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#!/usr/bin/env python
"""Test the GenBank parser and make sure everything is working smoothly.
"""
# standard library
import os
import copy
import cStringIO
# Biopython
from Bio import File
# GenBank stuff to test
from Bio import GenBank
from Bio.GenBank import utils
gb_file_dir = os.path.join(os.getcwd(), 'GenBank')
test_files = ['noref.gb', 'cor6_6.gb', 'iro.gb', 'pri1.gb', 'arab1.gb',
'protein_refseq.gb', 'extra_keywords.gb', 'one_of.gb',
'NT_019265.gb', 'origin_line.gb', 'blank_seq.gb',
'dbsource_wrap.gb', 'gbvrl1_start.seq', 'NC_005816.gb']
# We only test writing on a subset of the examples:
write_format_files = ['noref.gb', 'cor6_6.gb', 'iro.gb', 'pri1.gb', 'arab1.gb',
'extra_keywords.gb', 'one_of.gb', 'origin_line.gb']
# don't test writing on protein_refseq, since it is horribly nasty
# don't test writing on the CONTIG refseq, because the wrapping of
# locations won't work exactly
# don't test writing on blank_seq because it lacks a sequence type
# don't test dbsource_wrap because it is a junky RefSeq file
files_to_parse = []
for file in test_files:
files_to_parse.append(os.path.join(gb_file_dir, file))
# parse the bioperl test files
# comment this out for now -- there are a bunch of junky records in here
# that no longer exist in GenBank -- do we really need to support those?
# files_to_parse = [os.path.join(os.getcwd(), 'GenBank', 'bioperl_test.gb')]
# parse the biojava test files
# files_to_parse += [os.path.join(os.getcwd(), 'GenBank', 'biojava_test.gb')]
# test the parsers
feature_parser = GenBank.FeatureParser(debug_level = 0)
record_parser = GenBank.RecordParser(debug_level = 0)
all_parsers = [feature_parser, record_parser]
print "Testing parsers..."
for parser in all_parsers:
for filename in files_to_parse:
if not os.path.isfile(filename):
print "Missing test input file: %s" % filename
continue
handle = open(filename, 'r')
iterator = GenBank.Iterator(handle, parser)
while 1:
cur_record = iterator.next()
if cur_record is None:
break
if isinstance(parser, GenBank.FeatureParser):
print "***Record from %s with the FeatureParser" \
% filename.split(os.path.sep)[-1]
print "Seq:", repr(cur_record.seq)
print "Id:", cur_record.id
print "Name:", cur_record.name
print "Description", cur_record.description
print "Annotations***"
ann_keys = cur_record.annotations.keys()
ann_keys.sort()
for ann_key in ann_keys:
if ann_key != 'references':
print "Key: %s" % ann_key
print "Value: %s" % \
cur_record.annotations[ann_key]
else:
print "References*"
for reference in cur_record.annotations[ann_key]:
print str(reference)
print "Feaures"
for feature in cur_record.features:
print feature
print "DB cross refs", cur_record.dbxrefs
elif isinstance(parser, GenBank.RecordParser):
print "***Record from %s with the RecordParser" \
% filename.split(os.path.sep)[-1]
print "sequence length: %i" % len(cur_record.sequence)
print "locus:", cur_record.locus
print "definition:", cur_record.definition
print "accession:", cur_record.accession
for reference in cur_record.references:
print "reference title:", reference.title
for feature in cur_record.features:
print "feature key:", feature.key
print "location:", feature.location
print "num qualifiers:", len(feature.qualifiers)
for qualifier in feature.qualifiers:
print "key:", qualifier.key, "value:", qualifier.value
handle.close()
#The dictionaries code has been deprecated
#print "Testing dictionaries..."
#...
# test writing GenBank format
print "Testing writing GenBank format..."
def do_comparison(good_record, test_record):
"""Compare two records to see if they are the same.
Ths compares the two GenBank record, and will raise an AssertionError
if two lines do not match, showing the non-matching lines.
"""
good_handle = cStringIO.StringIO(good_record)
test_handle = cStringIO.StringIO(test_record)
while 1:
good_line = good_handle.readline()
test_line = test_handle.readline()
if not(good_line) and not(test_line):
break
if not(good_line):
raise AssertionError("Extra info in Test: `%s`" % test_line)
if not(test_line):
raise AssertionError("Extra info in Expected: `%s`" % good_line)
test_normalized = ' '.join([x for x in test_line.split() if x])
good_normalized = ' '.join([x for x in good_line.split() if x])
assert test_normalized == good_normalized, \
"Expected does not match Test.\nExpect:`%s`\nTest :`%s`\n" % \
(good_line, test_line)
def t_write_format():
record_parser = GenBank.RecordParser(debug_level = 0)
for file in write_format_files:
print "Testing GenBank writing for %s..." % os.path.basename(file)
cur_handle = open(os.path.join("GenBank", file), "r")
compare_handle = open(os.path.join("GenBank", file), "r")
iterator = GenBank.Iterator(cur_handle, record_parser)
compare_iterator = GenBank.Iterator(compare_handle)
while 1:
cur_record = iterator.next()
compare_record = compare_iterator.next()
if cur_record is None or compare_record is None:
break
print "\tTesting for %s" % cur_record.version
output_record = str(cur_record) + "\n"
do_comparison(compare_record, output_record)
cur_handle.close()
t_write_format()
def t_cleaning_features():
"""Test the ability to clean up feature values.
"""
parser = GenBank.FeatureParser(feature_cleaner = \
utils.FeatureValueCleaner())
handle = open(os.path.join("GenBank", "arab1.gb"))
iterator = GenBank.Iterator(handle, parser)
first_record = iterator.next()
# test for cleaning of translation
translation_feature = first_record.features[1]
test_trans = translation_feature.qualifiers["translation"][0]
assert test_trans.find(" ") == -1, \
"Did not clean spaces out of the translation"
assert test_trans.find("\012") == -1, \
"Did not clean newlines out of the translation"
print "Testing feature cleaning..."
t_cleaning_features()
def t_bioformat():
"""Test converting GenBank into different formats using Bioformat.
"""
from Bio import formats
from Bio import SeqRecord
test_file = os.path.join("GenBank", "iro.gb")
test_handle = open(test_file)
format = formats["sequence"].identify(test_handle)
assert format.name == "genbank-records", \
"Identified format incorrectly: %s" % format.name
all_records = []
for record in SeqRecord.io.readFile(test_handle):
all_records.append(record)
assert len(all_records) == 1
assert all_records[0].id == "AL109817.1", \
"Unexpected record id: %s" % all_records[0].id
assert all_records[0].seq[0:10] == "cacaggccca", \
"Unexpected sequence: %s" % all_records[0].seq
assert all_records[0].description == \
"Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 125195.", \
"Unexpected description: %s" % all_records[0].description
print "Testing format conversions..."
# t_bioformat() # XXX this is mucked up right now and still under work
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