Mercurial > repos > earlhaminst > ensembl_get_sequences

diff get_genetree.py @ 5:0fa1d1cc417d draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author earlhaminst
date Thu, 31 Oct 2019 07:50:07 -0400
parents 4b7261f484bb
children 7af66c2b3831
line wrap: on
line diff
--- a/get_genetree.py	Fri Apr 13 09:43:51 2018 -0400
+++ b/get_genetree.py	Thu Oct 31 07:50:07 2019 -0400
@@ -18,10 +18,6 @@
                   choices=['protein', 'cdna', 'none'], default='protein',
                   help='The type of sequence to bring back. Setting it to none results in no sequence being returned')
 
-parser.add_option('-g', '--species', type='choice',
-                  choices=['ensembl', 'ensemblgenomes'], default='ensembl',
-                  help='Specify the genome databases for vertebrates and other eukaryotic species')
-
 parser.add_option('-a', '--aligned', type='choice', choices=['0', '1'],
                   default='0', help='Return the aligned string if true. Otherwise, return the original sequence (no insertions)')
 parser.add_option('-c', '--cigar_line', type='choice', choices=['0', '1'],
@@ -35,7 +31,7 @@
 if options.input is None:
     raise Exception('-i option must be specified')
 
-server = 'http://rest.%s.org' % options.species
+server = 'http://rest.ensembl.org'
 
 if options.id_type == 'gene_id':
     ext = 'genetree/member/id'