def test_sequence_dumpmap_2(self):
expected_output = (
">crops|2IXY_2|Chains A,C|Source: MADEUP|No info|" +
"#Residues cropped: 3 (2 not from terminal segments) ; % cropped: 23.08 (15.38 not from terminal segments)"
+ os.linesep + "1 0" + os.linesep + "2 1" + os.linesep + "3 2" +
os.linesep + "4 0" + os.linesep + "5 3" + os.linesep + "6 4" +
os.linesep + "7 5" + os.linesep + "8 6" + os.linesep + "9 0" +
os.linesep + "10 7" + os.linesep + "11 8" + os.linesep +
"12 9" + os.linesep + "13 10" + os.linesep)
seq = ces.sequence(seqid=2,
oligomer='2IXY',
chains={'A', 'C'},
seq=_SEQUENCE_5,
header=_HEADER_1,
extrainfo='No info',
source='MADEUP')
seq.cropmap = _CROPMAP_1
seq.cropbackmap = _CROPMAP_2
seq.seqs['cropseq'] = _SEQUENCE_6
seq.seqs['fullseq'] = seq.seqs['mainseq']
seq.seqs['mainseq'] = seq.seqs['cropseq'].replace("+", "")
returned_output = seq.dumpmap(out='string')
self.assertEqual(expected_output, returned_output)
def test_oligoseq_purge_1(self):
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq_2 = ces.sequence(seq=_SEQUENCE_5_2, header=_HEADER_2)
expected_keys = set()
expected_seqs = set()
oseq = ces.oligoseq(oligomer_id=seq.oligomer_id, imer={seq.name: seq})
oseq.add_sequence(seq_2)
oseq.purge()
obtained_keys = set(oseq.imer.keys())
obtained_seqs = set(oseq.imer.values())
self.assertEqual(expected_keys, obtained_keys)
self.assertEqual(expected_seqs, obtained_seqs)
def test_sequence_length_1(self):
expected_length = 246
seq = ces.sequence(seq=_SEQUENCE_2)
obtained_length = seq.length()
self.assertEqual(expected_length, obtained_length)
def test_sequence_length_2(self):
expected_length = 13
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
obtained_length = seq.length()
self.assertEqual(expected_length, obtained_length)
def test_sequence_dump_1(self):
expected_output = (
">crops|1IXY_1|Chains C,D|Source: RCSB PDB|5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'|"
+ os.linesep + "GATACTNAGATAG" + os.linesep)
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
returned_output = seq.dump(out='string')
self.assertEqual(expected_output, returned_output)
def test_oligoseq_whatseq_1(self):
chains = [{'C', 'D'}, {'E', 'F'}]
expected_seqnum = ['1', '1', '2', '2']
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq_2 = ces.sequence(seq=_SEQUENCE_6_2.replace("+", ""),
header=_HEADER_2)
oseq = ces.oligoseq(oligomer_id=seq.oligomer_id, imer={seq.name: seq})
oseq.add_sequence(seq_2)
obtained_seqnum = []
for aset in chains:
for ch in aset:
obtained_seqnum.append(oseq.whatseq(ch))
self.assertListEqual(expected_seqnum, obtained_seqnum)
def test_sequence_ngaps_2(self):
expected_ngaps = [3, 3]
seq = ces.sequence(seq=_SEQUENCE_2)
seq.seqs['gapseq'] = [_SEQUENCE_7, _SEQUENCE_8]
obtained_ngaps = seq.ngaps()
self.assertEqual(expected_ngaps, obtained_ngaps)
def test_sequence_update_cropsheader_1(self):
expected_output = ">crops|1IXY_2|Chains C,D|Source: RCSB PDB|5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'|"
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq.name = '2'
seq.update_cropsheader()
returned_output = seq.crops_header
self.assertEqual(expected_output, returned_output)
def test_sequence_mainseq_1(self):
expected_seq = _SEQUENCE_5
seq = ces.sequence(seqid=1,
oligomer='1IXY',
chains={'C', 'D'},
seq=_SEQUENCE_5)
returned_seq = seq.mainseq()
self.assertEqual(expected_seq, returned_seq)
def test_sequence_guess_biotype_1(self):
expected_type = ces.guess_type(_SEQUENCE_3)
seq = ces.sequence(seqid=1,
oligomer='1IXY',
chains={'C', 'D'},
seq=_SEQUENCE_3)
returned_type = seq.guess_biotype()
self.assertEqual(expected_type, returned_type)
def test_sequence_addseq_1(self):
expected_seq = _SEQUENCE_3
seq = ces.sequence(seqid=1,
oligomer='1IXY',
chains={'C', 'D'},
seq=_SEQUENCE_5)
seq.addseq(newid="alternative", newseq=_SEQUENCE_3)
self.assertTrue("alternative" in seq.seqs)
self.assertEqual(seq.seqs["alternative"], expected_seq)
def test_sequence_cropinfo_1(self):
expected_info = '#Residues cropped: 3 (2 not from terminal segments) ; % cropped: 23.08 (15.38 not from terminal segments)'
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq.cropmap = _CROPMAP_1
seq.cropbackmap = _CROPMAP_2
seq.seqs['cropseq'] = _SEQUENCE_6
seq.seqs['fullseq'] = seq.seqs['mainseq']
seq.seqs['mainseq'] = seq.seqs['cropseq'].replace("+", "")
obtained_info = seq.cropinfo()
self.assertEqual(expected_info, obtained_info)
def test_sequence_ncrops_1(self):
expected_ncrops = 3
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq.cropmap = _CROPMAP_1
seq.cropbackmap = _CROPMAP_2
seq.seqs['cropseq'] = _SEQUENCE_6
seq.seqs['fullseq'] = seq.seqs['mainseq']
seq.seqs['mainseq'] = seq.seqs['cropseq'].replace("+", "")
obtained_ncrops = seq.ncrops()
self.assertEqual(expected_ncrops, obtained_ncrops)
def test_sequence_dump_2(self):
expected_output = (">crops|2IXY_2|Chains A,C|Source: MADEUP|No info" +
os.linesep + "GATACTNAGATAG" + os.linesep)
seq = ces.sequence(seqid=2,
oligomer='2IXY',
chains={'A', 'C'},
seq=_SEQUENCE_5,
header=_HEADER_1,
extrainfo='No info',
source='MADEUP')
returned_output = seq.dump(out='string')
self.assertEqual(expected_output, returned_output)
def test_sequence_delseq_2(self):
expected_seq = ""
seq = ces.sequence(seqid=1,
oligomer='1IXY',
chains={'C', 'D'},
seq=_SEQUENCE_5)
seq.addseq(newid="alternative", newseq=_SEQUENCE_3)
seq.delseq(wipeall=True)
self.assertFalse("alternative" in seq.seqs)
self.assertTrue("mainseq" in seq.seqs)
self.assertEqual(seq.seqs["mainseq"], expected_seq)
def test_sequence_dumpmap_1(self):
expected_output = (
">crops|1IXY_1|Chains C,D|Source: RCSB PDB|5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'|"
+
"#Residues cropped: 3 (2 not from terminal segments) ; % cropped: 23.08 (15.38 not from terminal segments)"
+ os.linesep + "1 0" + os.linesep + "2 1" + os.linesep + "3 2" +
os.linesep + "4 0" + os.linesep + "5 3" + os.linesep + "6 4" +
os.linesep + "7 5" + os.linesep + "8 6" + os.linesep + "9 0" +
os.linesep + "10 7" + os.linesep + "11 8" + os.linesep +
"12 9" + os.linesep + "13 10" + os.linesep)
seq = ces.sequence(seq=_SEQUENCE_5, header=_HEADER_1)
seq.cropmap = _CROPMAP_1
seq.cropbackmap = _CROPMAP_2
seq.seqs['cropseq'] = _SEQUENCE_6
seq.seqs['fullseq'] = seq.seqs['mainseq']
seq.seqs['mainseq'] = seq.seqs['cropseq'].replace("+", "")
returned_output = seq.dumpmap(out='string')
self.assertEqual(expected_output, returned_output)
def parseseq(instream, inset=None):
"""Parse sequence(s).
:param instream: Imported-to-string sequence file content (fasta format).
:type instream: str
:param inset: Sequence IDs to return, if None it returns them all, defaults to None.
:type inset: set or dict or str, optional
:raises TypeError: When inset a set [str]; or instream is not a string.
:return: Parsed sequences.
:rtype: dict [str, :class:`crops.elements.sequences.oligoseq`]
"""
if isinstance(instream, str) is False:
logging.critical('Input argument instream should be a string.')
raise TypeError
if inset is not None:
if (not isinstance(inset, str) and not isinstance(inset, dict)
and not isinstance(inset, set)):
logging.critical('Input argument inset should be a set or, '
'alternatively a string or a dictionary.')
raise TypeError
elif isinstance(inset, str):
temp = inset
inset = set()
inset.add(temp)
upperset = set()
for element in inset:
if not isinstance(element, str):
logging.critical('Elements in inseq should be strings.')
raise TypeError
upperset.add(element.upper())
newseqs = {}
newid = []
head = ''
chain = ''
ignore = False
ignore = False
indx = -1
inseqlines = instream.splitlines()
inseqlines.append('')
for raw in range(len(inseqlines)):
line = inseqlines[raw].rstrip()
if (not line or line.startswith(">")) and not ignore:
if indx >= 0:
if newid['mainid'] not in newseqs:
newseqs[newid['mainid']] = oligoseq(
oligomer_id=newid['mainid'])
aseq = sequence(seqid=newid['seqid'],
oligomer=newid['mainid'],
seq=chain,
chains=newid['chains'],
source=newid['source'],
header=head,
extrainfo=newid['comments'])
newseqs[newid['mainid']].add_sequence(aseq)
else:
pass
if line.startswith(">"):
newid = retrieve_id(line)
head = line
indx += 1
chain = ''
if inset is not None:
ignore = False if newid['mainid'] in upperset else True
elif line.startswith("#") or line.startswith(' #'):
continue
else:
if not ignore:
chain += str(line)
return newseqs
