Mercurial > repos > earlhaminst > ensembl_get_sequences

diff get_sequences.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
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line diff
--- a/get_sequences.py	Fri Apr 13 09:43:51 2018 -0400
+++ b/get_sequences.py	Thu Oct 31 07:50:07 2019 -0400
@@ -12,10 +12,6 @@
 parser = optparse.OptionParser()
 parser.add_option('-i', '--input', help='List of Ensembl IDs')
 
-parser.add_option('-s', '--species', type='choice',
-                  choices=['ensembl', 'ensemblgenomes'], default='ensembl',
-                  help='Specify the genome databases for vertebrates and other eukaryotic species')
-
 parser.add_option('-t', '--type', type='choice',
                   choices=['genomic', 'cds', 'cdna', 'protein'],
                   default='genomic', help='Type of sequence')
@@ -27,7 +23,7 @@
 if options.input is None:
     raise Exception('-i option must be specified')
 
-server = 'http://rest.%s.org' % options.species
+server = 'http://rest.ensembl.org'
 ext = 'sequence/id'
 
 headers = {'Content-Type': 'text/x-fasta', 'Accept': 'text/x-fasta'}