diff --git a/tools/uniprotxml_downloader/macros.xml b/tools/uniprotxml_downloader/macros.xml
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index 000000000..92302116a
--- /dev/null
+++ b/tools/uniprotxml_downloader/macros.xml
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diff --git a/tools/uniprotxml_downloader/uniprotxml_downloader.py b/tools/uniprotxml_downloader/uniprotxml_downloader.py
index f125315de..83f0d7aa5 100755
--- a/tools/uniprotxml_downloader/uniprotxml_downloader.py
+++ b/tools/uniprotxml_downloader/uniprotxml_downloader.py
@@ -11,7 +11,7 @@
#
#------------------------------------------------------------------------------
"""
-import optparse
+import argparse
import re
import sys
from urllib import parse
@@ -20,7 +20,7 @@
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry
-DEFAULT_TIMEOUT = 5 # seconds
+DEFAULT_TIMEOUT = 3600 # seconds
retry_strategy = Retry(
total=5,
backoff_factor=2,
@@ -46,15 +46,17 @@ def send(self, request, **kwargs):
def __main__():
# Parse Command Line
- parser = optparse.OptionParser()
- parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
- parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs')
- parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
- parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
- parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format')
- parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
- parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
- (options, args) = parser.parse_args()
+ parser = argparse.ArgumentParser()
+ parser.add_argument('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
+ parser.add_argument('-c', '--column', dest='column', type=int, default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs')
+ parser.add_argument('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
+ parser.add_argument('-r', '--reviewed', dest='reviewed', choices=['yes', 'no'], help='Only uniprot reviewed entries (default: reviewed and unreviewed entries)')
+ parser.add_argument('-f', '--format', dest='format', choices=['xml', 'fasta', "tab"], default='xml', help='output format')
+ parser.add_argument('--columns', dest='columns', help='columns for tabular output')
+ parser.add_argument('--include', dest='include', choices=['yes', 'no'], default="no", help='Include isoforms in FASTA output')
+ parser.add_argument('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
+ parser.add_argument('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
+ options = parser.parse_args()
taxids = set(options.taxon)
if options.input:
with open(options.input, 'r') as inputFile:
@@ -72,30 +74,34 @@ def __main__():
dest_path = options.output
else:
dest_path = "uniprot_%s.xml" % '_'.join(taxids)
- reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
+ reviewed = "AND reviewed:%s" % options.reviewed if options.reviewed else ''
try:
url = 'https://www.uniprot.org/uniprot/'
- query = "%s%s" % (taxon_query, reviewed)
+ query = "(%s) %s" % (taxon_query, reviewed)
params = {'query': query, 'force': 'yes', 'format': options.format}
+ if options.format == "tab" and options.columns:
+ params['columns'] = options.columns
+ if options.format == "fasta":
+ params['include'] = options.include
if options.debug:
print("%s ? %s" % (url, params), file=sys.stderr)
data = parse.urlencode(params)
- print(f"Retrieving: {url+data}")
+ print(f"Retrieving: {url}?{data}")
adapter = TimeoutHTTPAdapter(max_retries=retry_strategy)
http = requests.Session()
http.mount("https://", adapter)
- response = http.post(url, data=params)
+ response = http.post(url, data=params, stream=True)
+ if response.encoding is None:
+ response.encoding = 'utf-8'
http.close()
with open(dest_path, 'w') as fh:
- fh.write(response.text)
+ for line in response.iter_lines(decode_unicode=True):
+ fh.write(line + "\n")
if options.format == 'xml':
with open(dest_path, 'r') as contents:
- while True:
- line = contents.readline()
+ for line in contents:
if options.debug:
print(line, file=sys.stderr)
- if line is None:
- break
if line.startswith('
download proteome as XML or fasta
+
+ macros.xml
+
requests
@@ -11,9 +14,6 @@
python '$__tool_directory__/uniprotxml_downloader.py'
#if $taxid.input_choice == 'common':
--taxon $taxid.organism
- #if $taxid.reviewed:
- --reviewed=$taxid.reviewed
- #end if
#elif $taxid.input_choice == 'taxids':
#for $id in $taxid.taxons.split(','):
-t '$id'
@@ -22,10 +22,31 @@ python '$__tool_directory__/uniprotxml_downloader.py'
--input='${taxid.taxon_file}'
--column=#echo int(str($taxid.column)) - 1#
#end if
---format $format
+#if $reviewed:
+ --reviewed=$reviewed
+#end if
+--format $output_cond.out_format
+#if $output_cond.out_format == 'tab'
+ --columns '$output_cond.columns'
+#else if $output_cond.out_format == 'fasta'
+ --include $output_cond.include
+#end if
--output '${proteome}'
+&& cp '$ext_config' 'galaxy.json'
]]>
+
+
+
@@ -41,17 +62,6 @@ python '$__tool_directory__/uniprotxml_downloader.py'
-
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