# HG changeset patch
# User mvdbeek
# Date 1472116222 14400
# Node ID addfc494867e55bc0110e003c1a4d852f8855d80
# Parent 0738889ff4d2d818e93f8cfd5760de1c7ef1136f
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 0b08439873c2278b8116aba51b19718d0ef51482-dirty
diff -r 0738889ff4d2 -r addfc494867e data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Aug 18 07:34:44 2016 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py Thu Aug 25 05:10:22 2016 -0400
@@ -118,7 +118,7 @@
def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
unsorted_fh = open( unsorted_fasta_filename )
- sorted_fh = open( sorted_fasta_filename, 'wb+' )
+ sorted_fh = open( sorted_fasta_filename, 'w+' )
for name in sorted_names:
offset = fasta_offsets[ name ]
@@ -183,7 +183,7 @@
sorted_names = []
for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
sorted_names.append( id_repeat[ 'identifier' ] )
- handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector']
+ handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector']
if handle_not_listed.startswith( 'keep' ):
add_list = []
for name in current_order:
@@ -242,7 +242,7 @@
"""
UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
- COMPRESSED_EXTENSIONS = ['.tar.gz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
+ COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
email = params['param_dict']['__user_email__']
if not email:
@@ -256,7 +256,7 @@
ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
- ftp.close()
+ ftp.quit()
for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
for ext in COMPRESSED_EXTENSIONS:
@@ -328,7 +328,7 @@
def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
fasta_base_filename = "%s.fa" % sequence_id
fasta_filename = os.path.join( target_directory, fasta_base_filename )
- with open( fasta_filename, 'wb+' ) as fasta_writer:
+ with open( fasta_filename, 'w+' ) as fasta_writer:
if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
fasta_stream = fasta_stream[0]
diff -r 0738889ff4d2 -r addfc494867e data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Thu Aug 18 07:34:44 2016 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Thu Aug 25 05:10:22 2016 -0400
@@ -10,77 +10,68 @@
]]>
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
+
@@ -110,7 +101,7 @@
.. class:: infomark
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.