mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
94 lines
3.0 KiB
Python
94 lines
3.0 KiB
Python
import urllib, pkg_resources, os
|
|
pkg_resources.require( 'elementtree' )
|
|
from elementtree import ElementTree, ElementInclude
|
|
from xml.parsers.expat import ExpatError as XMLParseErrorThing
|
|
import sys
|
|
|
|
import pkg_resources
|
|
|
|
class GetListing:
|
|
def __init__( self, data ):
|
|
self.tree = ElementTree.parse( data )
|
|
self.root = self.tree.getroot()
|
|
ElementInclude.include(self.root)
|
|
|
|
def xml_text(self, name=None):
|
|
"""Returns the text inside an element"""
|
|
root = self.root
|
|
if name is not None:
|
|
# Try attribute first
|
|
val = root.get(name)
|
|
if val:
|
|
return val
|
|
# Then try as element
|
|
elem = root.find(name)
|
|
else:
|
|
elem = root
|
|
if elem is not None and elem.text:
|
|
text = ''.join(elem.text.splitlines())
|
|
return text.strip()
|
|
# No luck, return empty string
|
|
return ''
|
|
|
|
def dlcachefile( webenv, querykey, i, results ):
|
|
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]'
|
|
fp = urllib.urlopen( url )
|
|
search = GetListing( fp )
|
|
fp.close()
|
|
webenv = search.xml_text( 'WebEnv' )
|
|
querykey = search.xml_text( 'QueryKey' )
|
|
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&WebEnv=%s&query_key=%s&retstart=%d&retmax=%d' % ( webenv, querykey, i, results )
|
|
fp = urllib.urlopen( url )
|
|
cachefile = os.tmpfile()
|
|
for line in fp:
|
|
cachefile.write( line )
|
|
fp.close()
|
|
cachefile.flush()
|
|
cachefile.seek(0)
|
|
return cachefile
|
|
|
|
|
|
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]'
|
|
fp = urllib.urlopen( url )
|
|
results = GetListing( fp )
|
|
fp.close()
|
|
|
|
webenv = results.xml_text( 'WebEnv' )
|
|
querykey = results.xml_text( 'QueryKey' )
|
|
counts = int( results.xml_text( 'Count' ) )
|
|
results = 10000
|
|
found = 0
|
|
|
|
for i in range(0, counts + results, results):
|
|
rets = dict()
|
|
cache = dlcachefile( webenv, querykey, i, results )
|
|
try:
|
|
xmldoc = GetListing( cache )
|
|
except (IOError, XMLParseErrorThing):
|
|
cache = dlcachefile( webenv, querykey, i, results )
|
|
try:
|
|
xmldoc = GetListing( cache )
|
|
except (IOError, XMLParseErrorThing):
|
|
cache.close()
|
|
exit()
|
|
pass
|
|
finally:
|
|
cache.close()
|
|
entries = xmldoc.root.findall( 'DocSum' )
|
|
for entry in entries:
|
|
dbkey = None
|
|
children = entry.findall('Item')
|
|
for item in children:
|
|
rets[ item.get('Name') ] = item.text
|
|
if not rets['Caption'].startswith('NC_'):
|
|
continue
|
|
|
|
for ret in rets['Extra'].split('|'):
|
|
if not ret.startswith('NC_'):
|
|
continue
|
|
else:
|
|
dbkey = ret
|
|
break
|
|
if dbkey is not None:
|
|
print '\t'.join( [ dbkey, rets['Title'] ] )
|