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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.Seq import UnknownSeq
from Bio.SeqUtils.CheckSum import seguid
from Bio.SeqFeature import ExactPosition, FeatureLocation, SeqFeature
from Bio.SeqRecord import SeqRecord
def checksum_summary(record):
if isinstance(record.seq, UnknownSeq):
return repr(record.seq)
if len(record.seq) < 25:
short = record.seq.tostring()
else:
short = record.seq.tostring()[:19] \
+ "..." + record.seq.tostring()[-3:]
return "%s [%s] len %i" \
% (short, seguid(record.seq), len(record.seq))
def compare_reference(old_r, new_r):
"""Compare two Reference objects
Note new_r is assumed to be a BioSQL DBSeqRecord, due to limitations
of the BioSQL table structure.
"""
assert old_r.title == new_r.title, \
"%s vs %s" % (old_r.title, new_r.title)
assert old_r.authors == new_r.authors, \
"%s vs %s" % (old_r.authors, new_r.authors)
assert old_r.journal == new_r.journal, \
"%s vs %s" % (old_r.journal, new_r.journal)
assert old_r.medline_id == new_r.medline_id, \
"%s vs %s" % (old_r.medline_id, new_r.medline_id)
if old_r.pubmed_id and new_r.pubmed_id:
assert old_r.pubmed_id == new_r.pubmed_id
#Looking at BioSQL/BioSeq.py function _retrieve_reference
#it seems that it will get either the MEDLINE or PUBMED,
#but not both. I *think* the current schema does not allow
#us to store both... must confirm this.
#TODO - assert old_r.comment == new_r.comment
#Looking at the tables, I *think* the current schema does not
#allow us to store a reference comment. Must confirm this.
assert old_r.comment == new_r.comment or new_r.comment == ""
#TODO - assert old_r.consrtm == new_r.consrtm
#Looking at the tables, I *think* the current schema does not
#allow us to store a consortium.
assert old_r.consrtm == new_r.consrtm or new_r.consrtm == ""
if len(old_r.location) == 0:
assert len(new_r.location) == 0
else:
#BioSQL can only store ONE location!
#TODO - Check BioPerl with a GenBank file with multiple ref locations
assert isinstance(old_r.location[0], FeatureLocation)
assert isinstance(new_r.location[0], FeatureLocation)
assert old_r.location[0].start == new_r.location[0].start and \
old_r.location[0].end == new_r.location[0].end
return True
def compare_feature(old_f, new_f):
"""Compare two SeqFeature objects"""
assert isinstance(old_f, SeqFeature)
assert isinstance(new_f, SeqFeature)
assert old_f.type == new_f.type, \
"%s -> %s" % (old_f.type, new_f.type)
assert old_f.strand == new_f.strand, \
"%s -> %s" % (old_f.strand, new_f.strand)
assert old_f.ref == new_f.ref, \
"%s -> %s" % (old_f.ref, new_f.ref)
assert old_f.ref_db == new_f.ref_db, \
"%s -> %s" % (old_f.ref_db, new_f.ref_db)
#TODO - BioSQL does not store/retrieve feature's id (Bug 2526)
#assert old_f.id == new_f.id
assert new_f.id == "<unknown id>"
#TODO - Work out how the location_qualifier_value table should
#be used, given BioPerl seems to ignore it (Bug 2766)
#assert old_f.location_operator == new_f.location_operator, \
# "%s -> %s" % (old_f.location_operator, new_f.location_operator)
# We dont store fuzzy locations:
try:
assert str(old_f.location) == str(new_f.location), \
"%s -> %s" % (str(old_f.location), str(new_f.location))
except AssertionError, e:
if isinstance(old_f.location.start, ExactPosition) and \
isinstance(old_f.location.end, ExactPosition):
# Its not a problem with fuzzy locations, re-raise
raise e
else:
assert old_f.location.nofuzzy_start == \
new_f.location.nofuzzy_start, \
"%s -> %s" % (old_f.location.nofuzzy_start, \
new_f.location.nofuzzy_start)
assert old_f.location.nofuzzy_end == \
new_f.location.nofuzzy_end, \
"%s -> %s" % (old_f.location.nofuzzy_end, \
new_f.location.nofuzzy_end)
assert len(old_f.sub_features) == len(new_f.sub_features), \
"number of sub_features: %s -> %s" % \
(len(old_f.sub_features), len(new_f.sub_features))
for old_sub, new_sub in zip(old_f.sub_features, new_f.sub_features):
assert old_sub.type == new_sub.type, \
"%s -> %s" % (old_sub.type, new_sub.type)
assert old_sub.strand == new_sub.strand, \
"%s -> %s" % (old_sub.strand, new_sub.strand)
assert old_sub.ref == new_sub.ref, \
"%s -> %s" % (old_sub.ref, new_sub.ref)
assert old_sub.ref_db == new_sub.ref_db, \
"%s -> %s" % (old_sub.ref_db, new_sub.ref_db)
#TODO - Work out how the location_qualifier_value table should
#be used, given BioPerl seems to ignore it (Bug 2766)
#assert old_sub.location_operator == new_sub.location_operator, \
# "%s -> %s" % (old_sub.location_operator, new_sub.location_operator)
# Compare sub-feature Locations:
#
# BioSQL currently does not store fuzzy locations, but instead stores
# them as FeatureLocation.nofuzzy_start FeatureLocation.nofuzzy_end.
# The vast majority of cases will be comparisons of ExactPosition
# class locations, so we'll try that first and catch the exceptions.
try:
assert str(old_sub.location) == str(new_sub.location), \
"%s -> %s" % (str(old_sub.location), str(new_sub.location))
except AssertionError, e:
if isinstance(old_sub.location.start, ExactPosition) and \
isinstance(old_sub.location.end, ExactPosition):
# Its not a problem with fuzzy locations, re-raise
raise e
else:
#At least one of the locations is fuzzy
assert old_sub.location.nofuzzy_start == \
new_sub.location.nofuzzy_start, \
"%s -> %s" % (old_sub.location.nofuzzy_start, \
new_sub.location.nofuzzy_start)
assert old_sub.location.nofuzzy_end == \
new_sub.location.nofuzzy_end, \
"%s -> %s" % (old_sub.location.nofuzzy_end, \
new_sub.location.nofuzzy_end)
assert len(old_f.qualifiers) == len(new_f.qualifiers)
assert set(old_f.qualifiers.keys()) == set(new_f.qualifiers.keys())
for key in old_f.qualifiers.keys():
if isinstance(old_f.qualifiers[key], str):
if isinstance(new_f.qualifiers[key], str):
assert old_f.qualifiers[key] == new_f.qualifiers[key]
elif isinstance(new_f.qualifiers[key], list):
#Maybe a string turning into a list of strings?
assert [old_f.qualifiers[key]] == new_f.qualifiers[key], \
"%s -> %s" \
% (repr(old_f.qualifiers[key]),
repr(new_f.qualifiers[key]))
else:
assert False, "Problem with feature's '%s' qualifier" & key
else:
#Should both be lists of strings...
assert old_f.qualifiers[key] == new_f.qualifiers[key], \
"%s -> %s" % (old_f.qualifiers[key], new_f.qualifiers[key])
return True
def compare_sequence(old, new):
"""Compare two Seq or DBSeq objects"""
assert len(old) == len(new)
assert old.tostring() == new.tostring()
if isinstance(old, UnknownSeq):
assert isinstance(new, UnknownSeq)
else:
assert not isinstance(new, UnknownSeq)
l = len(old)
s = old.tostring()
assert isinstance(s, str)
#Don't check every single element; for long sequences
#this takes far far far too long to run!
#Test both positive and negative indices
if l < 50:
indices = range(-l,l)
else:
#A selection of end cases, and the mid point
indices = [-l,-1+1,-int(l/2),-1,0,1,int(l/2),l-2,l-1]
#Test element access,
for i in indices:
expected = s[i]
assert expected == old[i]
assert expected == new[i]
#Test slices
indices.append(l) #check copes with overflows
indices.append(l+1000) #check copes with overflows
for i in indices:
for j in indices:
expected = s[i:j]
assert expected == old[i:j].tostring(), \
"Slice %s vs %s" % (repr(expected), repr(old[i:j]))
assert expected == new[i:j].tostring(), \
"Slice %s vs %s" % (repr(expected), repr(new[i:j]))
#Slicing with step of 1 should make no difference.
#Slicing with step 3 might be useful for codons.
for step in [1,3]:
expected = s[i:j:step]
assert expected == old[i:j:step].tostring()
assert expected == new[i:j:step].tostring()
#Check automatic end points
expected = s[i:]
assert expected == old[i:].tostring()
assert expected == new[i:].tostring()
expected = s[:i]
assert expected == old[:i].tostring()
assert expected == new[:i].tostring()
#Check "copy" splice
assert s == old[:].tostring()
assert s == new[:].tostring()
return True
def compare_features(old_list, new_list):
assert isinstance(old_list, list)
assert isinstance(new_list, list)
assert len(old_list) == len(new_list)
for old_f, new_f in zip(old_list, new_list):
if not compare_feature(old_f, new_f):
return False
return True
def compare_record(old, new):
"""Compare two SeqRecord or DBSeqRecord objects"""
assert isinstance(old, SeqRecord)
assert isinstance(new, SeqRecord)
#Sequence:
compare_sequence(old.seq, new.seq)
#Basics:
assert old.id == new.id
assert old.name == new.name
assert old.description == new.description
assert old.dbxrefs == new.dbxrefs, \
"dbxrefs mismatch\nOld: %s\nNew: %s" \
% (old.dbxrefs, new.dbxrefs)
#Features:
if not compare_features(old.features, new.features):
return False
#Annotation:
#We are expecting to see some "extra" annotations appearing,
#such as 'cross_references', 'dates', 'data_file_division',
#'ncbi_taxon' and 'gi'.
#TODO - address these, see Bug 2681?
new_keys = set(new.annotations).difference(old.annotations)
new_keys = new_keys.difference(['cross_references', 'dates',
'data_file_division', 'ncbi_taxid', 'gi'])
assert not new_keys, "Unexpected new annotation keys: %s" \
% ", ".join(new_keys)
missing_keys = set(old.annotations).difference(new.annotations)
missing_keys = missing_keys.difference(['ncbi_taxid', # Can't store chimeras
])
assert not missing_keys, "Unexpectedly missing annotation keys: %s" \
% ", ".join(missing_keys)
#In the short term, just compare any shared keys:
for key in set(old.annotations.keys()).intersection(new.annotations.keys()):
if key == "references":
assert len(old.annotations[key]) == len(new.annotations[key])
for old_r, new_r in zip(old.annotations[key], new.annotations[key]):
compare_reference(old_r, new_r)
elif key == "comment":
#Turn them both into containing strings for comparison - due to
#line wrapping in GenBank etc we don't really expect the white
#space to be 100% the same.
if isinstance(old.annotations[key], list):
old_comment = " ".join(old.annotations[key])
else:
old_comment = old.annotations[key]
if isinstance(new.annotations[key], list):
new_comment = " ".join(new.annotations[key])
else:
new_comment = new.annotations[key]
old_comment = old_comment.replace("\n"," ").replace(" ", " ")
new_comment = new_comment.replace("\n"," ").replace(" ", " ")
assert old_comment == new_comment, \
"Comment annotation changed by load/retrieve\n" \
"Was:%s\nNow:%s" \
% (repr(old_comment), repr(new_comment))
elif key in ["taxonomy", "organism", "source"]:
#If there is a taxon id recorded, these fields get overwritten
#by data from the taxon/taxon_name tables. There is no
#guarantee that they will be identical after a load/retrieve.
assert isinstance(new.annotations[key], basestring) \
or isinstance(new.annotations[key], list)
elif type(old.annotations[key]) == type(new.annotations[key]):
assert old.annotations[key] == new.annotations[key], \
"Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s" \
% (key, old.annotations[key], new.annotations[key])
elif isinstance(old.annotations[key], str) \
and isinstance(new.annotations[key], list):
#Any annotation which is a single string gets turned into
#a list containing one string by BioSQL at the moment.
assert [old.annotations[key]] == new.annotations[key], \
"Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s" \
% (key, old.annotations[key], new.annotations[key])
elif isinstance(old.annotations[key], list) \
and isinstance(new.annotations[key], str):
assert old.annotations[key] == [new.annotations[key]], \
"Annotation '%s' changed by load/retrieve\nWas:%s\nNow:%s" \
% (key, old.annotations[key], new.annotations[key])
return True
def compare_records(old_list, new_list):
assert isinstance(old_list, list)
assert isinstance(new_list, list)
assert len(old_list) == len(new_list)
for old_r, new_r in zip(old_list, new_list):
if not compare_record(old_r, new_r):
return False
return True
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