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 main():
starttime = time.time()
parser = create_argument_parser()
args = parser.parse_args()
global logger
logger = pcl.pisacov_logger(level="info")
welcomemsg, starttime = pcl.welcome(command=__script__)
logger.info(welcomemsg)
# PARSE CONFIGURATION FILE:
invals = pco._initialise_inputs()
invals['INSEQ'] = None
invals['INIFS'] = None
invals['OUTROOT'] = None
invals['OUTCSVPATH'] = None
# READ INPUT ARGUMENTS
invals['INSEQ'] == ppaths.check_path(args.seqpath[0], 'file')
invals['INIFS'] = []
args.remove_insertions = False
for fp in args.dimers:
if '*' in fp:
invals['INIFS'] += ppaths.check_wildcard(fp)
else:
invals['INIFS'].append(ppaths.check_path(fp, 'file'))
invals['INIFS'] = list(dict.fromkeys(invals['INIFS']))
if args.hhblits_arguments is not None:
invals['HHBLITS_PARAMETERS'] = pco._check_hhparams(
args.hhblits_arguments)
else:
pass
if args.skip_conpred is True:
skipexec = True
if args.hhblits_arguments is not None:
logger.info('HHblits parameters given bypassed by --skip_conpred')
else:
skipexec = False
if args.outdir is None:
invals['OUTROOT'] = ppaths.check_path(os.path.dirname(invals['INSEQ']))
else:
invals['OUTROOT'] = ppaths.check_path(os.path.join(args.outdir[0], ''))
ppaths.mdir(invals['OUTROOT'])
if args.collection_file is None:
invals['OUTCSVPATH'] = ppaths.check_path(
os.path.join(invals['OUTROOT'],
("evcovsignal" + os.extsep + "full" + os.extsep +
"pisacov" + os.extsep + "csv")))
else:
invals['OUTCSVPATH'] = ppaths.check_path(args.collection_file[0])
if os.path.isfile(invals['OUTCSVPATH']) is False:
pic.csvheader(invals['OUTCSVPATH'], cropped=False)
# Define formats used
sources = pco._sources()
# Parse sequence and structure files
logger.info('Parsing sequence file...')
seqs = cps.parseseqfile(invals['INSEQ'])
if len(seqs) == 1:
if len(seqs) == 1:
for key in seqs:
pdbid = key.lower()
else:
raise Exception('More than one pdbid in sequence set.')
seq = seqs[pdbid]
outpdbdir = os.path.join(invals['OUTROOT'], pdbid, "")
# RENUMBERING
fseq = {}
fmsa = {}
if skipexec is False:
if invals['INIFS'] is not None:
logger.info('Renumbering interfaces provided ' +
'according to position in sequence.')
for path in invals['INIFS']:
instrc = os.path.join(invals['OUTROOT'], pdbid,
os.path.basename(path))
logger.info(pcl.running('CROPS-renumber'))
itime = datetime.datetime.now()
psc.renumcrops(invals['INSEQ'], path, invals['OUTROOT'])
copyfile(path, instrc)
logger.info(pcl.running('CROPS-renumber', done=itime))
ppaths.mdir(outpdbdir)
for i, iseq in seq.imer.items():
fiseq = pdbid + '_' + i + os.extsep + 'fasta'
fseq[i] = os.path.join(invals['OUTROOT'], pdbid, fiseq)
fiseq = pdbid + '_' + i + os.extsep + 'msa' + os.extsep + 'aln'
fmsa[i] = os.path.join(invals['OUTROOT'], pdbid, 'hhblits', fiseq)
if skipexec is False:
iseq.dump(fseq[i])
# EXECUTION OF EXTERNAL PROGRAMS
hhdir = os.path.join(invals['OUTROOT'], pdbid, 'hhblits', '')
dmpdir = os.path.join(invals['OUTROOT'], pdbid, 'dmp', '')
fstr = []
for file in invals['INIFS']:
fstr.append(
os.path.join(
invals['OUTROOT'],
(os.path.splitext(os.path.basename(file))[0] + os.extsep +
'crops' + os.extsep + 'seq' + os.extsep + 'pdb')))
if skipexec is False:
# MSA GENERATOR
ppaths.mdir(hhdir)
if invals['HHBLITS_PARAMETERS'] == ['3', '0.001', 'inf', '50', '99']:
logger.info(
'Generating Multiple Sequence Alignment using DeepMetaPSICOV default parameters... [AS RECOMMENDED]'
)
elif invals['HHBLITS_PARAMETERS'] == ['2', '0.001', '1000', '0', '90']:
logger.info(
'Generating Multiple Sequence Alignment using HHBlits default parameters...'
)
else:
logger.info(
'Generating Multiple Sequence Alignment using user-custom parameters...'
)
for i, iseq in seq.imer.items():
sfile = fseq[i]
afile = fmsa[i]
logger.info(pcl.running('HHBlits'))
itime = datetime.datetime.now()
themsa = psm.runhhblits(sfile, invals['HHBLITS_PARAMETERS'], hhdir)
logger.info(pcl.running('HHBlits', done=itime))
iseq.msa = themsa
# DEEP META PSICOV RUN
logger.info(
'Generating contact prediction lists via DeepMetaPSICOV...')
ppaths.mdir(dmpdir)
for i, iseq in seq.imer.items():
sfile = fseq[i]
afile = fmsa[i]
nsfile = os.path.join(dmpdir, os.path.basename(sfile))
if sfile != nsfile:
copyfile(sfile, nsfile)
logger.info(pcl.running('DeepMetaPSICOV'))
itime = datetime.datetime.now()
psd.rundmp(nsfile, afile, dmpdir)
logger.info(pcl.running('DeepMetaPSICOV', done=itime))
# GENERATE INTERFACE LIST
iflist = []
for filepath in fstr:
ifname = os.path.splitext(os.path.basename(filepath))[0]
iflist.append(pci.interface(name=ifname))
# CONTACT ANALYSIS AND MATCH
logger.info('Opening output csv files...')
resultdir = os.path.join(invals['OUTROOT'], pdbid, 'pisacov', '')
ppaths.mdir(resultdir)
csvfile = os.path.join(
resultdir, (pdbid + os.extsep + "evcovsignal" + os.extsep + "full" +
os.extsep + "pisacov" + os.extsep + "csv"))
pic.csvheader(csvfile, cropped=False, pisascore=False)
logger.info('Parsing sequence files...')
for i, fpath in fseq.items():
seq.imer[i].seqs['conkit'] = ckio.read(fpath, 'fasta')[0]
seq.imer[i].biotype = csq.guess_type(seq.imer[i].seqs['mainseq'])
logger.info('Parsing contact predictions lists...')
conpred = {}
matches = []
for s in seq.imer:
if s not in conpred:
conpred[s] = {}
for source, attribs in sources.items():
fc = os.path.splitext(os.path.basename(fseq[s]))[0]
fc += attribs[1]
confile = os.path.join(invals['OUTROOT'], pdbid, attribs[0], fc)
conpred[s][source] = ckio.read(confile, attribs[2])[0]
logger.info('Parsing crystal structure contacts...')
for i in range(len(iflist)):
inputmap = ckio.read(fstr[i], 'pdb')
if len(inputmap) == 4:
chnames = list(iflist[i].chains.keys())
chtypes = list(iflist[i].chains.values())
if (seq.whatseq(chnames[0]) != seq.whatseq(chnames[1])
or (chtypes[0] != 'Protein' or chtypes[1] != 'Protein')):
if chtypes[0] != "Protein" or chtypes[1] != "Protein":
logger.info(
'Interface ' + str(i) +
' is not a Protein-Protein interface. Ignoring.')
else:
logger.info('Interface ' + str(i) +
' is not a homodimer. Ignoring.')
iflist[i].structure = None
matches.append(None)
continue
s = seq.whatseq(chnames[0])
try:
iflist[i].structure = []
for m in range(len(inputmap)):
iflist[i].structure.append(inputmap[m].as_contactmap())
iflist[i].structure[m].id = inputmap[m].id
except Exception:
for m in range(len(inputmap)):
iflist[i].structure.append(inputmap[m]) # ConKit LEGACY.
matches.append({})
for source, attribs in sources.items():
matches[i][source] = pcc.contact_atlas(
name=pdbid + '_' + str(s),
conpredmap=conpred[s][source],
strmap=iflist[i].structure,
sequence=seq.imer[s],
removeintra=True)
else:
iflist[i].structure = None
matches.append(None)
continue
logger.info('Computing results and writing them to file...')
for i in range(len(iflist)):
if matches[i] is None:
continue
results = [pdbid, str(i + 1)]
results.append(matches[i]['psicov'].chain1)
results.append(matches[i]['psicov'].chain2)
sid = seq.whatseq(matches[i]['psicov'].chain1)
results.append(str(sid))
results.append(str(seq.imer[sid].length()))
results.append(str(seq.imer[sid].cropmsa.meff))
results.append(str(seq.imer[sid].ncrops()))
results.append(str(seq.imer[sid].full_length()))
for source, attribs in sources.items():
appresults = pcs.list_scores(matches[i][source], tag=source)
results += appresults
pic.lineout(results, csvfile)
pic.lineout(results, invals['OUTCSVPATH'])
endmsg = pcl.ok(starttime, command=__script__)
logger.info(endmsg)
return
def test_guess_type_4(self):
expected_type = "RNA"
obtained_type = ces.guess_type(_SEQUENCE_4)
self.assertEqual(obtained_type, expected_type)
def test_guess_type_2(self):
expected_type = "Protein"
obtained_type = ces.guess_type(_SEQUENCE_2)
self.assertEqual(obtained_type, expected_type)