.	Name=intron00028;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62669299	62671283	.	+	.	Name=intron00029;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62671361	62671958	.	+	.	Name=intron00030;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62672085	62673958	.	+	.	Name=intron00031;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62674160	62678497	.	+	.	Name=intron00032;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62678579	62679702	.	+	.	Name=intron00033;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62679808	62683727	.	+	.	Name=intron00034;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62683916	62685193	.	+	.	Name=intron00035;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	intron	62672085	62674007	.	+	.	Name=intron00036;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	intron	62674160	62678497	.	+	.	Name=intron00037;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	intron	62678579	62679702	.	+	.	Name=intron00038;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	intron	62679808	62683727	.	+	.	Name=intron00039;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	intron	62683916	62685193	.	+	.	Name=intron00040;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	intron	62672085	62674007	.	+	.	Name=intron00041;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	intron	62674160	62678497	.	+	.	Name=intron00042;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	intron	62678579	62679702	.	+	.	Name=intron00043;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	intron	62679808	62683727	.	+	.	Name=intron00044;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	intron	62683916	62685193	.	+	.	Name=intron00045;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	CDS	62596855	62596942	.	+	0	Name=MGP_PahariEiJ_P0009933;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	CDS	62596943	62596974	.	+	2	Name=MGP_PahariEiJ_P0009933;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	CDS	62624028	62624354	.	+	0	Name=MGP_PahariEiJ_P0009933;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	CDS	62626425	62626620	.	+	0	Name=MGP_PahariEiJ_P0009933;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	CDS	62596855	62596942	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62596943	62596974	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62624028	62624354	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62626425	62626619	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62637350	62637435	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62640661	62640767	.	+	1	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62641047	62641178	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62641726	62641853	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62641962	62642214	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62651557	62651792	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62657151	62657339	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62660198	62660807	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62662196	62662302	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62663624	62663750	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62665452	62665636	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62668992	62669298	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62671284	62671360	.	+	2	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62671959	62672084	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62673959	62674159	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62678498	62678578	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62679703	62679807	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62683728	62683915	.	+	0	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62685194	62685509	.	+	1	Name=MGP_PahariEiJ_P0009934;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	CDS	62674016	62674159	.	+	0	Name=MGP_PahariEiJ_P0009938;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	CDS	62678498	62678578	.	+	0	Name=MGP_PahariEiJ_P0009938;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	CDS	62679703	62679807	.	+	0	Name=MGP_PahariEiJ_P0009938;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	CDS	62683728	62683915	.	+	0	Name=MGP_PahariEiJ_P0009938;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	CDS	62685194	62685509	.	+	1	Name=MGP_PahariEiJ_P0009938;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62596741	62596942	.	+	.	Name=MGP_PahariEiJ_E0009933.1;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	exon	62596943	62596974	.	+	.	Name=MGP_PahariEiJ_E0009933.2;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	exon	62624028	62624354	.	+	.	Name=MGP_PahariEiJ_E0009933.3;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	exon	62626425	62626623	.	+	.	Name=MGP_PahariEiJ_E0009933.4;Parent=MGP_PahariEiJ_T0009933.1
+13	Ensembl	exon	62596741	62596942	.	+	.	Name=MGP_PahariEiJ_E0009933.1;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62596943	62596974	.	+	.	Name=MGP_PahariEiJ_E0009933.2;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62624028	62624354	.	+	.	Name=MGP_PahariEiJ_E0009933.3;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62626425	62626619	.	+	.	Name=MGP_PahariEiJ_E0009934.4;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62637350	62637435	.	+	.	Name=MGP_PahariEiJ_E0009934.5;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62640661	62640767	.	+	.	Name=MGP_PahariEiJ_E0009934.6;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62641047	62641178	.	+	.	Name=MGP_PahariEiJ_E0009934.7;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62641726	62641853	.	+	.	Name=MGP_PahariEiJ_E0009934.8;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62641962	62642214	.	+	.	Name=MGP_PahariEiJ_E0009934.9;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62651557	62651792	.	+	.	Name=MGP_PahariEiJ_E0009934.10;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62657151	62657339	.	+	.	Name=MGP_PahariEiJ_E0009934.11;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62660198	62660807	.	+	.	Name=MGP_PahariEiJ_E0009934.12;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62662196	62662302	.	+	.	Name=MGP_PahariEiJ_E0009934.13;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62663624	62663750	.	+	.	Name=MGP_PahariEiJ_E0009934.14;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62665452	62665636	.	+	.	Name=MGP_PahariEiJ_E0009934.15;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62668992	62669298	.	+	.	Name=MGP_PahariEiJ_E0009934.16;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62671284	62671360	.	+	.	Name=MGP_PahariEiJ_E0009934.17;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62671959	62672084	.	+	.	Name=MGP_PahariEiJ_E0009934.18;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62673959	62674159	.	+	.	Name=MGP_PahariEiJ_E0009934.19;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62678498	62678578	.	+	.	Name=MGP_PahariEiJ_E0009934.20;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62679703	62679807	.	+	.	Name=MGP_PahariEiJ_E0009934.21;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62683728	62683915	.	+	.	Name=MGP_PahariEiJ_E0009934.22;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62685194	62686932	.	+	.	Name=MGP_PahariEiJ_E0009934.23;Parent=MGP_PahariEiJ_T0009934.1
+13	Ensembl	exon	62596766	62596974	.	+	.	Name=MGP_PahariEiJ_E0009935.1;Parent=MGP_PahariEiJ_T0009935.1
+13	Ensembl	exon	62624028	62625799	.	+	.	Name=MGP_PahariEiJ_E0009935.2;Parent=MGP_PahariEiJ_T0009935.1
+13	Ensembl	exon	62660839	62660878	.	+	.	Name=MGP_PahariEiJ_E0009936.1;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62662196	62662388	.	+	.	Name=MGP_PahariEiJ_E0009936.2;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62663624	62663750	.	+	.	Name=MGP_PahariEiJ_E0009936.3;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62665452	62665636	.	+	.	Name=MGP_PahariEiJ_E0009936.4;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62668992	62669298	.	+	.	Name=MGP_PahariEiJ_E0009936.5;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62671284	62671360	.	+	.	Name=MGP_PahariEiJ_E0009936.6;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62671959	62672084	.	+	.	Name=MGP_PahariEiJ_E0009936.7;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62673959	62674159	.	+	.	Name=MGP_PahariEiJ_E0009936.8;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62678498	62678578	.	+	.	Name=MGP_PahariEiJ_E0009936.9;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62679703	62679807	.	+	.	Name=MGP_PahariEiJ_E0009936.10;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62683728	62683915	.	+	.	Name=MGP_PahariEiJ_E0009936.11;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62685194	62686932	.	+	.	Name=MGP_PahariEiJ_E0009936.12;Parent=MGP_PahariEiJ_T0009936.1
+13	Ensembl	exon	62671962	62672084	.	+	.	Name=MGP_PahariEiJ_E0009937.1;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62674008	62674159	.	+	.	Name=MGP_PahariEiJ_E0009937.2;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62678498	62678578	.	+	.	Name=MGP_PahariEiJ_E0009936.9;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62679703	62679807	.	+	.	Name=MGP_PahariEiJ_E0009936.10;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62683728	62683915	.	+	.	Name=MGP_PahariEiJ_E0009936.11;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62685194	62686919	.	+	.	Name=MGP_PahariEiJ_E0009937.6;Parent=MGP_PahariEiJ_T0009937.1
+13	Ensembl	exon	62671962	62672084	.	+	.	Name=MGP_PahariEiJ_E0009937.1;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62674008	62674159	.	+	.	Name=MGP_PahariEiJ_E0009938.2;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62678498	62678578	.	+	.	Name=MGP_PahariEiJ_E0009934.20;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62679703	62679807	.	+	.	Name=MGP_PahariEiJ_E0009934.21;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62683728	62683915	.	+	.	Name=MGP_PahariEiJ_E0009934.22;Parent=MGP_PahariEiJ_T0009938.1
+13	Ensembl	exon	62685194	62686918	.	+	.	Name=MGP_PahariEiJ_E0009938.6;Parent=MGP_PahariEiJ_T0009938.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa	Thu Oct 31 08:16:51 2019 -0400
@@ -0,0 +1,99 @@
+>MGP_PahariEiJ_T0009933.1 cds chromosome:PAHARI_EIJ_v1.1:13:62596741:62626623:1 gene:MGP_PahariEiJ_G0008413.1 gene_biotype:polymorphic_pseudogene transcript_biotype:protein_coding gene_symbol:Atp10d description:ATPase, class V, type 10D [Source:MGI Symbol;Acc:MGI:2450125]
+AAGACAAATGGCTGGCTTGGAAGCGTAACTCTCACCGCCCTTTGGATCCCTGCTCGCTTC
+TCTTTTGGCACTTTGGGATCCGAGGTAACCATGCGGTGATGAGCGGCCCGGGAGGGACAG
+ATCACCTGAACCAGCCGGGTCTCCCTGCGTCTTGGACATGACTGAGCTTCTGCAGTGGGC
+CAGACATCACTGGCGTCGGCTGAGCCATGGGAGAACCCAGGGTGAAGATGAGAGGCCGTA
+CAACTACGCCTCCCTGCTGGCCTGTGGGGGCAAGTCCCCCCGGACCCCCAGGCCTGCAGG
+AAAGCACCGTGTCGTTATTCCTCACCTTCAGTGCTTCAGGGATGAGTACGAGAGGTTTTC
+TGGAACCTACGTGAATAACCGGATACGGACGACCAAGTACACACTCCTGAACTTTGTGCC
+AAGGAACTTATTTGAACAGTTTCACAGGGCTGCCAATTTATATTTCCTGTTCCTCGTGGT
+CCTGAACTGGGTGCCTTTGGTAGAAGCCTTCCAAAAGGAAATCACCATGCTGCCTCTGGT
+GGTGGTCCTCACAATTATTGCAATTAAAGATGGCTTGGAAGACTACCGGAAGTACAAAAT
+TGACAAGCAGATCAACAACTTAATAACCAAGGTTTACAGTAGG
+>MGP_PahariEiJ_T0009934.1 cds chromosome:PAHARI_EIJ_v1.1:13:62596741:62686932:1 gene:MGP_PahariEiJ_G0008413.1 gene_biotype:polymorphic_pseudogene transcript_biotype:polymorphic_pseudogene gene_symbol:Atp10d description:ATPase, class V, type 10D [Source:MGI Symbol;Acc:MGI:2450125]
+AAGACAAATGGCTGGCTTGGAAGCGTAACTCTCACCGCCCTTTGGATCCCTGCTCGCTTC
+TCTTTTGGCACTTTGGGATCCGAGGTAACCATGCGGTGATGAGCGGCCCGGGAGGGACAG
+ATCACCTGAACCAGCCGGGTCTCCCTGCGTCTTGGACATGACTGAGCTTCTGCAGTGGGC
+CAGACATCACTGGCGTCGGCTGAGCCATGGGAGAACCCAGGGTGAAGATGAGAGGCCGTA
+CAACTACGCCTCCCTGCTGGCCTGTGGGGGCAAGTCCCCCCGGACCCCCAGGCCTGCAGG
+AAAGCACCGTGTCGTTATTCCTCACCTTCAGTGCTTCAGGGATGAGTACGAGAGGTTTTC
+TGGAACCTACGTGAATAACCGGATACGGACGACCAAGTACACACTCCTGAACTTTGTGCC
+AAGGAACTTATTTGAACAGTTTCACAGGGCTGCCAATTTATATTTCCTGTTCCTCGTGGT
+CCTGAACTGGGTGCCTTTGGTAGAAGCCTTCCAAAAGGAAATCACCATGCTGCCTCTGGT
+GGTGGTCCTCACAATTATTGCAATTAAAGATGGCTTGGAAGACTACCGGAAGTACAAAAT
+TGACAAGCAGATCAACAACTTAATAACCAAGGTTTACAGTAGGACTCTGAAGTTGATCCT
+GAGAAGTTCTCCAGTAGGATAGAATGTGAAAGCCCAAACAATGACCTCAGCAGATTCCGA
+GGTTTCCTGGAACATGCCAATAAAGACCGTGTGGGCCTCAGCAAAGAGAATTTATTGCTC
+CGCGGGTGCACCATCAGAAACACAGAGGCTGTGGTGGGCATTGTGGTCTATGCAGGTCAT
+GAAACCAAAGCAATGCTGAACAACAGTGGGCCACGGTATAAGCGCAGTAAGTTAGAGAGA
+AGAGCAAATACAGACGTCCTCTGGTGTGTCCTGCTTCTGATCGTCATGTGCTTAACTGGT
+GCACTGGGTCACGGCATATGGCTGAGCAGGTATGAGAACATGCTCTTTTTTAACATCCCT
+GAGCCGGACGGACGTGTCCTATCACCTGTGCTGACTGGGTTCTATGTGTTCTGGACCATG
+ATCATCTTGCTGCAGGTCCTGATCCCCATTTCTCTCTACGTGTCCATTGAGATCGTGAAG
+CTGGGACAGATCTATTTCATCCAGAGCGATGTAGATTTCTACAACGAGAAAATGGATTCG
+ACCATTCAGTGCCGAGCCCTAAACATCACTGAGGACCTTGGGCAGATTCAATACCTCTTT
+TCTGATAAGACAGGAACCCTCACAGAGAATAAGATGGTGTTTCGGAGGTGCAGTGTAGCA
+GGGTTTGACTACTGCCATGAAGAAAACGCCAGGAGGCTCGAGTCCTATCAGGAAGCTGTC
+TCTGAAGAGGAGGAACGCGCAGACACTCTCGGCGGCTCCCTCAGCAACGTGGCGAGACCC
+AGAGCCCAGGGCTGCAGGACAGTTCACAGTGGGCTTCCGGGAAAACCCCCGGCTCACCTC
+TCCGGGAGCACCTCTGCTGTAGGAGACGCAGAAGGATCCGGGGAAGTGCCTCATTCCAGA
+CAGGCTGCCTTCAGTAGTCCCATGGAAACAGACGTGGTACCAGATACCAGACTTTTAGAC
+AAATTTAGCCAGATTACCCCTCAGCTGCTCACTGGACTGGATGGGACCTTGCAGAGCTCA
+TCACTGGAGACCTTGTACATCATGGACTTCTTTATTGCACTGGCAATTTGCAACACGGTG
+GTGGTTTCTGCCCCAAACCAACCTCGGCAAAAGATTGGGCTCTCCTCACTGGGTGGAATG
+CCCATCAAGTCCTTGGACGAGATTAAAAACATCTTCCAGAAATTGTCTGTCCGGAGATCA
+AGTTCACCATCCCTTGCCAGCGGGAAGGATTCATCCTCTGGGACTCCCTGTGCCTTTGTG
+AGCAGAATCTCTTTCTTTAGTCGACCAAAACTGTCACCTCCTATGGAGGACGAGTCTTCC
+CAAATGGATGAAATCCCCCAGGCCAGTAACTCAGCTTGCTGTACAGAAACGGAGGCACAA
+AACAGTGCCTTAGGACTCAGCGTCGGCTCCGCGGAAGCCCTAAATGGACCACCGCCCTTG
+GCTTCCAACCTGTGTTATGAGGCGGAGAGTCCAGATGAAGCAGCCTTGGTGTATGCCGCC
+AGAGCTTATCATTGCACTTTACAGTCTCGGACCCCAGAGCAGGTCATGGTGGAGTTTGCA
+GCTTTGGGCTCATTAACATTTCAACTCCTACACATCCTGCCCTTTGACTCAGTAAGGAAA
+AGAATGTCGGTGGTGGTCCGGCACCCTCTTTCCAAACAAGTCGTGGTGTATACAAAAGGC
+GCTGATTCCGTGATCATGGAGCTGCTGTCTATGGCTTCCTCGGATGGAACAAATCTGGAA
+GAACAACAGATGATAATAAGGGAGAGAACGCAGAGGCACCTGGACGAGTATGCCAGACGA
+GGGCTGCGCACTCTGTGTGTTGCAAAGAAGGTCATGAGTGACACGGAATATGCAGAGTGG
+CTGAGGAATCACTTCCTAGCTGAAACCAGCATTGACAACAGGGAGGAGCTGCTAGTTGAG
+TCTGCCATGAGACTAGAAAACAAACTCACGTTACTTGGTGCTACTGGCATTGAAGATCGT
+CTGCAGGAGGGGGTCCCTGAGTCTATAGAAGCCCTTCACCAAGCTGGCATCAAGATCTGG
+ATGCTGACAGGGGACAAGCAGGAGACAGCTGTCAACATAGCTTATGCATGCAGACTCCTG
+GAACCAGATGACAAGCTCTTCATCCTCAATACACAAAGTGAGGATGCCTGTGGGATGCTG
+ATGAGTGCAATTTTGGAAGAACTTCAGAAGAGAGCTCAGGTGTCTCCGGAGCTGGCATCA
+CCAAGAAAGAACTTTCCTCAGCCCCCTGACCCTCAGGGCCAGGGACGTGCGGGACTTGTT
+ATCACTGGGAAGAGCCTGGAGTTTGCCCTGCAGGAGAGTCTACAAAGACAGTTCCTTGAG
+CTGACTGCATGGTGCCAAGCTGTGATCTGCTGCCGAGCCACCCCCCTTCAAAAGAGTGAG
+GTGGTGAAATTGGTTCGAAACCATCTCCATGTGATGACCCTAGCCATTGGTGACGGTGCC
+AATGATGTTAGCATGATACAAGTGGCTGACATTGGGATCGGTGTCTCAGGTCAAGAAGGC
+ATGCAGGCTGTGATGGCCAGTGACTTCGCCATCTCTCAGTTCAGACATCTCAGCAAGCTT
+CTCCTCGTGCACGGGCACTGGTGTTACACCCGGCTCTCCAACATGATTCTCTATTTTTTC
+TACAAGAATGTGGCCTATGTGAATCTCCTTTTCTGGTACCAGTTCTTTTGTGGGTTTTCA
+GGAACATCGATGACTGACTACTGGGTGCTGATCTTCTTCAACCTCCTCTTCACATCTGTC
+CCCCCCATCATTTATGGCGTTTTGGAGAAAGATGTGTCAGCAGAGACCCTCCTGCAGCTG
+CCTGAACTTTACCGGAGTGGTCAGCGATCAGAGGAATACTTGCCCGTCACTTTCTGGATC
+ACCTTGTTGGATGCCTTTTATCAAAGCCTGGTCTGCTTCTTTGTGCCTTACTTTACCTAC
+CAGGGCTCTGACATTGACATCTTTACCTTTGGGAATCCCCTGAACACGGCGGCTCTGTTC
+ATCATTCTCCTCCACCTGGTGATCGAAAGCAAGAGTTTGACTTGGATCCACATGCTGGTC
+ATTGTTGGGAGCATCTTGTCCTACTTTTTCTTTGCCTTGGCTTTTGGAGCCTTATGTGTC
+ACTTGCAACCCACCCTCCAACCCCTACGGGATCATGCAGAAGCACATGCTAGACCCTGTG
+TTCTACTTAGTTTGTGTTCTTACAACCTTCGTAGCACTCCTGCCCAGGTTTGCCTACCGA
+GTTCTTCAGGGATCCATGTTTCCATCTCCAGTTCTCAGAGCCAAGTACTTTGACCGACTA
+CCTCCAGAGGAGAGAGCTGAAGCTCTCAAGAGGTGGAGAGGGACTGCAAAGATCAATCAC
+GTGGCATCTCAGCATGCCAGCCAATCAGCTGCTAAGTCAGGAAGACCCACGCCTGGGTCT
+TCTGCTGTCCTTGCAATGAAGACAGCAACAGTGCGTACTGTTGAGCAGAGCACATGTGAA
+ACTGCGCTAGACCATGGCTGCTCTGAACCTGGGGCCTCCAGGACGACTGGACCCTCAGCA
+AGT
+>MGP_PahariEiJ_T0009938.1 cds chromosome:PAHARI_EIJ_v1.1:13:62671962:62686918:1 gene:MGP_PahariEiJ_G0008413.1 gene_biotype:polymorphic_pseudogene transcript_biotype:protein_coding gene_symbol:Atp10d description:ATPase, class V, type 10D [Source:MGI Symbol;Acc:MGI:2450125]
+ATGACTGACTACTGGGTGCTGATCTTCTTCAACCTCCTCTTCACATCTGTCCCCCCCATC
+ATTTATGGCGTTTTGGAGAAAGATGTGTCAGCAGAGACCCTCCTGCAGCTGCCTGAACTT
+TACCGGAGTGGTCAGCGATCAGAGGAATACTTGCCCGTCACTTTCTGGATCACCTTGTTG
+GATGCCTTTTATCAAAGCCTGGTCTGCTTCTTTGTGCCTTACTTTACCTACCAGGGCTCT
+GACATTGACATCTTTACCTTTGGGAATCCCCTGAACACGGCGGCTCTGTTCATCATTCTC
+CTCCACCTGGTGATCGAAAGCAAGAGTTTGACTTGGATCCACATGCTGGTCATTGTTGGG
+AGCATCTTGTCCTACTTTTTCTTTGCCTTGGCTTTTGGAGCCTTATGTGTCACTTGCAAC
+CCACCCTCCAACCCCTACGGGATCATGCAGAAGCACATGCTAGACCCTGTGTTCTACTTA
+GTTTGTGTTCTTACAACCTTCGTAGCACTCCTGCCCAGGTTTGCCTACCGAGTTCTTCAG
+GGATCCATGTTTCCATCTCCAGTTCTCAGAGCCAAGTACTTTGACCGACTACCTCCAGAG
+GAGAGAGCTGAAGCTCTCAAGAGGTGGAGAGGGACTGCAAAGATCAATCACGTGGCATCT
+CAGCATGCCAGCCAATCAGCTGCTAAGTCAGGAAGACCCACGCCTGGGTCTTCTGCTGTC
+CTTGCAATGAAGACAGCAACAGTGCGTACTGTTGAGCAGAGCACATGTGAAACTGCGCTA
+GACCATGGCTGCTCTGAACCTGGGGCCTCCAGGACGACTGGACCCTCAGCAAGT
Binary file test-data/test5.sqlite has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6.fasta	Thu Oct 31 08:16:51 2019 -0400
@@ -0,0 +1,15 @@
+>MGP_PahariEiJ_T0009938.1_muspahari
+ATGACTGACTACTGGGTGCTGATCTTCTTCAACCTCCTCTTCACATCTGTCCCCCCCATC
+ATTTATGGCGTTTTGGAGAAAGATGTGTCAGCAGAGACCCTCCTGCAGCTGCCTGAACTT
+TACCGGAGTGGTCAGCGATCAGAGGAATACTTGCCCGTCACTTTCTGGATCACCTTGTTG
+GATGCCTTTTATCAAAGCCTGGTCTGCTTCTTTGTGCCTTACTTTACCTACCAGGGCTCT
+GACATTGACATCTTTACCTTTGGGAATCCCCTGAACACGGCGGCTCTGTTCATCATTCTC
+CTCCACCTGGTGATCGAAAGCAAGAGTTTGACTTGGATCCACATGCTGGTCATTGTTGGG
+AGCATCTTGTCCTACTTTTTCTTTGCCTTGGCTTTTGGAGCCTTATGTGTCACTTGCAAC
+CCACCCTCCAACCCCTACGGGATCATGCAGAAGCACATGCTAGACCCTGTGTTCTACTTA
+GTTTGTGTTCTTACAACCTTCGTAGCACTCCTGCCCAGGTTTGCCTACCGAGTTCTTCAG
+GGATCCATGTTTCCATCTCCAGTTCTCAGAGCCAAGTACTTTGACCGACTACCTCCAGAG
+GAGAGAGCTGAAGCTCTCAAGAGGTGGAGAGGGACTGCAAAGATCAATCACGTGGCATCT
+CAGCATGCCAGCCAATCAGCTGCTAAGTCAGGAAGACCCACGCCTGGGTCTTCTGCTGTC
+CTTGCAATGAAGACAGCAACAGTGCGTACTGTTGAGCAGAGCACATGTGAAACTGCGCTA
+GACCATGGCTGCTCTGAACCTGGGGCCTCCAGGACGACTGGACCCTCAGCAAGT
Binary file test-data/test6.sqlite has changed