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#!/usr/bin/env python
"""Test for the SProt parser on SwissProt files.
"""
import os
from Bio import SeqIO
from Bio import SwissProt
from Bio.SeqRecord import SeqRecord
from Bio.SwissProt import SProt
test_files = ['sp001', 'sp002', 'sp003', 'sp004', 'sp005',
'sp006', 'sp007', 'sp008', 'sp009', 'sp010',
'sp011', 'sp012', 'sp013', 'sp014', 'sp015']
# test the record parser
for test_file in test_files:
print "\ntesting %s..." % test_file
datafile = os.path.join('SwissProt', test_file)
print "*Using SequenceParser"
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
assert isinstance(seq_record, SeqRecord)
print seq_record.id
print seq_record.name
print seq_record.description
print repr(seq_record.seq)
print "*Using RecordParser"
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# test a couple of things on the record -- this is not exhaustive
print record.entry_name
print record.accessions
print record.organism_classification
print record.seqinfo
print "***Features:"
for feature in record.features:
print feature
print "***References:"
for ref in record.references:
print "authors:", ref.authors
print "title:", ref.title
print "references:", ref.references
#Check the two parsers agree on the essentials
assert seq_record.seq.tostring() == record.sequence
assert seq_record.description == record.description
assert seq_record.name == record.entry_name
assert seq_record.id in record.accessions
#Now try using the Iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
assert len(records) == 1
assert isinstance(records[0], SeqRecord)
#Check matches what we got earlier without the iterator:
assert records[0].seq.tostring() == seq_record.seq.tostring()
assert records[0].description == seq_record.description
assert records[0].name == seq_record.name
assert records[0].id == seq_record.id
# With the RecordParser
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
assert len(records) == 1
assert isinstance(records[0], SProt.Record)
#Check matches what we got earlier without the iterator:
assert records[0].sequence == record.sequence
assert records[0].description == record.description
assert records[0].entry_name == record.entry_name
assert records[0].accessions == record.accessions
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