def get(self, gi):
"""
Look up genbank records by their GI
"""
taxonomyFileName = os.path.join(self.options.dbcache, gi + ".tax")
fastaFileName = os.path.join(self.options.dbcache, gi + ".fasta")
if (os.path.exists(taxonomyFileName)
and os.path.getsize(taxonomyFileName) != 0
and os.path.exists(fastaFileName)
and os.path.getsize(fastaFileName) != 0):
retrievalStatus = "(c)"
taxonomy = utils.safeReadTaxonomyCache(taxonomyFileName)
sequence = utils.safeReadFastaCache(fastaFileName)
else:
retrievalStatus = "(d)"
taxonXref = None
seqLength = None
successful = False
for tries in range(10):
try:
Entrez.email = self.options.email
Entrez.tool = 'sapwebserver'
fp = Entrez.efetch(db="nucleotide", id=gi, retmode="xml")
# Get the cross ref to the taxonomy database:
taxonXrefRE = re.compile(
"<GBQualifier_value>taxon:(\d+)</GBQualifier_value>")
seqLengthRE = re.compile(
"<GBSeq_length>(\d+)</GBSeq_length>")
sequenceRE = re.compile(
"<GBSeq_sequence>([a-zA-Z]+)</GBSeq_sequence>")
taxonXref = None
seqLength = None
sequence = None
while taxonXref is None or sequence is None:
line = fp.readline()
if not line:
break
taxonMatch = taxonXrefRE.search(line)
lengthMatch = seqLengthRE.search(line)
sequenceMatch = sequenceRE.search(line)
if taxonMatch:
if taxonXref is None:
taxonXref = taxonMatch.group(1)
# else:
# print "There was more than one taxon xref for %s. Picking the first one (%s)." % (gi, taxonXref)
if lengthMatch:
seqLength = lengthMatch.group(1)
if sequenceMatch:
sequence = sequenceMatch.group(1)
if not (taxonXref and sequence):
# Give it another try:
continue
except KeyboardInterrupt:
sys.exit()
except MemoryError:
# Write an empty file to cache to keep the script from
# trying to download the sequence next time.
utils.writeFile(fastaFileName, '')
return None, retrievalStatus.replace(")", "!M)")
except:
## print ' retrieving failed - retrying'
time.sleep(tries * 5)
continue
else:
successful = True
fp.close()
break
if not successful:
return None, retrievalStatus.replace(")", "!D2)")
if not (taxonXref and gi and sequence):
# The entry did not have a cross ref to the taxonomy database:
return None, retrievalStatus.replace(")", "!T2)")
# Make an object to hold the taxonomy:
taxonomy = Taxonomy.Taxonomy()
try:
taxonomy.populateFromNCBI(
dbid=taxonXref,
# allow_unclassified=self.options.unclassified,
minimaltaxonomy=self.options.minimaltaxonomy)
except Taxonomy.NCBIPopulationError, X:
return None, retrievalStatus.replace(")", " !%s)" % X.status)
# Dump the taxonomy object to a file:
fp = open(taxonomyFileName, 'w')
pickle.dump(taxonomy, fp)
fp.close()
# Upcase the sequence:
sequence = sequence.upper()
# Cache the sequence:
fastaEntry = ">%s\n%s\n" % (gi, sequence)
utils.writeFile(fastaFileName, fastaEntry)
def get(self, gi):
"""
Look up genbank records by their GI
"""
taxonomyFileName = os.path.join(self.options.dbcache, gi + ".tax")
fastaFileName = os.path.join(self.options.dbcache, gi + ".fasta")
if (os.path.exists(taxonomyFileName) and os.path.getsize(taxonomyFileName) != 0 and
os.path.exists(fastaFileName) and os.path.getsize(fastaFileName) != 0):
retrievalStatus = "(c)"
taxonomy = utils.safeReadTaxonomyCache(taxonomyFileName)
sequence = utils.safeReadFastaCache(fastaFileName)
else:
retrievalStatus = "(d)"
taxonXref = None
seqLength = None
successful = False
for tries in range(10):
try:
Entrez.email = self.options.email
Entrez.tool = 'sapwebserver'
fp = Entrez.efetch(db="nucleotide", id=gi, retmode="xml")
# Get the cross ref to the taxonomy database:
taxonXrefRE = re.compile("<GBQualifier_value>taxon:(\d+)</GBQualifier_value>")
seqLengthRE = re.compile("<GBSeq_length>(\d+)</GBSeq_length>")
sequenceRE = re.compile("<GBSeq_sequence>([a-zA-Z]+)</GBSeq_sequence>")
taxonXref = None
seqLength = None
sequence = None
while taxonXref is None or sequence is None:
line = fp.readline()
if not line:
break
taxonMatch = taxonXrefRE.search(line)
lengthMatch = seqLengthRE.search(line)
sequenceMatch = sequenceRE.search(line)
if taxonMatch:
if taxonXref is None:
taxonXref = taxonMatch.group(1)
# else:
# print "There was more than one taxon xref for %s. Picking the first one (%s)." % (gi, taxonXref)
if lengthMatch:
seqLength = lengthMatch.group(1)
if sequenceMatch:
sequence = sequenceMatch.group(1)
if not (taxonXref and sequence):
# Give it another try:
continue
except KeyboardInterrupt:
sys.exit()
except MemoryError:
# Write an empty file to cache to keep the script from
# trying to download the sequence next time.
utils.writeFile(fastaFileName, '')
return None, retrievalStatus.replace(")", "!M)")
except:
## print ' retrieving failed - retrying'
time.sleep(tries * 5)
continue
else:
successful = True
fp.close()
break
if not successful:
return None, retrievalStatus.replace(")", "!D2)")
if not (taxonXref and gi and sequence):
# The entry did not have a cross ref to the taxonomy database:
return None, retrievalStatus.replace(")", "!T2)")
# Make an object to hold the taxonomy:
taxonomy = Taxonomy.Taxonomy()
try:
taxonomy.populateFromNCBI(dbid=taxonXref,
# allow_unclassified=self.options.unclassified,
minimaltaxonomy=self.options.minimaltaxonomy)
except Taxonomy.NCBIPopulationError, X:
return None, retrievalStatus.replace(")", " !%s)" % X.status)
# Dump the taxonomy object to a file:
fp = open(taxonomyFileName, 'w')
pickle.dump(taxonomy, fp)
fp.close()
# Upcase the sequence:
sequence = sequence.upper()
# Cache the sequence:
fastaEntry = ">%s\n%s\n" % (gi, sequence)
utils.writeFile(fastaFileName, fastaEntry)
