Mercurial > repos > gga > apollo_fetch_jbrowse

changeset 13:6905bb3ce9db draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:13:41 -0400
parents 30ea2be4a236
children b7c44671f012
files create_features_from_gff3.py export.py fetch_organism_jbrowse.py macros.xml test-data/create_org/output.json test-data/create_org/output2.json test-data/export/cdna.fa test-data/export/cds.fa test-data/export/pep.fa test-data/load_gff3/output.tsv test-data/load_gff3/output.txt
diffstat 11 files changed, 727 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/create_features_from_gff3.py	Fri Apr 24 09:03:01 2020 -0400
+++ b/create_features_from_gff3.py	Mon Jun 29 09:13:41 2020 -0400
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 import argparse
+import json
 import logging
 
 from apollo import accessible_organisms
@@ -16,6 +17,8 @@
     parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
     parser.add_argument('email', help='User Email')
     parser.add_argument('--source', help='URL where the input dataset can be found.')
+    parser.add_argument('--use_name', action='store_true', help='Use the given name instead of generating one.')
+    parser.add_argument('--disable_cds_recalculation', action='store_true', help='Disable CDS recalculation and instead use the one provided.')
     OrgOrGuess(parser)
 
     parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
@@ -42,4 +45,5 @@
     if not orgs:
         raise Exception("You do not have write permission on this organism")
 
-    wa.annotations.load_gff3(org_cn, args.gff3, args.source)
+    load_result = wa.annotations.load_gff3(org_cn, args.gff3, args.source, use_name=args.use_name, disable_cds_recalculation=args.disable_cds_recalculation)
+    print(json.dumps(load_result, indent=2))
--- a/export.py	Fri Apr 24 09:03:01 2020 -0400
+++ b/export.py	Mon Jun 29 09:13:41 2020 -0400
@@ -52,28 +52,28 @@
 
         uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
         if 'error' in uuid_gff or 'uuid' not in uuid_gff:
-            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_gff)
+            raise Exception("Apollo failed to prepare the GFF3 file for download: %s" % uuid_gff)
         args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))
 
         time.sleep(1)
 
         uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
         if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
-            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_vcf)
+            raise Exception("Apollo failed to prepare the VCF file for download: %s" % uuid_vcf)
         args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))
 
         time.sleep(1)
 
         uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna')
         if 'error' in uuid_fa or 'uuid' not in uuid_fa:
-            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
+            raise Exception("Apollo failed to prepare the cdna FASTA file for download: %s" % uuid_fa)
         args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
 
         time.sleep(1)
 
         uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds')
         if 'error' in uuid_fa or 'uuid' not in uuid_fa:
-            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
+            raise Exception("Apollo failed to prepare the cds FASTA file for download: %s" % uuid_fa)
         args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))
 
         time.sleep(1)
--- a/fetch_organism_jbrowse.py	Fri Apr 24 09:03:01 2020 -0400
+++ b/fetch_organism_jbrowse.py	Mon Jun 29 09:13:41 2020 -0400
@@ -57,7 +57,7 @@
 
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
+    parser = argparse.ArgumentParser(description='Script to fetch organism data dir from apollo')
     OrgOrGuess(parser)
     parser.add_argument('target_dir', help='Target directory')
     parser.add_argument('email', help='User Email')
--- a/macros.xml	Fri Apr 24 09:03:01 2020 -0400
+++ b/macros.xml	Mon Jun 29 09:13:41 2020 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@WRAPPER_VERSION@">4.2.1</token>
+  <token name="@WRAPPER_VERSION@">4.2.3</token>
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="4.2.1">apollo</requirement>
+      <requirement type="package" version="4.2.3">apollo</requirement>
       <yield/>
     </requirements>
   </xml>
--- a/test-data/create_org/output.json	Fri Apr 24 09:03:01 2020 -0400
+++ b/test-data/create_org/output.json	Mon Jun 29 09:13:41 2020 -0400
@@ -1,7 +1,7 @@
 {
   "commonName": "Test org",
   "blatdb": "/data/temporary/apollo_data/1384-Test_org/searchDatabaseData/genome.2bit",
-  "metadata": "{\"creator\":\"20\"}",
+  "metadata": "{\"creator\":\"xx\"}",
   "annotationCount": 0,
   "currentOrganism": true,
   "obsolete": false,
@@ -11,6 +11,6 @@
   "valid": true,
   "genus": "genus",
   "species": null,
-  "id": 23,
+  "id": "xx",
   "nonDefaultTranslationTable": null
 }
--- a/test-data/create_org/output2.json	Fri Apr 24 09:03:01 2020 -0400
+++ b/test-data/create_org/output2.json	Mon Jun 29 09:13:41 2020 -0400
@@ -1,7 +1,7 @@
 {
   "commonName": "Test org",
   "blatdb": "/data/temporary/apollo_data/1384-Test_org/searchDatabaseData/genome.2bit",
-  "metadata": "{\"creator\":\"20\"}",
+  "metadata": "{\"creator\":\"xx\"}",
   "annotationCount": 0,
   "currentOrganism": true,
   "obsolete": false,
@@ -11,6 +11,6 @@
   "valid": true,
   "genus": "genus2",
   "species": "sp",
-  "id": 23,
+  "id": "xx",
   "nonDefaultTranslationTable": null
 }
--- a/test-data/export/cdna.fa	Fri Apr 24 09:03:01 2020 -0400
+++ b/test-data/export/cdna.fa	Mon Jun 29 09:13:41 2020 -0400
@@ -1,4 +1,4 @@
->ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 690 residues [Merlin:2-691 + strand] [cdna] name=Unknown
+>df4157db-1481-4120-858c-e6a4c0f78547 (mRNA) 690 residues [Merlin:2-691 + strand] [cdna] name=Merlin_1_mRNA-00001
 CGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGAG
 CATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCCT
 CTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTAT
@@ -11,13 +11,13 @@
 CTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGAA
 TCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGAC
 ATTGATGACATGCCACGTAAGTTCCGCTAG
->f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 288 residues [Merlin:752-1039 + strand] [cdna] name=Unknown
+>eedd9b31-f1dd-487c-a3ab-6435b2214685 (mRNA) 288 residues [Merlin:752-1039 + strand] [cdna] name=mrna-name-00001
 ATGAAATCAATTTTTCGTATCAACGGTGTAGAAATTGTAGTTGAAGATGTAGTTCCTATG
 TCTTATGAATTCAATGAAGTTGTTTTCAAAGAGCTTAAGAAAATTTTAGGCGATAAGAAG
 CTTCAAAGTACTCCAATTGGACGTTTTGGAATGAAAGAAAACGTTGATACTTATATTGAA
 AGTGTAGTGACAGGGCAGTTAGAAGGTGAATTTTCTGTAGCAGTTCAAACTGTAGAAAAT
 GATGAAGTTATTTTAACTTTACCAGCTTTCGTAATTTTCCGCAAATAA
->12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 945 residues [Merlin:1067-2011 - strand] [cdna] name=Unknown
+>8cd6db6d-b818-4b65-b6f2-de79844a5641 (mRNA) 945 residues [Merlin:1067-2011 - strand] [cdna] name=Merlin_3_mRNA-00001
 ATGCTAACTTTAGATGAATTTAAAAACCAAGCGGGTAATATAGACTTTCAGCGTACTAAT
 ATGTTTAGTTGTGTATTTGCAACTACTCCGTCAGCAAAGTCTCAACAATTACTCGATCAA
 TTTGGCGGTATGCTCTTTAATAACCTTCCGTTGAATAATGACTGGCTTGGATTAACACAA
@@ -34,7 +34,7 @@
 GATTGGATTGAAGATAGAGCTGTTAATTCTATAACTGGAATTAATAGTGAAATGTCTCTT
 AATGGAAGTTTAAGTAGATTATCTAGACTTGGAGGAGCTGCTGGAGGGTTGTCTCACGTC
 ATTAATTCGACCCGAAACTCTACTTCGAAAATACTTGGATTGTAA
->58fc8255-95ed-4417-a373-238f826810ac (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cdna] name=Unknown
+>125a44c4-44da-4854-9d3b-ae2aa0221120 (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cdna] name=Merlin_4_mRNA-00001
 ATGAGCATTAAAGTCAGAGAATTAGATGATAAGACTGATGCTTTAATTAGCGGAGTTAAA
 ACCTCCGCTGGTCAAAGTTCACAATCAGCAAAAATAAAATCCACTATAACTGCGCAATAT
 CCGTCTGAACGTTCAGCTGGTAATGACACATCTGGTTCTTTACGAGTTCATGATCTTTAT
@@ -53,7 +53,7 @@
 TGTCAAATTCAGAGTATCCGTTTTGATAAAACTCCAAATGGAAACTTTAACGGTTTAGCT
 ATAGCTCCAAACCTGCCAAGTACATTCACATTAGAAATTACTATGCGTGAAATCTTGACA
 TTGAACCGAGCTTCAGTATATGCGGAAGGATTCTGA
->c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cdna] name=multiexongene
+>87414073-7db0-4a60-903f-5e3593e55884 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cdna] name=Merlin_5_mRNA-00001
 ATGAAAAGCGAAAACATGTCCACAATGAGACGTCGTAAAGTTATCGCTGATTCAAAGGGT
 GAAAGAGATGCAGCCTCGACTGCATCTGATCAAGTAGACTCTTTAGAATTAATCGGCCTT
 AAACTTGATGATGTACAAAGCGCTAATGAACTAGTTGCTGAAGTAATTGAAGAAAAGGGC
@@ -82,7 +82,7 @@
 AAAGCTGAAAATGCTAAAGAGCAATCTAAAAAATCAACCGGTGATATGAATGTTGCTAAC
 ACTCAGGTTAATAACGTAAATAATAGTAAGACTATTCACCAGGTTCAAACAGTCACGGCT
 ACTCCAGCTCCTGGAGTATTCGGGGCAACAGGAGTTAATTAA
->2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 1056 residues [Merlin:5011-6066 - strand] [cdna] name=cds-not-under-exon
+>1dcb3fc3-3307-4476-9c8a-04d252f9371f (mRNA) 1056 residues [Merlin:5011-6066 - strand] [cdna] name=Merlin_42_mRNA-00001
 CTTTAATGACGCTGGTGAATCAATAAAAGAGATGATCGGTGCAATTTATGAATCAAAACC
 TCTTATAGCACCTGCGATGAACACAATCAACACATATGTTCCTCGAGTTCCATGGACGAG
 TAACATAACTGAATACAAGAAATATGTTCGAGATGTTGCATTAGCAGTAGATAATGACCA
--- a/test-data/export/cds.fa	Fri Apr 24 09:03:01 2020 -0400
+++ b/test-data/export/cds.fa	Mon Jun 29 09:13:41 2020 -0400
@@ -1,4 +1,4 @@
->ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 690 residues [Merlin:2-691 + strand] [cds] name=Unknown
+>df4157db-1481-4120-858c-e6a4c0f78547 (mRNA) 690 residues [Merlin:2-691 + strand] [cds] name=Merlin_1_mRNA-00001
 CGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGAG
 CATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCCT
 CTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTAT
@@ -11,12 +11,30 @@
 CTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGAA
 TCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGAC
 ATTGATGACATGCCACGTAAGTTCCGCTAG
->f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 9 residues [Merlin:752-1039 + strand] [cds] name=Unknown
-AAATTTTAG
->12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 108 residues [Merlin:1067-2011 - strand] [cds] name=Unknown
-CACCTCAATTATCACTGCCGGTACTCAACAGCTGGTAAGAAAGTCTGGTGTATCGAAATA
-TCTTATTGGAGCAATGAGCAATCGTGTTGTTCAGTCTTTATTAGGTGA
->58fc8255-95ed-4417-a373-238f826810ac (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cds] name=Unknown
+>eedd9b31-f1dd-487c-a3ab-6435b2214685 (mRNA) 288 residues [Merlin:752-1039 + strand] [cds] name=mrna-name-00001
+ATGAAATCAATTTTTCGTATCAACGGTGTAGAAATTGTAGTTGAAGATGTAGTTCCTATG
+TCTTATGAATTCAATGAAGTTGTTTTCAAAGAGCTTAAGAAAATTTTAGGCGATAAGAAG
+CTTCAAAGTACTCCAATTGGACGTTTTGGAATGAAAGAAAACGTTGATACTTATATTGAA
+AGTGTAGTGACAGGGCAGTTAGAAGGTGAATTTTCTGTAGCAGTTCAAACTGTAGAAAAT
+GATGAAGTTATTTTAACTTTACCAGCTTTCGTAATTTTCCGCAAATAA
+>8cd6db6d-b818-4b65-b6f2-de79844a5641 (mRNA) 945 residues [Merlin:1067-2011 - strand] [cds] name=Merlin_3_mRNA-00001
+ATGCTAACTTTAGATGAATTTAAAAACCAAGCGGGTAATATAGACTTTCAGCGTACTAAT
+ATGTTTAGTTGTGTATTTGCAACTACTCCGTCAGCAAAGTCTCAACAATTACTCGATCAA
+TTTGGCGGTATGCTCTTTAATAACCTTCCGTTGAATAATGACTGGCTTGGATTAACACAA
+GGTGAGTTCACATCAGGACTCACCTCAATTATCACTGCCGGTACTCAACAGCTGGTAAGA
+AAGTCTGGTGTATCGAAATATCTTATTGGAGCAATGAGCAATCGTGTTGTTCAGTCTTTA
+TTAGGTGAATTTGAAGTCGGAACTTATTTGTTAGACTTCTTTAACATGGCTTATCCGCAA
+TCTGGATTGATGATTTATTCGGTCAAAATTCCAGAGAACAGATTGTCTCATGAAATGGAT
+TTCAACCATAACTCACCGAATATTAGAATAACTGGACGTGAACTCGATCCGTTAACTATA
+TCATTCAGAATGGATCCCGAAGCAAGTAACTATCGTGCAATGCAAGATTGGGTGAACTCC
+GTTCAAGACCCGGTTACTGGATTGCGAGCATTACCAACTGACGTCGAAGCTGACATTCAG
+GTTAACCTTCATGCTCGAAATGGATTACCTCATACTGTGATAATGTTCACAGGTTGTGTT
+CCTGTTGCGTGTGGAGCTCCTGAGCTTACATATGAAGGAGATAACCAAATTGCGGTTTTC
+GATGTTACATTTGCTTACAGAGTAATGCAAACGGGTGCTGTTGGACGTCAAGCTGCTCTT
+GATTGGATTGAAGATAGAGCTGTTAATTCTATAACTGGAATTAATAGTGAAATGTCTCTT
+AATGGAAGTTTAAGTAGATTATCTAGACTTGGAGGAGCTGCTGGAGGGTTGTCTCACGTC
+ATTAATTCGACCCGAAACTCTACTTCGAAAATACTTGGATTGTAA
+>125a44c4-44da-4854-9d3b-ae2aa0221120 (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cds] name=Merlin_4_mRNA-00001
 ATGAGCATTAAAGTCAGAGAATTAGATGATAAGACTGATGCTTTAATTAGCGGAGTTAAA
 ACCTCCGCTGGTCAAAGTTCACAATCAGCAAAAATAAAATCCACTATAACTGCGCAATAT
 CCGTCTGAACGTTCAGCTGGTAATGACACATCTGGTTCTTTACGAGTTCATGATCTTTAT
@@ -35,7 +53,7 @@
 TGTCAAATTCAGAGTATCCGTTTTGATAAAACTCCAAATGGAAACTTTAACGGTTTAGCT
 ATAGCTCCAAACCTGCCAAGTACATTCACATTAGAAATTACTATGCGTGAAATCTTGACA
 TTGAACCGAGCTTCAGTATATGCGGAAGGATTCTGA
->c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cds] name=multiexongene
+>87414073-7db0-4a60-903f-5e3593e55884 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cds] name=Merlin_5_mRNA-00001
 ATGAAAAGCGAAAACATGTCCACAATGAGACGTCGTAAAGTTATCGCTGATTCAAAGGGT
 GAAAGAGATGCAGCCTCGACTGCATCTGATCAAGTAGACTCTTTAGAATTAATCGGCCTT
 AAACTTGATGATGTACAAAGCGCTAATGAACTAGTTGCTGAAGTAATTGAAGAAAAGGGC
@@ -64,5 +82,17 @@
 AAAGCTGAAAATGCTAAAGAGCAATCTAAAAAATCAACCGGTGATATGAATGTTGCTAAC
 ACTCAGGTTAATAACGTAAATAATAGTAAGACTATTCACCAGGTTCAAACAGTCACGGCT
 ACTCCAGCTCCTGGAGTATTCGGGGCAACAGGAGTTAATTAA
->2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 6 residues [Merlin:5011-6066 - strand] [cds] name=cds-not-under-exon
-CTTTAA
+>1dcb3fc3-3307-4476-9c8a-04d252f9371f (mRNA) 777 residues [Merlin:5011-6066 - strand] [cds] name=Merlin_42_mRNA-00001
+TTTAATGACGCTGGTGAATCAATAAAAGAGATGATCGGTGCAATTTATGAATCAAAACCT
+CTTATAGCACCTGCGATGAACACAATCAACACATATGTTCCTCGAGTTCCATGGACGAGT
+AACATAACTGAATACAAGAAATATGTTCGAGATGTTGCATTAGCAGTAGATAATGACCAA
+TTCGTTTTTGTATGGGAAGATATCTATGGCTTGAACATGATGGATTATGACGCAATGATT
+AACCAAGAATCAATCAAGGTTATTGTCGGTGAACCACGCACAATAGGTCAATTTGTCGGT
+GAGCTGGAATATAATCTCGCTTATGACTTCCAGTGGTTAACGAAGGCTAATGCCCATACA
+CGCGATCCTATTTTTAACGCTACAATCTATTCACACTCATTCTTGGATAATAACCTTCCT
+AGAATAGTAACAGGTGATGGACAGAATAGCATCTTCGTTTCTCGCTCGGGTGCATATTCT
+GAAATGACTTATCGAAATGGATATGAAGAAGCTATCAGGCTTCAGACTATGGCACAATAC
+GACGGTTATGCAACTTGTAAAATGGTTGGAGACTTTGAAATGACTCCTGGAGATAAGATT
+AATTTCTTTGATCCAAAGAAACAATTCAAAGCTGATTTTTACATTGATGAAGTAATTCAT
+GAAGTAAGTAATAACCAAAGCATAACTACACTTTATATGTTTACTAACTCTCGTAAGTTG
+GAAACAGTAGAACCAATAAAGGTTAAAAATGAACTTAAATCTGATACTACCACTTAA
--- a/test-data/export/pep.fa	Fri Apr 24 09:03:01 2020 -0400
+++ b/test-data/export/pep.fa	Mon Jun 29 09:13:41 2020 -0400
@@ -1,20 +1,26 @@
->ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 229 residues [Merlin:2-691 + strand] [peptide] name=Unknown
+>df4157db-1481-4120-858c-e6a4c0f78547 (mRNA) 229 residues [Merlin:2-691 + strand] [peptide] name=Merlin_1_mRNA-00001
 RLDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIY
 TAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIV
 PGSLTEYPEEAEVILPRGTLLKINKITTQVDKRSNKFMVEGSIVPPSEQIDESVEIYDGD
 LFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR
->f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 2 residues [Merlin:752-1039 + strand] [peptide] name=Unknown
-KF
->12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 35 residues [Merlin:1067-2011 - strand] [peptide] name=Unknown
-HLNYHCRYSTAGKKVWCIEISYWSNEQSCCSVFIR
->58fc8255-95ed-4417-a373-238f826810ac (mRNA) 351 residues [Merlin:2011-3066 - strand] [peptide] name=Unknown
+>eedd9b31-f1dd-487c-a3ab-6435b2214685 (mRNA) 95 residues [Merlin:752-1039 + strand] [peptide] name=mrna-name-00001
+MKSIFRINGVEIVVEDVVPMSYEFNEVVFKELKKILGDKKLQSTPIGRFGMKENVDTYIE
+SVVTGQLEGEFSVAVQTVENDEVILTLPAFVIFRK
+>8cd6db6d-b818-4b65-b6f2-de79844a5641 (mRNA) 314 residues [Merlin:1067-2011 - strand] [peptide] name=Merlin_3_mRNA-00001
+MLTLDEFKNQAGNIDFQRTNMFSCVFATTPSAKSQQLLDQFGGMLFNNLPLNNDWLGLTQ
+GEFTSGLTSIITAGTQQLVRKSGVSKYLIGAMSNRVVQSLLGEFEVGTYLLDFFNMAYPQ
+SGLMIYSVKIPENRLSHEMDFNHNSPNIRITGRELDPLTISFRMDPEASNYRAMQDWVNS
+VQDPVTGLRALPTDVEADIQVNLHARNGLPHTVIMFTGCVPVACGAPELTYEGDNQIAVF
+DVTFAYRVMQTGAVGRQAALDWIEDRAVNSITGINSEMSLNGSLSRLSRLGGAAGGLSHV
+INSTRNSTSKILGL
+>125a44c4-44da-4854-9d3b-ae2aa0221120 (mRNA) 351 residues [Merlin:2011-3066 - strand] [peptide] name=Merlin_4_mRNA-00001
 MSIKVRELDDKTDALISGVKTSAGQSSQSAKIKSTITAQYPSERSAGNDTSGSLRVHDLY
 KNGLLFTAYDMNSRTTGDMRSMRLGEMKRTANSVVKSITGTNTNKVDKIPVVNILLPRSK
 SDVESVSHKFNDVGDSLISRGGGTATGVLSNVASTAVFGGLESLTQGLMADHNEQIYNTA
 RSMYGGADNRTKVFTWDLTPRSVQDLIAIIEIYEYFNYYSYGETGTSTYAKEVKSQLDEW
 YKSTFLDTLTPDEANKNDTVFEKITSFLSNVIVVSNPTVWFVRNFGTTSKFDGRAEVFGP
 CQIQSIRFDKTPNGNFNGLAIAPNLPSTFTLEITMREILTLNRASVYAEGF
->c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 553 residues [Merlin:3066-4796 - strand] [peptide] name=multiexongene
+>87414073-7db0-4a60-903f-5e3593e55884 (mRNA) 553 residues [Merlin:3066-4796 - strand] [peptide] name=Merlin_5_mRNA-00001
 MKSENMSTMRRRKVIADSKGERDAASTASDQVDSLELIGLKLDDVQSANELVAEVIEEKG
 NNLIDSVDNVAEGTELAAEASERTTESIKTLTGVASTISDKLSKLASMLESKVQAVEQKV
 QESGASASTGLSVIEDKLPDPDEPFFPPVPQEPENNKKDQKKDDKKPTDMLGDLLKTTKG
@@ -25,5 +31,9 @@
 YIGDVDPENPTNMQSLEKAYNSAKKSISDSAISDQPATKKELDKRFQRVESKYQKLKEDN
 TPKPAAPATSEDNQRVQNIQKAENAKEQSKKSTGDMNVANTQVNNVNNSKTIHQVQTVTA
 TPAPGVFGATGVN
->2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 1 residues [Merlin:5011-6066 - strand] [peptide] name=cds-not-under-exon
-L
+>1dcb3fc3-3307-4476-9c8a-04d252f9371f (mRNA) 258 residues [Merlin:5011-6066 - strand] [peptide] name=Merlin_42_mRNA-00001
+FNDAGESIKEMIGAIYESKPLIAPAMNTINTYVPRVPWTSNITEYKKYVRDVALAVDNDQ
+FVFVWEDIYGLNMMDYDAMINQESIKVIVGEPRTIGQFVGELEYNLAYDFQWLTKANAHT
+RDPIFNATIYSHSFLDNNLPRIVTGDGQNSIFVSRSGAYSEMTYRNGYEEAIRLQTMAQY
+DGYATCKMVGDFEMTPGDKINFFDPKKQFKADFYIDEVIHEVSNNQSITTLYMFTNSRKL
+ETVEPIKVKNELKSDTTT
--- a/test-data/load_gff3/output.tsv	Fri Apr 24 09:03:01 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# Feature ID	Apollo ID	Success	Messages
-Merlin_1	a036ab4f-512d-45e3-b19e-1fe83984a185	success
-Merlin_2	4a3f5c6b-03fc-43d1-8d6d-1a7075931cc6	success
-Merlin_3	de819682-eb71-4b98-a532-032d59354b95	success
-Merlin_4	423ca5cc-d570-4ae8-8527-6a52e0a6862b	success
-Merlin_5	f1b5327d-79ca-40f0-b4b3-90ea03d79a56	success
-Merlin_42	3629a7fe-03bb-420d-85d3-f23e55430abd	success
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/load_gff3/output.txt	Mon Jun 29 09:13:41 2020 -0400
@@ -0,0 +1,646 @@
+{
+  "Merlin_1_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "Merlin_1_mRNA",
+    "uniquename": "d33cb6e8-0809-442f-84ff-015aff163846",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039041,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "Merlin_1_mRNA-00001",
+        "uniquename": "d33cb6e8-0809-442f-84ff-015aff163846-CDS",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039071,
+        "sequence": "Merlin",
+        "parent_id": "d33cb6e8-0809-442f-84ff-015aff163846",
+        "name": "d33cb6e8-0809-442f-84ff-015aff163846-CDS",
+        "location": {
+          "strand": 1,
+          "is_fmin_partial": true,
+          "id": 459,
+          "fmin": 1,
+          "fmax": 691
+        },
+        "id": 458,
+        "properties": [],
+        "date_last_modified": 1593424039095
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_1_mRNA-00001",
+        "uniquename": "0356ce47-8746-4557-9f45-2b08625ebc63",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039029,
+        "sequence": "Merlin",
+        "parent_id": "d33cb6e8-0809-442f-84ff-015aff163846",
+        "name": "0356ce47-8746-4557-9f45-2b08625ebc63",
+        "location": {
+          "strand": 1,
+          "id": 455,
+          "fmin": 1,
+          "fmax": 691
+        },
+        "id": 454,
+        "properties": [],
+        "date_last_modified": 1593424039078
+      }
+    ],
+    "parent_id": "436dee83-9e76-44c3-94a8-37ac15c57e8e",
+    "name": "Merlin_1_mRNA-00001",
+    "location": {
+      "strand": 1,
+      "id": 453,
+      "fmin": 1,
+      "fmax": 691
+    },
+    "id": 452,
+    "properties": [],
+    "date_last_modified": 1593424039249
+  },
+  "Merlin_2_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "mrna-name",
+    "uniquename": "d5d0e6eb-458d-4402-b2ee-c19e4c1e0666",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039315,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "mrna-name-00001",
+        "uniquename": "d5d0e6eb-458d-4402-b2ee-c19e4c1e0666-CDS",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039321,
+        "sequence": "Merlin",
+        "parent_id": "d5d0e6eb-458d-4402-b2ee-c19e4c1e0666",
+        "name": "d5d0e6eb-458d-4402-b2ee-c19e4c1e0666-CDS",
+        "location": {
+          "strand": 1,
+          "id": 471,
+          "fmin": 751,
+          "fmax": 1039
+        },
+        "id": 470,
+        "properties": [],
+        "date_last_modified": 1593424039334
+      },
+      {
+        "owner": "None",
+        "parent_name": "mrna-name-00001",
+        "uniquename": "46e2b6ce-5cf2-4472-b858-9535a374f535",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039312,
+        "sequence": "Merlin",
+        "parent_id": "d5d0e6eb-458d-4402-b2ee-c19e4c1e0666",
+        "name": "46e2b6ce-5cf2-4472-b858-9535a374f535",
+        "location": {
+          "strand": 1,
+          "id": 467,
+          "fmin": 751,
+          "fmax": 1039
+        },
+        "id": 466,
+        "properties": [],
+        "date_last_modified": 1593424039328
+      }
+    ],
+    "parent_id": "9d2661e7-c095-426e-a9ce-0e0f9d68c1ca",
+    "name": "mrna-name-00001",
+    "location": {
+      "strand": 1,
+      "id": 465,
+      "fmin": 751,
+      "fmax": 1039
+    },
+    "id": 464,
+    "properties": [],
+    "date_last_modified": 1593424039356
+  },
+  "Merlin_3_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "Merlin_3_mRNA",
+    "uniquename": "c1e84840-7b7e-4c45-b044-e6ffaa89cb5d",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039392,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "Merlin_3_mRNA-00001",
+        "uniquename": "3fc60774-85c1-4cbd-aca3-1a1a74a2cbf3",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039390,
+        "sequence": "Merlin",
+        "parent_id": "c1e84840-7b7e-4c45-b044-e6ffaa89cb5d",
+        "name": "3fc60774-85c1-4cbd-aca3-1a1a74a2cbf3",
+        "location": {
+          "strand": -1,
+          "id": 479,
+          "fmin": 1066,
+          "fmax": 2011
+        },
+        "id": 478,
+        "properties": [],
+        "date_last_modified": 1593424039410
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_3_mRNA-00001",
+        "uniquename": "c1e84840-7b7e-4c45-b044-e6ffaa89cb5d-CDS",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039403,
+        "sequence": "Merlin",
+        "parent_id": "c1e84840-7b7e-4c45-b044-e6ffaa89cb5d",
+        "name": "c1e84840-7b7e-4c45-b044-e6ffaa89cb5d-CDS",
+        "location": {
+          "strand": -1,
+          "id": 483,
+          "fmin": 1066,
+          "fmax": 2011
+        },
+        "id": 482,
+        "properties": [],
+        "date_last_modified": 1593424039416
+      }
+    ],
+    "parent_id": "6a3cfa63-9957-44c2-855e-8914d14c6773",
+    "name": "Merlin_3_mRNA-00001",
+    "location": {
+      "strand": -1,
+      "id": 477,
+      "fmin": 1066,
+      "fmax": 2011
+    },
+    "id": 476,
+    "properties": [],
+    "date_last_modified": 1593424039439
+  },
+  "Merlin_4_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "Merlin_4_mRNA",
+    "uniquename": "4b3f4451-6feb-4a89-85ee-002c03679c4b",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039555,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "Merlin_4_mRNA-00001",
+        "uniquename": "4b3f4451-6feb-4a89-85ee-002c03679c4b-CDS",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039563,
+        "sequence": "Merlin",
+        "parent_id": "4b3f4451-6feb-4a89-85ee-002c03679c4b",
+        "name": "4b3f4451-6feb-4a89-85ee-002c03679c4b-CDS",
+        "location": {
+          "strand": -1,
+          "id": 503,
+          "fmin": 2010,
+          "fmax": 3066
+        },
+        "id": 502,
+        "properties": [],
+        "date_last_modified": 1593424039575
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_4_mRNA-00001",
+        "uniquename": "4322d1af-5aa0-4777-9bd2-20d87b807d1e",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039553,
+        "sequence": "Merlin",
+        "parent_id": "4b3f4451-6feb-4a89-85ee-002c03679c4b",
+        "name": "4322d1af-5aa0-4777-9bd2-20d87b807d1e",
+        "location": {
+          "strand": -1,
+          "id": 499,
+          "fmin": 2010,
+          "fmax": 3066
+        },
+        "id": 498,
+        "properties": [],
+        "date_last_modified": 1593424039569
+      }
+    ],
+    "parent_id": "71eafcd2-8ef6-4a71-88c2-bcac2f342e28",
+    "name": "Merlin_4_mRNA-00001",
+    "location": {
+      "strand": -1,
+      "id": 497,
+      "fmin": 2010,
+      "fmax": 3066
+    },
+    "id": 496,
+    "properties": [],
+    "date_last_modified": 1593424039596
+  },
+  "Merlin_5_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "Merlin_5_mRNA",
+    "uniquename": "19b80336-a138-4276-96e1-116a7787afe8",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039700,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "Merlin_5_mRNA-00001",
+        "uniquename": "19b80336-a138-4276-96e1-116a7787afe8-non_canonical_five_prime_splice_site-4363",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "non_canonical_five_prime_splice_site"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039756,
+        "sequence": "Merlin",
+        "parent_id": "19b80336-a138-4276-96e1-116a7787afe8",
+        "name": "19b80336-a138-4276-96e1-116a7787afe8-non_canonical_five_prime_splice_site-4363",
+        "location": {
+          "strand": -1,
+          "id": 532,
+          "fmin": 4363,
+          "fmax": 4363
+        },
+        "id": 531,
+        "properties": [],
+        "date_last_modified": 1593424039803
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_5_mRNA-00001",
+        "uniquename": "19b80336-a138-4276-96e1-116a7787afe8-non_canonical_three_prime_splice_site-4296",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "non_canonical_three_prime_splice_site"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039767,
+        "sequence": "Merlin",
+        "parent_id": "19b80336-a138-4276-96e1-116a7787afe8",
+        "name": "19b80336-a138-4276-96e1-116a7787afe8-non_canonical_three_prime_splice_site-4296",
+        "location": {
+          "strand": -1,
+          "id": 535,
+          "fmin": 4296,
+          "fmax": 4296
+        },
+        "id": 534,
+        "properties": [],
+        "date_last_modified": 1593424039804
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_5_mRNA-00001",
+        "uniquename": "f192c0c8-c043-474a-9cba-fe593340a28f",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039691,
+        "sequence": "Merlin",
+        "parent_id": "19b80336-a138-4276-96e1-116a7787afe8",
+        "name": "f192c0c8-c043-474a-9cba-fe593340a28f",
+        "location": {
+          "strand": -1,
+          "id": 522,
+          "fmin": 3065,
+          "fmax": 4296
+        },
+        "id": 521,
+        "properties": [],
+        "date_last_modified": 1593424039696
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_5_mRNA-00001",
+        "uniquename": "31a23617-42b1-4bf1-a65d-45eccdd17e8e",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039699,
+        "sequence": "Merlin",
+        "parent_id": "19b80336-a138-4276-96e1-116a7787afe8",
+        "name": "31a23617-42b1-4bf1-a65d-45eccdd17e8e",
+        "location": {
+          "strand": -1,
+          "id": 525,
+          "fmin": 4365,
+          "fmax": 4796
+        },
+        "id": 524,
+        "properties": [],
+        "date_last_modified": 1593424039716
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_5_mRNA-00001",
+        "uniquename": "19b80336-a138-4276-96e1-116a7787afe8-CDS",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039710,
+        "sequence": "Merlin",
+        "parent_id": "19b80336-a138-4276-96e1-116a7787afe8",
+        "name": "19b80336-a138-4276-96e1-116a7787afe8-CDS",
+        "location": {
+          "strand": -1,
+          "id": 529,
+          "fmin": 3065,
+          "fmax": 4796
+        },
+        "id": 528,
+        "properties": [],
+        "date_last_modified": 1593424039722
+      }
+    ],
+    "parent_id": "f380f7b1-2b7d-45cd-8d0b-2519b1b0afee",
+    "name": "Merlin_5_mRNA-00001",
+    "location": {
+      "strand": -1,
+      "id": 520,
+      "fmin": 3065,
+      "fmax": 4796
+    },
+    "id": 519,
+    "properties": [],
+    "date_last_modified": 1593424039810
+  },
+  "Merlin_42_mRNA": {
+    "owner": "admin@local.host",
+    "parent_name": "Merlin_42_mRNA",
+    "uniquename": "0e34cfa5-6f64-4111-9c2f-37655f6f1b92",
+    "type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "mRNA"
+    },
+    "parent_type": {
+      "cv": {
+        "name": "sequence"
+      },
+      "name": "gene"
+    },
+    "date_creation": 1593424039850,
+    "sequence": "Merlin",
+    "children": [
+      {
+        "owner": "None",
+        "parent_name": "Merlin_42_mRNA-00001",
+        "uniquename": "6596e6e2-a894-4c0b-98c1-298c65f0c021",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "exon"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039841,
+        "sequence": "Merlin",
+        "parent_id": "0e34cfa5-6f64-4111-9c2f-37655f6f1b92",
+        "name": "6596e6e2-a894-4c0b-98c1-298c65f0c021",
+        "location": {
+          "strand": -1,
+          "id": 543,
+          "fmin": 5010,
+          "fmax": 6066
+        },
+        "id": 542,
+        "properties": [],
+        "date_last_modified": 1593424039847
+      },
+      {
+        "owner": "None",
+        "parent_name": "Merlin_42_mRNA-00001",
+        "uniquename": "a42c4166-5211-49b9-9110-e5fd41c9d2cb",
+        "type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "CDS"
+        },
+        "parent_type": {
+          "cv": {
+            "name": "sequence"
+          },
+          "name": "mRNA"
+        },
+        "date_creation": 1593424039849,
+        "sequence": "Merlin",
+        "parent_id": "0e34cfa5-6f64-4111-9c2f-37655f6f1b92",
+        "name": "a42c4166-5211-49b9-9110-e5fd41c9d2cb",
+        "location": {
+          "strand": -1,
+          "id": 546,
+          "fmin": 5288,
+          "fmax": 6065,
+          "is_fmax_partial": true
+        },
+        "id": 545,
+        "properties": [],
+        "date_last_modified": 1593424039867
+      }
+    ],
+    "parent_id": "f7843db6-26da-44f9-ae05-6bb92ca573f6",
+    "name": "Merlin_42_mRNA-00001",
+    "location": {
+      "strand": -1,
+      "id": 541,
+      "fmin": 5010,
+      "fmax": 6066
+    },
+    "id": 540,
+    "properties": [],
+    "date_last_modified": 1593424039879
+  }
+}