def loadXRef(self): ### Load Identifier XRef Data
'''Load Identifier XRef Data.'''
try: ### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if rje.exists('%s.xref.tdt' %
self.info['Basefile']) and not self.opt['Force']:
return self.db().addTable('%s.xref.tdt' %
self.info['Basefile'],
mainkeys=['#'],
datakeys='All',
name='XRef')
if not rje.checkForFile(self.info['XRef']): return False
changehead = {
'Ensembl Gene ID': 'EnsG',
'Ensembl Protein ID': 'EnsP',
'Associated Gene Name': 'Gene',
'Associated Gene DB': 'GeneDB',
'UniProt/SwissProt ID': 'UniprotID',
'UniProt/SwissProt Accession': 'UniProt',
'SGD Gene': 'SGD'
}
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
xref = self.db().addTable(self.info['XRef'],
mainkeys='All',
datakeys='All',
name='XRef')
for field in changehead:
if field in xref.fields():
xref.renameField(field, changehead[field])
xref.saveToFile('%s.xref.tdt' % self.info['Basefile'])
return xref
except:
self.errorLog(rje_zen.Zen().wisdom())
raise # Delete this if method error not terrible
def setup(self): ### Main class setup method.
'''Main class setup method.'''
try:### ~ [0] Setup File names etc. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if self.getStr('SaveDis').lower() in ['','none']:
base = 'peptides'
if rje.checkForFile(self.getStr('Peptides')): base = rje.baseFile(self.getStr('Peptides'))
if self.baseFile().lower() not in ['','none']: base = self.baseFile()
self.baseFile(base)
self.setStr({'SaveDis':'%s.%s.%s' % (base,self.getStr('PeptDis'),self.getStr('PeptCluster'))})
if self.getStr('OutMatrix') in ['tdt','csv','png','phylip']: self.str['SaveDis'] += '.%s' % self.getStr('OutMatrix')[:3]
else: self.str['SaveDis'] += '.txt'
self.dict['Output']['peptides'] = string.join(self.list['Peptides'],'\n')
### ~ [1] Setup Distance Matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['AADis'] = rje_dismatrix.DisMatrix(self.log,['nsf2nwk=T']+self.cmd_list)
self.obj['AADis'].info['Name'] = 'Pairwise AA distances'
self.obj['PeptDis'] = rje_dismatrix.DisMatrix(self.log,['nsf2nwk=T']+self.cmd_list)
self.obj['PeptDis'].info['Name'] = 'Pairwise peptide distances'
### ~ [2] Optional loading of AA Distance Matrix ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if self.getStr('AADis').lower() not in ['','none']: self.obj['AADis'].loadMatrix(self.getStr('AADis'))
else:
self.obj['AAProp'] = aaprop = rje_aaprop.AAPropMatrix(self.log,self.cmd_list)
#aaprop.readAAProp() # Does this on loading!
for aa in aaprop.pdif: self.obj['AADis'].addDis(aa[0],aa[1],aaprop.pdif[aa])
return True
except: self.errorLog('Problem during %s setup.' % self); return False # Setup failed
def processHHPID(self): ### Process HHPID interactions
'''Process HHPID interactions.'''
try: ### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if rje.checkForFile('%s.HHPIDMap.tdt' % self.basefile()):
mdb = self.db().addTable('%s.HHPIDMap.tdt' % self.basefile(),
['HIV', 'Gene'],
'All',
name='HHPIDMap')
return mdb
hdb = self.db('HHPID')
gdb = self.db('GeneMap')
pdb = self.db('PPI')
mdb = self.db().joinTables(name='HHPIDMap',
join=[(hdb, 'Entrez'), (gdb, 'Entrez')],
newkey=['#'],
empties=False,
keeptable=True)
for field in mdb.fields()[0:]:
if field not in [
'#', 'AccHIV', 'EntrezHIV', 'HIV', 'Entrez', 'Gene',
'Symbol', 'UniProt', 'EnsEMBL', 'EnsLoci'
]:
mdb.dropField(field)
mdb.compress(['HIV', 'Gene'], default='str')
mdb.dropField('#')
mdb.saveToFile()
### ~ [2] Save viral accession numbers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
open('%s.hivacc' % self.getStr('Basefile'), 'w').write(
'%s\n' % string.join(rje.sortKeys(mdb.index('AccHIV')), '\n'))
return mdb
except:
self.errorLog('%s.processHHPID error' % self)
return False
def hmmSearch(self,hmm,dbase=None,outfile=None,wait=True): ### Performs HMMer Search using object attributes
'''
Performs HMMer Search using object attributes.
>> hmm:str = Name of HMM file
>> dbase:str = Name of DBase file [self.info['SearchDB']]
>> outfile:str = Name of Output file file [self.info['HMMOut']]
>> wait:boolean = whether to wait for HMMer. [True]
<< returns outfile or None if fails
'''
try:### ~ [1] ~ Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
## ~ [1a] ~ Input files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not rje.checkForFile(hmm): self.printLog('#ERR','HMM file %s is missing!' % hmm); return None
if not dbase: dbase = self.info['SearchDB']
if not rje.checkForFile(dbase): self.printLog('#ERR','Database file "%s" is missing!' % dbase); return None
## ~ [1b] ~ Output file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not outfile or outfile.lower() in ['','none']: # Make an outfile per search
outfile = '%s.%s.hmmer' % (rje.baseFile(hmm,True),rje.baseFile(dbase,True))
resfile = outfile
if not os.path.exists(outfile) and self.opt['GZip'] and os.path.exists('%s.gz' % outfile) and not self.opt['Force']:
resfile = '%s.gz' % outfile
if not self.opt['Force'] and rje.isYounger(resfile,hmm) == resfile and rje.isYounger(resfile,dbase) == resfile:
self.printLog('#HMM','HMM results file "%s" exists.' % resfile)
return outfile # Already exists
else: rje.backup(self,outfile,unlink=True)
### ~ [2] ~ HMM Search ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if self.opt['HMMPFam']:
_command = 'hmmpfam --cut_ga %s %s %s > %s' % (string.join(self.list['HMMOptions']),hmm,dbase,outfile)
else: _command = 'hmmsearch %s %s %s > %s' % (string.join(self.list['HMMOptions']),hmm,dbase,outfile)
self.log.printLog('#HMM',_command)
if not wait: os.system(self.info['HMMerPath'] + _command + ' &')
elif not os.path.exists(outfile) or self.opt['Force']: open(outfile,'a').write(os.popen(self.info['HMMerPath'] + _command).read())
self.printLog('#HMM','Outfile produced for %s: %s.' % (hmm,outfile))
if self.opt['GZip']:
rje.backup(self,'%s.gz' % outfile,unlink=True)
os.system('gzip %s' % outfile)
self.printLog('#GZIP','%s gzipped to save space' % outfile)
return outfile
except:
self.log.errorLog('Fatal Error during hmmSearch(%s)' % hmm)
return None
def loadPPI(self): ### Load pairwise interaction data
'''Load pairwise interaction data.'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not rje.checkForFile(self.info['PPIFile']): return False
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for line in open(self.info['PPIFile'],'r').readlines():
try: [pa,pb] = string.split(rje.chomp(line))[:2]
except: continue
for ppi in [(pa,pb),(pb,pa)]:
if ppi[0] not in self.dict['PPI']: self.dict['PPI'][ppi[0]] = []
if ppi[1] not in self.dict['PPI'][ppi[0]]: self.dict['PPI'][ppi[0]].append(ppi[1])
self.progLog('\r#PPI','Loading PPI data: %s proteins' % rje.integerString(len(self.dict['PPI'])))
self.printLog('\r#PPI','Loaded PPI data for %s proteins' % rje.integerString(len(self.dict['PPI'])))
except: self.errorLog(rje_zen.Zen().wisdom()); raise # Delete this if method error not terrible
def loadXRef(self): ### Load Identifier XRef Data
'''Load Identifier XRef Data.'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if rje.exists('%s.xref.tdt' % self.info['Basefile']) and not self.opt['Force']:
return self.db().addTable('%s.xref.tdt' % self.info['Basefile'],mainkeys=['#'],datakeys='All',name='XRef')
if not rje.checkForFile(self.info['XRef']): return False
changehead = {'Ensembl Gene ID':'EnsG','Ensembl Protein ID':'EnsP','Associated Gene Name':'Gene',
'Associated Gene DB':'GeneDB','UniProt/SwissProt ID':'UniprotID',
'UniProt/SwissProt Accession':'UniProt','SGD Gene':'SGD'}
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
xref = self.db().addTable(self.info['XRef'],mainkeys='All',datakeys='All',name='XRef')
for field in changehead:
if field in xref.fields(): xref.renameField(field,changehead[field])
xref.saveToFile('%s.xref.tdt' % self.info['Basefile']); return xref
except: self.errorLog(rje_zen.Zen().wisdom()); raise # Delete this if method error not terrible
def loadPillars(self): ### Load YGOB Pillar data
'''Load YGOB Pillar data.'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not rje.checkForFile(self.info['Pillars']): return False
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for line in self.loadFromFile(filename=self.info['Pillars'],chomplines=True):
pillars = string.split(line)
#self.deBug('%s = %d' % (pillars,len(pillars)))
if len(pillars) < 17: continue
pillars = pillars[:5] + pillars[6:] # Remove ancestral gene
while '---' in pillars: pillars.remove('---')
#self.deBug('%s = %d' % (pillars,len(pillars)))
if pillars: self.list['Pillars'].append(pillars)
self.progLog('\r#YGOB','Loading Pillar data: %s loci' % rje.integerString(len(self.list['Pillars'])))
self.printLog('\r#YGOB','Loaded Pillar data for %s loci' % rje.integerString(len(self.list['Pillars'])))
except: self.errorLog(rje_zen.Zen().wisdom()); raise # Delete this if method error not terrible
def processHHPID(self): ### Process HHPID interactions
'''Process HHPID interactions.'''
try:### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if rje.checkForFile('%s.HHPIDMap.tdt' % self.basefile()):
mdb = self.db().addTable('%s.HHPIDMap.tdt' % self.basefile(),['HIV','Gene'],'All',name='HHPIDMap')
return mdb
hdb = self.db('HHPID')
gdb = self.db('GeneMap')
pdb = self.db('PPI')
mdb = self.db().joinTables(name='HHPIDMap',join=[(hdb,'Entrez'),(gdb,'Entrez')],newkey=['#'],empties=False,keeptable=True)
for field in mdb.fields()[0:]:
if field not in ['#','AccHIV','EntrezHIV','HIV','Entrez','Gene','Symbol','UniProt','EnsEMBL','EnsLoci']: mdb.dropField(field)
mdb.compress(['HIV','Gene'],default='str'); mdb.dropField('#')
mdb.saveToFile()
### ~ [2] Save viral accession numbers ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
open('%s.hivacc' % self.getStr('Basefile'),'w').write('%s\n' % string.join(rje.sortKeys(mdb.index('AccHIV')),'\n'))
return mdb
except: self.errorLog('%s.processHHPID error' % self); return False
def loadPillars(self): ### Load YGOB Pillar data
'''Load YGOB Pillar data.'''
try: ### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not rje.checkForFile(self.info['Pillars']): return False
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for line in self.loadFromFile(filename=self.info['Pillars'],
chomplines=True):
pillars = string.split(line)
#self.deBug('%s = %d' % (pillars,len(pillars)))
if len(pillars) < 17: continue
pillars = pillars[:5] + pillars[6:] # Remove ancestral gene
while '---' in pillars:
pillars.remove('---')
#self.deBug('%s = %d' % (pillars,len(pillars)))
if pillars: self.list['Pillars'].append(pillars)
self.progLog(
'\r#YGOB', 'Loading Pillar data: %s loci' %
rje.integerString(len(self.list['Pillars'])))
self.printLog(
'\r#YGOB', 'Loaded Pillar data for %s loci' %
rje.integerString(len(self.list['Pillars'])))
except:
self.errorLog(rje_zen.Zen().wisdom())
raise # Delete this if method error not terrible
def loadPPI(self): ### Load pairwise interaction data
'''Load pairwise interaction data.'''
try: ### ~ [1] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not rje.checkForFile(self.info['PPIFile']): return False
### ~ [2] Load data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for line in open(self.info['PPIFile'], 'r').readlines():
try:
[pa, pb] = string.split(rje.chomp(line))[:2]
except:
continue
for ppi in [(pa, pb), (pb, pa)]:
if ppi[0] not in self.dict['PPI']:
self.dict['PPI'][ppi[0]] = []
if ppi[1] not in self.dict['PPI'][ppi[0]]:
self.dict['PPI'][ppi[0]].append(ppi[1])
self.progLog(
'\r#PPI', 'Loading PPI data: %s proteins' %
rje.integerString(len(self.dict['PPI'])))
self.printLog(
'\r#PPI', 'Loaded PPI data for %s proteins' %
rje.integerString(len(self.dict['PPI'])))
except:
self.errorLog(rje_zen.Zen().wisdom())
raise # Delete this if method error not terrible
def hmmSearch(
self,
hmm,
dbase=None,
outfile=None,
wait=True): ### Performs HMMer Search using object attributes
'''
Performs HMMer Search using object attributes.
>> hmm:str = Name of HMM file
>> dbase:str = Name of DBase file [self.info['SearchDB']]
>> outfile:str = Name of Output file file [self.info['HMMOut']]
>> wait:boolean = whether to wait for HMMer. [True]
<< returns outfile or None if fails
'''
try: ### ~ [1] ~ Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
## ~ [1a] ~ Input files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not rje.checkForFile(hmm):
self.printLog('#ERR', 'HMM file %s is missing!' % hmm)
return None
if not dbase: dbase = self.info['SearchDB']
if not rje.checkForFile(dbase):
self.printLog('#ERR', 'Database file "%s" is missing!' % dbase)
return None
## ~ [1b] ~ Output file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not outfile or outfile.lower() in [
'', 'none'
]: # Make an outfile per search
outfile = '%s.%s.hmmer' % (rje.baseFile(
hmm, True), rje.baseFile(dbase, True))
resfile = outfile
if not os.path.exists(
outfile) and self.opt['GZip'] and os.path.exists(
'%s.gz' % outfile) and not self.opt['Force']:
resfile = '%s.gz' % outfile
if not self.opt['Force'] and rje.isYounger(
resfile, hmm) == resfile and rje.isYounger(
resfile, dbase) == resfile:
self.printLog('#HMM',
'HMM results file "%s" exists.' % resfile)
return outfile # Already exists
else:
rje.backup(self, outfile, unlink=True)
### ~ [2] ~ HMM Search ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if self.opt['HMMPFam']:
_command = 'hmmpfam --cut_ga %s %s %s > %s' % (string.join(
self.list['HMMOptions']), hmm, dbase, outfile)
else:
_command = 'hmmsearch %s %s %s > %s' % (string.join(
self.list['HMMOptions']), hmm, dbase, outfile)
self.log.printLog('#HMM', _command)
if not wait: os.system(self.info['HMMerPath'] + _command + ' &')
elif not os.path.exists(outfile) or self.opt['Force']:
open(outfile, 'a').write(
os.popen(self.info['HMMerPath'] + _command).read())
self.printLog('#HMM',
'Outfile produced for %s: %s.' % (hmm, outfile))
if self.opt['GZip']:
rje.backup(self, '%s.gz' % outfile, unlink=True)
os.system('gzip %s' % outfile)
self.printLog('#GZIP', '%s gzipped to save space' % outfile)
return outfile
except:
self.log.errorLog('Fatal Error during hmmSearch(%s)' % hmm)
return None
def pairwiseAQ(self,seqlist=None,query=None,focus=[0,0]): ### Performs PAQ on seqlist, adding seq.info['PAQ']
'''
Performs PAQ on seqlist, adding seq.info['PAQ']
>> seqlist:rje_seq.SeqList Object
- NB. This object will itself have sequences removed from it, so beware!
- A new info key will be added: PAQ = PAQ sequences with alignment Xs
>> focus:list of range positions [X:Y] to look at. If Y=0 then [X:].
'''
### <PAQ0> ### Setup
try:
_stage = '<0> Setup'
haqlist = seqlist # SeqList Object to store individually Xd sequences
if not query:
query = haqlist.obj['QuerySeq']
if self.opt['NoQuery'] or not query:
query = haqlist.seq[random.randint(0,haqlist.seqNum()-1)]
self.log.printLog('#QRY','Temp (random) query %s assigned for PAQ' % query.shortName())
#!# paqx = [False] * seqlist.seq[0].seqLen() # List of whether a column of the alignment is bad (has an X) [True] or not [False]
#!# - make this a method?!
pwaq = {} # Dictionary of lists of pairwise alignements
block_align = {} # Dictionary of whether residue in block of sequence that is well-aligned or not
for seq in haqlist.seq:
block_align[seq] = [False] * seq.seqLen()
seq.info['PAQ'] = seq.info['Sequence'][0:]
if seq.info.has_key('SAQX') and len(seq.info['SAQX']) == seq.seqLen(): #!# Should no longer be issues due to length changes following realignment
seq.info['Sequence'] = seq.info['SAQX'][0:]
elif seq.info.has_key('SAQX'):
self.log.errorLog('Cannot use SAQX for %s in PAQ as wrong length.' % seq.shortName(),printerror=False)
for otherseq in haqlist.seq:
pwaq[(seq,otherseq)] = [False] * seq.seqLen()
### <PAQ1> ### Directional Pairwise Comparisons of sequences
_stage = '<1> Pairwise Comparisons'
infotxt = 'PAQ%d: Pairwise Comparisons ...' % self.stat['PAQCyc']
#print self.stat
for seq in haqlist.seq:
for otherseq in haqlist.seq:
myinfo = '%s %.1f%% %.1f%% ' % (infotxt,(100.0 * haqlist.seq.index(seq) / haqlist.seqNum()),(100.0 * haqlist.seq.index(otherseq) / haqlist.seqNum()))
self.log.printLog('\r#PAQ',myinfo,log=False,newline=False)
for r in range(seq.seqLen()):
ar = seq.info['Sequence'][r]
## <i> ## Look for PW aligned block
_stage = '<1-i> Pairwise Comparisons'
if ar not in ['-','X']: # Start of test block
blen = 0 # Block length (PAQBlock) = AAs
win = 0 # Window length = all sequence
matchx = 0 # Score for residues in window
while blen < self.stat['PAQBlock'] and (r+win) < seq.seqLen(): # This time we allow overshoots in both directions
ar = seq.info['Sequence'][r+win]
at = otherseq.info['Sequence'][r+win]
if 'X' in [ar,at]: # Hit Bad Region: Abort
break
else: # Better region
if ar != '-':
blen += 1 # Increase Block
matchx += self._saqCon(ar,at)
win += 1
## <ii> ## Update pwaq if block good
_stage = '<1-ii> Pairwise Comparisons'
if matchx >= self.stat['PAQMatch']:
for w in range(win):
if seq.info['Sequence'][r+w] in ['-','X']:
pwaq[(seq,otherseq)][r+w] = False
else:
pwaq[(seq,otherseq)][r+w] = True
self.log.printLog('\r#PAQ','%s 100.0% 100.0%. ' % infotxt,log=False)
### <PAQ2> ### Link back to Query
_stage = '<2> Linking to Query'
### <PAQ2a> ### Network of Pairwise Quality alignments
_stage = '<2a> Linking to Query'
#self.verbose(1,3,'PAQ%d: Linking Residues to Query (%s)' % (self.stat['PAQCyc'],query.shortName()),0)
infotxt = 'PAQ%d: Linking Residues to Query (%s) ...' % (self.stat['PAQCyc'],query.shortName())
for r in range(query.seqLen()):
_stage = '<2a> Linking to Query'
self.log.printLog('\r#PAQ','%s %.1f%%' % (infotxt,(100.0 * r / query.seqLen())),log=False,newline=False)
qok = {} # Dictionary of whether residue in seq OK, i.e. linked to query
for seq in haqlist.seq:
qok[seq] = False
qok[query] = True
sok = [0,1] # List of OK sequence for residue
while sok[-2] != sok[-1]:
## <i> ## Match pairs, starting with query
_stage = '<2a-i> Linking to Query'
for seq in haqlist.seq:
if qok[seq]:
for otherseq in haqlist.seq:
if pwaq[(seq,otherseq)][r] or pwaq[(otherseq,seq)][r]:
qok[otherseq] = True
## <ii> ## Update sok
_stage = '<2a-ii> Linking to Query'
sok.append(0)
for seq in haqlist.seq:
if qok[seq]:
sok[-1] += 1
block_align[seq][r] = True
_stage = '<2a-iii> Linking to Query'
if sok[-1] == 1: # Only query OK!
block_align[query][r] = False
self.log.printLog('\r#PAQ','%s 100.0%%' % infotxt,log=False)
### <PAQ2b> ### Allow for divergence (Conserved Anchors)
_stage = '<2b> Anchors'
if self.opt['Anchors']:
infotxt = 'PAQ%d: Accounting for divergence within aligned regions ...' % self.stat['PAQCyc']
## <i> ## Setup gapped list
gapped = [False] * query.seqLen() # Whether column of alignment is gapped
for seq in haqlist.seq:
self.log.printLog('\r#PAQ','%s %.1f%% ' % (infotxt,(50.0 * haqlist.seq.index(seq) / haqlist.seqNum())),log=False,newline=False)
(start,end) = (0,seq.seqLen())
while seq.info['Sequence'][start] == '-':
start += 1
while seq.info['Sequence'][end-1] == '-':
end -=1
for r in range(start,end):
if seq.info['Sequence'][r] == '-':
gapped[r] = True
## <ii> ## Correction
for seq in haqlist.seq:
self.log.printLog('\r#PAQ','%s %.1f%% ' % (infotxt,(50 + (50.0 * haqlist.seq.index(seq) / haqlist.seqNum()))),log=False,newline=False)
for r in range(seq.seqLen()):
if block_align[seq][r] or gapped[r]: # No need for correction
continue
# Move in both directions: if good residues (or sequence end) reached before gaps then reinstate
winf = 0
fwd = True
fok = False
winb = 0
bwd = True
bok = False
while fwd or bwd:
# End of seqs
if (r + winf) >= seq.seqLen():
fwd = False
if (r - winb) < 0:
bwd = False
# Gaps/OK
if fwd:
if gapped[r+winf]:
fok = False
fwd = False
elif block_align[seq][r+winf]:
fwd = False
else:
winf += 1
if bwd:
if gapped[r-winb]:
bok = False
bwd = False
elif block_align[seq][r-winb]:
bwd = False
else:
winb += 1
if fok and bok: # Reinstate
for w in range(r-winb,r+winf+1):
block_align[seq][w] = True
self.log.printLog('\r#PAQ','%s 100.0%% ' % infotxt,log=False)
### <PAQ3> ### X out badly-aligned blocks
_stage = '<3> Making bad sequence blocks'
for seq in haqlist.seq:
newseq = ''
for r in range(seq.seqLen()):
if block_align[seq][r] or seq.info['Sequence'][r] == '-':
newseq += seq.info['Sequence'][r]
else: # Bad residue
newseq += 'X'
seq.info['Sequence'] = newseq[0:]
#!# Add saving of data in 'datafull' option
### <PAQ4> ### Remove sequences and/or badly-aligned regions
_stage = '<4> Removing sequences/regions'
self.verbose(0,4,'PAQ%d: Removing bad sequences and/or dodgy regions...' % self.stat['PAQCyc'],0)
## <PAQ4a> ## Process Query first - only interested in good regions within query
if self.opt['NoQuery']: # No preprocessing of Query
self.verbose(0,4,'no Master Query processing...',0)
else:
haqlist.mapX(query, qtrim=True, focus=focus) # Replaces other sequence ends and query X columns with Xs
self.verbose(0,4,'Query (%s) processed...' % query.shortName(),0)
self.verbose(0,3,'',1)
if self.opt['ManPAQ']:
haqlist.saveFasta(seqfile='%s.manpaq.fas' % haqlist.info['Basefile'])
## <PAQ4b> ## Cycle through other sequences (worst first) until no more good residues are lost
goodres = [0, self._getGood(haqlist.seq)] # List of number of 'good' residues
goodseq = [0, haqlist.seqNum()]
while goodres[-1] != goodres[-2] or goodseq[-1] != goodseq[-2]:
colgood = [0] * haqlist.seq[0].seqLen() # Good residues per column
for r in range(haqlist.seq[0].seqLen()):
for seq in haqlist.seq:
if seq.info['Sequence'][r] != '-' and seq.info['Sequence'][r] != 'X':
colgood[r] += 1
## <i> ## Compare relative loss of masking and losing each sequence
keepx = {} # Dictionary of seq:number of lost residues if seq kept
losex = {} # Dictionary of seq:number of lost residues if seq lost
badkx = -1 # Biggest loss if kept
badlx = -1 # Biggest loss if lost
bads = None # Worst sequence
for seq in haqlist.seq:
if seq == query and self.opt['NoQuery'] == False:
continue # Next sequence
# Calculate keepx and losex
keepx[seq] = 0
for r in range(seq.seqLen()):
if seq.info['Sequence'][r] == 'X':
keepx[seq] += colgood[r]
#?# In Perl HAQESAC there was an option to ignore Orphans in this calculation. Reinstate?
losex[seq] = self._getGood([seq])
# Update bads if worse
if keepx[seq] > badkx:
badkx = keepx[seq]
badlx = losex[seq]
bads = seq
elif keepx[seq] == badkx and losex[seq] < badlx:
badlx = losex[seq]
bads = seq
## <ii> ## Remove bad sequences and/or regions
if badkx > 0:
if self.opt['ManPAQ']:
default = 'N'
if badkx * self.stat['PAQKeepLen'] > badlx * self.stat['PAQKeepSeq']: # Lose sequence!
default = 'Y'
if rje.yesNo('%s worst: -%s aa if kept vs -%s aa if lost. Remove?' % (bads.shortName(),rje.integerString(badkx),rje.integerString(badlx)),default):
seqlist.removeSeq(text='PAQ%d: -%s aa if kept vs -%s aa if lost. (Manual decision.)' % (self.stat['PAQCyc'],rje.integerString(badkx),rje.integerString(badlx)),seq=bads)
else: # X out
haqlist.mapX(bads)
else:
self.verbose(1,3,'%s worst: -%s aa if kept vs -%s aa if lost.' % (bads.shortName(),rje.integerString(badkx),rje.integerString(badlx)),1)
#!# Add option for upweighting certain sequence type? (e.g. vs fragment or hypothetical?)
if badkx * self.stat['PAQKeepLen'] > badlx * self.stat['PAQKeepSeq']: # Lose sequence!
seqlist.removeSeq(text='PAQ%d: -%s aa if kept vs -%s aa if lost.' % (self.stat['PAQCyc'],rje.integerString(badkx),rje.integerString(badlx)),seq=bads)
else: # X out
haqlist.mapX(bads)
### <iii> ### Recalculate goodres
goodres.append(self._getGood(haqlist.seq))
goodseq.append(haqlist.seqNum())
self.verbose(1,3,'%d -> %d "good" aa' % (goodres[-2],goodres[-1]),1)
### <PAQ5> ### Reinstate UnX'd sequence:
_stage = '<5> Replacing sequences'
for seq in haqlist.seq:
[seq.info['PAQ'],seq.info['Sequence']] = [seq.info['Sequence'],seq.info['PAQ']]
if self.opt['ManPAQ'] and rje.checkForFile('%s.manpaq.fas' % haqlist.info['Basefile']):
os.unlink('%s.manpaq.fas' % haqlist.info['Basefile'])
except:
self.log.errorLog('rje_haq.py ~ Problem with pairwiseAQ %s.' % _stage, True)
def singleSeqAQ(self,
seqlist,
focus=[
0, -1
]): ### Performs SAQ on seqlist, adding seq.info['SAQ']
'''
Performs SAQ on seqlist, adding seq.info['SAQ'].
>> seqlist:rje_seq.SeqList Object
- NB. This object will itself have sequences removed from it, so beware!
- A new info key will be added: SAQX = SAQ sequences with individual Xs
- A new info key will be added: SAQ = SAQ sequences with aligment Xs
>> focus:list of range positions [X:Y] to look at. If Y=0 then [X:].
'''
### <SAQ1> ### Setup
try:
_stage = '<1> Setup'
haqlist = seqlist # SeqList Object to store individually Xd sequences
query = haqlist.obj['QuerySeq']
if self.opt['NoQuery']:
query = None
badres = [-1, 0] # List of how many bad residues in total dataset
block_align = {
} # Dictionary of whether residue in block of sequence that is well-aligned or not
res_align = {
} # Dictionary of whether residue of sequence is well-aligned or not
res_gap = {
} # Dictionary of whether residue of sequence is a gap or not
gap_align = {
} # Dictionary of whether residue of sequence is a gap in a well-aligned block or not
for seq in haqlist.seq:
seq.info['SAQ'] = seq.info['Sequence'][
0:] # Note! Sequence is modified and SAQ not, then they are swapped at end!
block_align[seq] = [False] * seq.seqLen()
res_align[seq] = [False] * seq.seqLen()
res_gap[seq] = [False] * seq.seqLen()
gap_align[seq] = [False] * seq.seqLen()
### <SAQ2> ### Repeated cycles of defining well- and badly-aligned blocks
#X#self.deBug(self.stat)
_stage = '<2> BlockID'
while badres[-1] != badres[-2]: # Change in number of bad residues
total_res = 0
badres.append(
0) # badres[-1] is the current number of bad residues
infotxt = 'SAQ%d-%d: Calculating "bad" residues ...' % (
self.stat['SAQCyc'], len(badres) - 2)
for seq in haqlist.seq:
myinfo = '%s %.1f%%' % (infotxt,
(100.0 * haqlist.seq.index(seq) /
haqlist.seqNum()))
self.log.printLog('\r#SAQ',
myinfo,
log=False,
newline=False)
#self.verbose(0,3,'\r%45s' % myinfo,0)
## <SAQ2a> ## For each sequence, mark residues as aligned or gapped
_stage = '<2a> Mark Residues'
for r in range(seq.seqLen()):
gap_align[seq][r] = False
res_align[seq][r] = False
if block_align[seq][r] or len(
badres
) == 3: # After first cycle, look only at well-aligned blocks (well-aligned for sequence not whole alignment)
a = seq.info['Sequence'][r]
res_gap[seq][r] = False
if a == '-':
res_gap[seq][r] = True
gap_align[seq][r] = True
else: # 'X' handled by self._saqCon
conx = 0 # Matches with good regions of otherseqs (*including self*)
for otherseq in haqlist.seq[0:]:
if otherseq == seq: # > so self not counted!
continue
if len(otherseq.info['Sequence']) != len(
seq.info['Sequence']):
self.log.errorLog(
'Sequence lengths do not match - should be aligned!',
printerror=False)
raise ValueError
if (block_align[otherseq][r]
or len(badres) == 3):
conx += self._saqCon(
a, otherseq.info['Sequence'][r])
#if seq == query and r > 590:
# print seq.shortName(),r,conx,'vs',self.stat['SAQCon'],
if conx >= self.stat['SAQCon']:
res_align[seq][r] = True
#if seq == query and r > 590:
# print r, res_align[seq][r]
## <SAQ2b> ## Marked regions of well-aligned residues for each sequence
_stage = '<2b> Mark Regions'
## <i> ## Clear first
_stage = '<2b-i> Mark Regions'
for r in range(seq.seqLen()):
block_align[seq][r] = False
## <ii> ## Recalculate
_stage = '<2b-ii> Mark Regions'
for r in range(seq.seqLen()):
_stage = '<2b-ii> Blocks'
if res_align[seq][r]: # Start of potential block
blen = 0 # Block length (SAQBlock) = AAs
win = 0 # Window length = all sequence
matchx = 1 # Good residues in window (first residue must be good!) (SAQMatch)
while blen < self.stat[
'SAQBlock'] and matchx < self.stat[
'SAQMatch']:
win += 1
if (r + win
) >= seq.seqLen() or seq.info['Sequence'][
r +
win] == 'X': # Hit Bad Region: Abort
break
else: # Better region
if gap_align[seq][r + win]: # Decent gap
continue
else:
blen += 1 # Increase Block
if res_align[seq][r +
win]: # Good residue
matchx += 1
#if seq == query and r > 590:
# print seq.shortName(),r,matchx,'vs',self.stat['SAQMatch'],
if matchx >= self.stat['SAQMatch']:
for w in range((win + 1)):
block_align[seq][r + w] = True
#if seq == query and r > 590:
# print r, block_align[seq][r]
## <iii> ## Update bad residue count
for r in range(seq.seqLen()):
_stage = '<2b-iii> Mark Regions'
#print seq.shortName(), r, seq.seqLen(), block_align[seq][r], res_gap[seq][r], badres[-1] # Bad residue
if not block_align[seq][r] and not res_gap[seq][
r]: # Bad residue
badres[-1] += 1
if not res_gap[seq][r]:
total_res += 1
myinfo = '%s 100.0%%' % infotxt
myinfo += ' => %s bad of %s total residues' % (
rje.integerString(
badres[-1]), rje.integerString(total_res))
self.log.printLog('\r#SAQ', myinfo)
#self.verbose(0,3,'\r%45s' % myinfo,0)
if badres[-1] == total_res:
self.log.errorLog('All residues marked as bad in SAQ!',
printerror=False,
quitchoice=True)
# Now have all residues in all sequences marked as good (block_align=True) or bad (block_align=False)
### <SAQ3> ### X out badly-aligned blocks
_stage = '<3> X-Out'
self.log.printLog('#SAQ',
'SAQ%d-%d: Masking "bad" residues ...' %
(self.stat['SAQCyc'], len(badres) - 2),
log=False,
newline=False)
#self.verbose(0,3,'SAQ%d-%d: Masking "bad" residues ...' % (self.stat['SAQCyc'],len(badres)-2),0)
for seq in haqlist.seq:
newseq = ''
for r in range(seq.seqLen()):
if block_align[seq][r] or seq.info['Sequence'][
r] == '-': #!# Was backwards? res_gap[seq][r] == False:
newseq += seq.info['Sequence'][r]
else: # Bad residue
newseq += 'X'
seq.info['Sequence'] = newseq[0:]
seq.info['SAQX'] = newseq[
0:] # Stores Xd sequences for individuals for use in PAQ
#!# Add saving of data in 'datafull' option
### <SAQ4> ### Remove sequences and/or badly-aligned regions
_stage = '<4> Removal'
self.log.printLog(
'\r#SAQ',
'SAQ%d-%d: Removing bad sequences and/or dodgy regions...' %
(self.stat['SAQCyc'], len(badres) - 2),
log=False,
newline=False)
#self.verbose(0,3,'\rSAQ%d-%d: Removing bad sequences and/or dodgy regions...' % (self.stat['SAQCyc'],len(badres)-2),0)
## <SAQ4a> ## Process Query first - only interested in good regions within query
_stage = '<4a> Query Removal'
if self.opt[
'NoQuery'] or query == None: # No preprocessing of Query
self.verbose(0, 4, 'no Master Query processing...', 0)
else:
haqlist.mapX(
query, qtrim=True, focus=focus
) # Replaces other sequence ends and query X columns with Xs
self.verbose(0, 4,
'Query (%s) processed...' % query.shortName(), 0)
self.verbose(0, 3, '', 1)
if self.opt['ManSAQ']:
haqlist.saveFasta(seqfile='%s.mansaq.fas' %
haqlist.info['Basefile'])
## <SAQ4b> ## Cycle through other sequences (worst first) until no more good residues or sequences are lost
_stage = '<4b> Seq Removal'
goodres = [0, self._getGood(haqlist.seq)
] # List of number of 'good' residues
goodseq = [0, haqlist.seqNum()]
while goodres[-1] != goodres[-2] or goodseq[-1] != goodseq[-2]:
colgood = [
0
] * haqlist.seq[0].seqLen() # Good residues per column
for r in range(haqlist.seq[0].seqLen()):
for seq in haqlist.seq:
if seq.info['Sequence'][r] != '-' and seq.info[
'Sequence'][r] != 'X':
colgood[r] += 1
## <i> ## Compare relative loss of masking and losing each sequence
keepx = {
} # Dictionary of seq:number of lost residues if seq kept
losex = {
} # Dictionary of seq:number of lost residues if seq lost
badkx = -1 # Biggest loss if kept
badlx = -1 # Biggest loss if lost
bads = None # Worst sequence
for seq in haqlist.seq:
if seq == query and self.opt['NoQuery'] == False:
continue # Next sequence
# Calculate keepx and losex
keepx[seq] = 0
for r in range(seq.seqLen()):
if seq.info['Sequence'][r] == 'X':
keepx[seq] += colgood[r]
losex[seq] = self._getGood([seq])
# Update bads if worse
if keepx[seq] > badkx:
badkx = keepx[seq]
badlx = losex[seq]
bads = seq
elif keepx[seq] == badkx and losex[seq] < badlx:
badlx = losex[seq]
bads = seq
## <ii> ## Remove bad sequences and/or regions
if badkx > 0:
if self.opt['ManSAQ']:
default = 'N'
if badkx * self.stat['SAQKeepLen'] > badlx * self.stat[
'SAQKeepSeq']: # Lose sequence!
default = 'Y'
if rje.yesNo(
'%s worst: -%s aa if kept vs -%s aa if lost. Remove?'
% (bads.shortName(), rje.integerString(badkx),
rje.integerString(badlx)), default):
seqlist.removeSeq(
text=
'SAQ%d: -%s aa if kept vs -%s aa if lost. (Manual decision.)'
%
(self.stat['SAQCyc'], rje.integerString(badkx),
rje.integerString(badlx)),
seq=bads)
else: # X out
haqlist.mapX(bads)
else:
self.verbose(
1, 3,
'%s worst: -%s aa if kept vs -%s aa if lost.' %
(bads.shortName(), rje.integerString(badkx),
rje.integerString(badlx)), 1)
#!# Add option for upweighting certain sequence type? (e.g. vs fragment or hypothetical?)
if badkx * self.stat['SAQKeepLen'] > badlx * self.stat[
'SAQKeepSeq']: # Lose sequence!
haqlist.removeSeq(
text='SAQ%d: -%s aa if kept vs -%s aa if lost.'
%
(self.stat['SAQCyc'], rje.integerString(badkx),
rje.integerString(badlx)),
seq=bads)
else: # X out
haqlist.mapX(bads)
### <iii> ### Recalculate goodres
goodres.append(self._getGood(haqlist.seq))
goodseq.append(haqlist.seqNum())
#X#self.verbose(1,3,'%d -> %d "good" aa' % (goodres[-2],goodres[-1]),1)
### <SAQ5> ### Reinstate UnX'd sequence:
_stage = '<4b> Seq Removal'
for seq in haqlist.seq:
#print seq.info
[seq.info['SAQ'], seq.info['Sequence']
] = [seq.info['Sequence'], seq.info['SAQ']]
if self.opt['ManSAQ'] and rje.checkForFile(
'%s.mansaq.fas' % haqlist.info['Basefile']):
os.unlink('%s.mansaq.fas' % haqlist.info['Basefile'])
except:
self.log.errorLog('Problem with singleSeqAQ() %s.' % _stage,
quitchoice=True)
def loadOrthAln(callobj,seq,gopher=True): ### Identifies file, loads and checks alignment.
'''
Identifies file, loads and checks alignment. If the identified file is not actually aligned, then RJE_SEQ will try to
align the proteins using MUSCLE or ClustalW.
>> callobj:Object containing settings for stats generation (MotifList, generally).
>> seq:Sequence being analysed.
>> gopher:bool [True] = whether to try to generate alignment with GOPHER if callobj.opt['Gopher']
<< aln = SeqList object containing alignment with queryseq
'''
try:
### Setup Attributes ###
v = callobj.stat['Verbose']
alndir = rje.makePath(callobj.info['AlnDir'])
alnext = callobj.info['AlnExt']
### Identify File ###
if alnext[0] != '.': alnext = '.%s' % alnext
alnstart = [seq.info['AccNum'],seq.info['ID'],seq.shortName(),None]
if v > 2: callobj.log.printLog('#PRESTO','%s' % callobj.opt) #!# Old debugging? #!#
if callobj.opt['Gopher'] and callobj.opt['FullForce']:
if v > 0: callobj.log.printLog('#ALN','FullForce=T. Will call Gopher for %s regardless of existing files' % seq.shortName())
alnstart = [None]
for file in alnstart:
if file:
file = '%s%s%s' % (alndir,file,alnext)
if rje.checkForFile(file): break # File found
else:
#!# Sort out logging and see if Gopher can be used directly rather than just run() #!#
### Run GOPHER ###
if gopher and callobj.opt['Gopher']: #!# Add working version for PRESTO and SlimPickings #!#
callobj.deBug('Run GOPHER in %s' % callobj.info['GopherDir'])
mydir = os.getcwd()
os.chdir(callobj.info['GopherDir'])
callobj.log.printLog('\n#GOPHER','Running GOPHER on %s' % seq.shortName())
try: #!# Add log.silent() method? #!#
gcmd = ['orthtree'] + callobj.cmd_list + ['gnspacc=T','i=-1']
solo_gopher = gopher_V2.GopherFork(log=callobj.log,cmd_list=gcmd)
solo_gopher.info['Name'] = seq.shortName()
solo_gopher.obj['Sequence'] = seq
solo_gopher.obj['BLAST'] = gopher_V2.Gopher(callobj.log,gcmd).setupBlast() #!# Contemplate setting up Gopher in callobj #!#
solo_gopher.obj['BLAST'].log = callobj.log
solo_gopher.run('orthalign') #X#gopher_V2.Gopher(callobj.log,gcmd).setMode())
except:
os.chdir(mydir)
callobj.log.errorLog('Problem with Gopher run!')
return None
if not 'old_school':
inputseq = 'tmp%s.fas' % rje.randomString(8)
TMP = open(inputseq,'w')
TMP.write('>%s\n%s\n' % (seq.info['Name'],seq.info['Sequence']))
TMP.close()
gcmd = ['orthtree'] + callobj.cmd_list + ['gopher=%s' % inputseq, 'gnspacc=T','i=-1']
try:
mygopher = gopher_V2.Gopher(log=callobj.log,cmd_list=gcmd)
mygopher.run()
except:
os.chdir(mydir)
callobj.log.errorLog('Problem with Gopher run!',printerror=False)
return None
rje_blast.cleanupDB(callobj,dbfile=inputseq,deletesource=True)
os.chdir(mydir)
if callobj.opt['Gopher']:
file = '%s%s%s' % (alndir,seq.info['AccNum'],alnext)
if not os.path.exists(file):
file = None
if not file:
callobj.log.printLog('#ALN','No alignment file found for %s in %s.' % (seq.shortName(),alndir),screen=False)
return None
### Load Alignment ###
callobj.log.stat['Verbose'] = v - 1
alncmd = ['seqin=None','query=%s' % seq.shortName(),'accnr=F','seqnr=F','autofilter=F','align=T','gnspacc=F']
aln = rje_seq.SeqList(log=callobj.log,cmd_list=callobj.cmd_list+alncmd)
#X#print file
aln.loadSeqs(seqfile=file,seqtype='Protein',aln=True,nodup=None)
callobj.log.stat['Verbose'] = v
## Check Query ##
qry = aln.obj['QuerySeq']
if not qry:
if aln.querySeq(query=seq.info['AccNum']):
qry = aln.obj['QuerySeq']
else:
callobj.log.printLog('#ALN','Problem finding %s in %s.' % (seq.shortName(),file),screen=False)
return None
### Check Alignment ###
if aln.seqNum() < 2:
callobj.log.printLog('#ALN','Not enough sequences for %s in %s.' % (seq.shortName(),file),screen=False)
return None
if aln._checkAln(aln=True,realign=True):
return aln
else:
callobj.log.printLog('#ERR','%s not aligned!!!' % (file))
return None
except:
callobj.log.errorLog('Something bad has happened in rje_motif_stats.loadOrthAln()')
callobj.log.stat['Verbose'] = v
return None
def pairwiseAQ(
self,
seqlist=None,
query=None,
focus=[0, 0]): ### Performs PAQ on seqlist, adding seq.info['PAQ']
'''
Performs PAQ on seqlist, adding seq.info['PAQ']
>> seqlist:rje_seq.SeqList Object
- NB. This object will itself have sequences removed from it, so beware!
- A new info key will be added: PAQ = PAQ sequences with alignment Xs
>> focus:list of range positions [X:Y] to look at. If Y=0 then [X:].
'''
### <PAQ0> ### Setup
try:
_stage = '<0> Setup'
haqlist = seqlist # SeqList Object to store individually Xd sequences
if not query:
query = haqlist.obj['QuerySeq']
if self.opt['NoQuery'] or not query:
query = haqlist.seq[random.randint(0, haqlist.seqNum() - 1)]
self.log.printLog(
'#QRY', 'Temp (random) query %s assigned for PAQ' %
query.shortName())
#!# paqx = [False] * seqlist.seq[0].seqLen() # List of whether a column of the alignment is bad (has an X) [True] or not [False]
#!# - make this a method?!
pwaq = {} # Dictionary of lists of pairwise alignements
block_align = {
} # Dictionary of whether residue in block of sequence that is well-aligned or not
for seq in haqlist.seq:
block_align[seq] = [False] * seq.seqLen()
seq.info['PAQ'] = seq.info['Sequence'][0:]
if seq.info.has_key('SAQX') and len(
seq.info['SAQX']
) == seq.seqLen(
): #!# Should no longer be issues due to length changes following realignment
seq.info['Sequence'] = seq.info['SAQX'][0:]
elif seq.info.has_key('SAQX'):
self.log.errorLog(
'Cannot use SAQX for %s in PAQ as wrong length.' %
seq.shortName(),
printerror=False)
for otherseq in haqlist.seq:
pwaq[(seq, otherseq)] = [False] * seq.seqLen()
### <PAQ1> ### Directional Pairwise Comparisons of sequences
_stage = '<1> Pairwise Comparisons'
infotxt = 'PAQ%d: Pairwise Comparisons ...' % self.stat['PAQCyc']
#print self.stat
for seq in haqlist.seq:
for otherseq in haqlist.seq:
myinfo = '%s %.1f%% %.1f%% ' % (
infotxt,
(100.0 * haqlist.seq.index(seq) / haqlist.seqNum()),
(100.0 * haqlist.seq.index(otherseq) /
haqlist.seqNum()))
self.log.printLog('\r#PAQ',
myinfo,
log=False,
newline=False)
for r in range(seq.seqLen()):
ar = seq.info['Sequence'][r]
## <i> ## Look for PW aligned block
_stage = '<1-i> Pairwise Comparisons'
if ar not in ['-', 'X']: # Start of test block
blen = 0 # Block length (PAQBlock) = AAs
win = 0 # Window length = all sequence
matchx = 0 # Score for residues in window
while blen < self.stat['PAQBlock'] and (
r + win
) < seq.seqLen(
): # This time we allow overshoots in both directions
ar = seq.info['Sequence'][r + win]
at = otherseq.info['Sequence'][r + win]
if 'X' in [ar, at]: # Hit Bad Region: Abort
break
else: # Better region
if ar != '-':
blen += 1 # Increase Block
matchx += self._saqCon(ar, at)
win += 1
## <ii> ## Update pwaq if block good
_stage = '<1-ii> Pairwise Comparisons'
if matchx >= self.stat['PAQMatch']:
for w in range(win):
if seq.info['Sequence'][r +
w] in ['-', 'X']:
pwaq[(seq, otherseq)][r + w] = False
else:
pwaq[(seq, otherseq)][r + w] = True
self.log.printLog('\r#PAQ',
'%s 100.0% 100.0%. ' % infotxt,
log=False)
### <PAQ2> ### Link back to Query
_stage = '<2> Linking to Query'
### <PAQ2a> ### Network of Pairwise Quality alignments
_stage = '<2a> Linking to Query'
#self.verbose(1,3,'PAQ%d: Linking Residues to Query (%s)' % (self.stat['PAQCyc'],query.shortName()),0)
infotxt = 'PAQ%d: Linking Residues to Query (%s) ...' % (
self.stat['PAQCyc'], query.shortName())
for r in range(query.seqLen()):
_stage = '<2a> Linking to Query'
self.log.printLog('\r#PAQ',
'%s %.1f%%' % (infotxt,
(100.0 * r / query.seqLen())),
log=False,
newline=False)
qok = {
} # Dictionary of whether residue in seq OK, i.e. linked to query
for seq in haqlist.seq:
qok[seq] = False
qok[query] = True
sok = [0, 1] # List of OK sequence for residue
while sok[-2] != sok[-1]:
## <i> ## Match pairs, starting with query
_stage = '<2a-i> Linking to Query'
for seq in haqlist.seq:
if qok[seq]:
for otherseq in haqlist.seq:
if pwaq[(seq, otherseq)][r] or pwaq[(otherseq,
seq)][r]:
qok[otherseq] = True
## <ii> ## Update sok
_stage = '<2a-ii> Linking to Query'
sok.append(0)
for seq in haqlist.seq:
if qok[seq]:
sok[-1] += 1
block_align[seq][r] = True
_stage = '<2a-iii> Linking to Query'
if sok[-1] == 1: # Only query OK!
block_align[query][r] = False
self.log.printLog('\r#PAQ', '%s 100.0%%' % infotxt, log=False)
### <PAQ2b> ### Allow for divergence (Conserved Anchors)
_stage = '<2b> Anchors'
if self.opt['Anchors']:
infotxt = 'PAQ%d: Accounting for divergence within aligned regions ...' % self.stat[
'PAQCyc']
## <i> ## Setup gapped list
gapped = [
False
] * query.seqLen() # Whether column of alignment is gapped
for seq in haqlist.seq:
self.log.printLog(
'\r#PAQ',
'%s %.1f%% ' %
(infotxt,
(50.0 * haqlist.seq.index(seq) / haqlist.seqNum())),
log=False,
newline=False)
(start, end) = (0, seq.seqLen())
while seq.info['Sequence'][start] == '-':
start += 1
while seq.info['Sequence'][end - 1] == '-':
end -= 1
for r in range(start, end):
if seq.info['Sequence'][r] == '-':
gapped[r] = True
## <ii> ## Correction
for seq in haqlist.seq:
self.log.printLog(
'\r#PAQ',
'%s %.1f%% ' %
(infotxt,
(50 +
(50.0 * haqlist.seq.index(seq) / haqlist.seqNum()))),
log=False,
newline=False)
for r in range(seq.seqLen()):
if block_align[seq][r] or gapped[
r]: # No need for correction
continue
# Move in both directions: if good residues (or sequence end) reached before gaps then reinstate
winf = 0
fwd = True
fok = False
winb = 0
bwd = True
bok = False
while fwd or bwd:
# End of seqs
if (r + winf) >= seq.seqLen():
fwd = False
if (r - winb) < 0:
bwd = False
# Gaps/OK
if fwd:
if gapped[r + winf]:
fok = False
fwd = False
elif block_align[seq][r + winf]:
fwd = False
else:
winf += 1
if bwd:
if gapped[r - winb]:
bok = False
bwd = False
elif block_align[seq][r - winb]:
bwd = False
else:
winb += 1
if fok and bok: # Reinstate
for w in range(r - winb, r + winf + 1):
block_align[seq][w] = True
self.log.printLog('\r#PAQ',
'%s 100.0%% ' % infotxt,
log=False)
### <PAQ3> ### X out badly-aligned blocks
_stage = '<3> Making bad sequence blocks'
for seq in haqlist.seq:
newseq = ''
for r in range(seq.seqLen()):
if block_align[seq][r] or seq.info['Sequence'][r] == '-':
newseq += seq.info['Sequence'][r]
else: # Bad residue
newseq += 'X'
seq.info['Sequence'] = newseq[0:]
#!# Add saving of data in 'datafull' option
### <PAQ4> ### Remove sequences and/or badly-aligned regions
_stage = '<4> Removing sequences/regions'
self.verbose(
0, 4, 'PAQ%d: Removing bad sequences and/or dodgy regions...' %
self.stat['PAQCyc'], 0)
## <PAQ4a> ## Process Query first - only interested in good regions within query
if self.opt['NoQuery']: # No preprocessing of Query
self.verbose(0, 4, 'no Master Query processing...', 0)
else:
haqlist.mapX(
query, qtrim=True, focus=focus
) # Replaces other sequence ends and query X columns with Xs
self.verbose(0, 4,
'Query (%s) processed...' % query.shortName(), 0)
self.verbose(0, 3, '', 1)
if self.opt['ManPAQ']:
haqlist.saveFasta(seqfile='%s.manpaq.fas' %
haqlist.info['Basefile'])
## <PAQ4b> ## Cycle through other sequences (worst first) until no more good residues are lost
goodres = [0, self._getGood(haqlist.seq)
] # List of number of 'good' residues
goodseq = [0, haqlist.seqNum()]
while goodres[-1] != goodres[-2] or goodseq[-1] != goodseq[-2]:
colgood = [
0
] * haqlist.seq[0].seqLen() # Good residues per column
for r in range(haqlist.seq[0].seqLen()):
for seq in haqlist.seq:
if seq.info['Sequence'][r] != '-' and seq.info[
'Sequence'][r] != 'X':
colgood[r] += 1
## <i> ## Compare relative loss of masking and losing each sequence
keepx = {
} # Dictionary of seq:number of lost residues if seq kept
losex = {
} # Dictionary of seq:number of lost residues if seq lost
badkx = -1 # Biggest loss if kept
badlx = -1 # Biggest loss if lost
bads = None # Worst sequence
for seq in haqlist.seq:
if seq == query and self.opt['NoQuery'] == False:
continue # Next sequence
# Calculate keepx and losex
keepx[seq] = 0
for r in range(seq.seqLen()):
if seq.info['Sequence'][r] == 'X':
keepx[seq] += colgood[r]
#?# In Perl HAQESAC there was an option to ignore Orphans in this calculation. Reinstate?
losex[seq] = self._getGood([seq])
# Update bads if worse
if keepx[seq] > badkx:
badkx = keepx[seq]
badlx = losex[seq]
bads = seq
elif keepx[seq] == badkx and losex[seq] < badlx:
badlx = losex[seq]
bads = seq
## <ii> ## Remove bad sequences and/or regions
if badkx > 0:
if self.opt['ManPAQ']:
default = 'N'
if badkx * self.stat['PAQKeepLen'] > badlx * self.stat[
'PAQKeepSeq']: # Lose sequence!
default = 'Y'
if rje.yesNo(
'%s worst: -%s aa if kept vs -%s aa if lost. Remove?'
% (bads.shortName(), rje.integerString(badkx),
rje.integerString(badlx)), default):
seqlist.removeSeq(
text=
'PAQ%d: -%s aa if kept vs -%s aa if lost. (Manual decision.)'
%
(self.stat['PAQCyc'], rje.integerString(badkx),
rje.integerString(badlx)),
seq=bads)
else: # X out
haqlist.mapX(bads)
else:
self.verbose(
1, 3,
'%s worst: -%s aa if kept vs -%s aa if lost.' %
(bads.shortName(), rje.integerString(badkx),
rje.integerString(badlx)), 1)
#!# Add option for upweighting certain sequence type? (e.g. vs fragment or hypothetical?)
if badkx * self.stat['PAQKeepLen'] > badlx * self.stat[
'PAQKeepSeq']: # Lose sequence!
seqlist.removeSeq(
text='PAQ%d: -%s aa if kept vs -%s aa if lost.'
%
(self.stat['PAQCyc'], rje.integerString(badkx),
rje.integerString(badlx)),
seq=bads)
else: # X out
haqlist.mapX(bads)
### <iii> ### Recalculate goodres
goodres.append(self._getGood(haqlist.seq))
goodseq.append(haqlist.seqNum())
self.verbose(1, 3,
'%d -> %d "good" aa' % (goodres[-2], goodres[-1]),
1)
### <PAQ5> ### Reinstate UnX'd sequence:
_stage = '<5> Replacing sequences'
for seq in haqlist.seq:
[seq.info['PAQ'], seq.info['Sequence']
] = [seq.info['Sequence'], seq.info['PAQ']]
if self.opt['ManPAQ'] and rje.checkForFile(
'%s.manpaq.fas' % haqlist.info['Basefile']):
os.unlink('%s.manpaq.fas' % haqlist.info['Basefile'])
except:
self.log.errorLog(
'rje_haq.py ~ Problem with pairwiseAQ %s.' % _stage, True)
def buildPam(self): ### Builds PAM Matrix in memory
'''Builds PAM matrix in memory.'''
try:
### Check for Alternative PAM Matrix ###
if self.info['AltPam'].lower() not in ['','none']:
self.altPAM()
self.verbose(0,3,"Reading PAM1 matrix from %s" % self.info['Name'],2)
### <a> ### Open file & Read Lines
pamfiles = [self.info['Name'],rje.makePath(self.info['Path']) + self.info['Name'],rje.makePath(self.info['Path']) + rje.makePath('../data/') + self.info['Name']]
self.info['Name'] = None
for pfile in pamfiles:
if rje.checkForFile(pfile):
file_lines = open(pfile, 'r').readlines()
self.info['Name'] = pfile
break
if not self.info['Name']:
for pfile in pamfiles: self.printLog('#ERR','File "%s" not found' % pfile)
self.printLog('#ERR','No PAM file found!')
raise ValueError
### <b> ### Read in alphabet
self.verbose(0,3,file_lines[0],1)
if file_lines[0].upper().find('X') >= 0:
self.opt['X-Value'] = False
if file_lines[0].find('-') >= 0:
self.opt['GapValue'] = False
self.alphabet = file_lines[0].split()
### <c> ### Make PAM0
## <i> ## Clear dics
zeropamp = {}
for r in self.alphabet:
for c in self.alphabet:
zeropamp[r + c] = 0
zeropamp[r + r] = 1
if self.opt['X-Value']:
zeropamp['X' + r] = 1
zeropamp[r + 'X'] = 1
if self.opt['GapValue']:
zeropamp['-' + r] = 1
zeropamp[r + '-'] = 1
if self.opt['X-Value']:
zeropamp['XX'] = 1
if self.opt['GapValue']:
zeropamp['--'] = 1
if self.opt['X-Value'] and self.opt['GapValue']:
zeropamp['-X'] = 1
zeropamp['X-'] = 1
## <ii> ## New Matrix
newmatrix = PAM(pam=0,rawpamp=zeropamp,alpha=self.alphabet)
self.matrix.append(newmatrix)
## <d> ## Read in PAM1
rawpamp = {}
line = 1
for r in self.alphabet:
pamline = file_lines[line].split()
if len(pamline) != (len(self.alphabet)+1):
self.log.errorLog("%s has wrong format! Does not match %s" % (pamline, self.alphabet),printerror=False,quitchoice=True)
raise
for c in range(int(len(self.alphabet))):
prob = float(pamline[c+1])
rawpamp[r + self.alphabet[c]] = prob
if self.opt['X-Value']:
rawpamp['X' + r] = 1
rawpamp[r + 'X'] = 1
if self.opt['GapValue']:
rawpamp['-' + r] = 1
rawpamp[r + '-'] = 1
line += 1
if self.opt['X-Value']:
rawpamp['XX'] = 1
if self.opt['GapValue']:
rawpamp['--'] = 1
if self.opt['X-Value'] and self.opt['GapValue']:
rawpamp['-X'] = 1
rawpamp['X-'] = 1
newmatrix = PAM(pam=1,rawpamp=rawpamp,alpha=self.alphabet)
self.matrix.append(newmatrix)
## <e> ## Raise to pammax
self.log.printLog('\r#PAM','Building PAM Matrices <= %d: ' % self.stat['PamMax'],log=False,newline=False)
self.pamUp()
self.log.printLog('\r#PAM','Building PAM Matrices <= %d: Complete.' % self.stat['PamMax'])
except:
self.log.errorLog('Fatal Error in PamCtrl.buildPam().')
raise
def singleSeqAQ(self,seqlist,focus=[0,-1]): ### Performs SAQ on seqlist, adding seq.info['SAQ']
'''
Performs SAQ on seqlist, adding seq.info['SAQ'].
>> seqlist:rje_seq.SeqList Object
- NB. This object will itself have sequences removed from it, so beware!
- A new info key will be added: SAQX = SAQ sequences with individual Xs
- A new info key will be added: SAQ = SAQ sequences with aligment Xs
>> focus:list of range positions [X:Y] to look at. If Y=0 then [X:].
'''
### <SAQ1> ### Setup
try:
_stage = '<1> Setup'
haqlist = seqlist # SeqList Object to store individually Xd sequences
query = haqlist.obj['QuerySeq']
if self.opt['NoQuery']:
query = None
badres = [-1,0] # List of how many bad residues in total dataset
block_align = {} # Dictionary of whether residue in block of sequence that is well-aligned or not
res_align = {} # Dictionary of whether residue of sequence is well-aligned or not
res_gap = {} # Dictionary of whether residue of sequence is a gap or not
gap_align = {} # Dictionary of whether residue of sequence is a gap in a well-aligned block or not
for seq in haqlist.seq:
seq.info['SAQ'] = seq.info['Sequence'][0:] # Note! Sequence is modified and SAQ not, then they are swapped at end!
block_align[seq] = [False] * seq.seqLen()
res_align[seq] = [False] * seq.seqLen()
res_gap[seq] = [False] * seq.seqLen()
gap_align[seq] = [False] * seq.seqLen()
### <SAQ2> ### Repeated cycles of defining well- and badly-aligned blocks
#X#self.deBug(self.stat)
_stage = '<2> BlockID'
while badres[-1] != badres[-2]: # Change in number of bad residues
total_res = 0
badres.append(0) # badres[-1] is the current number of bad residues
infotxt = 'SAQ%d-%d: Calculating "bad" residues ...' % (self.stat['SAQCyc'],len(badres)-2)
for seq in haqlist.seq:
myinfo = '%s %.1f%%' % (infotxt,(100.0 * haqlist.seq.index(seq) / haqlist.seqNum()))
self.log.printLog('\r#SAQ',myinfo,log=False,newline=False)
#self.verbose(0,3,'\r%45s' % myinfo,0)
## <SAQ2a> ## For each sequence, mark residues as aligned or gapped
_stage = '<2a> Mark Residues'
for r in range(seq.seqLen()):
gap_align[seq][r] = False
res_align[seq][r] = False
if block_align[seq][r] or len(badres) == 3: # After first cycle, look only at well-aligned blocks (well-aligned for sequence not whole alignment)
a = seq.info['Sequence'][r]
res_gap[seq][r] = False
if a == '-':
res_gap[seq][r] = True
gap_align[seq][r] = True
else: # 'X' handled by self._saqCon
conx = 0 # Matches with good regions of otherseqs (*including self*)
for otherseq in haqlist.seq[0:]:
if otherseq == seq: # > so self not counted!
continue
if len(otherseq.info['Sequence']) != len(seq.info['Sequence']):
self.log.errorLog('Sequence lengths do not match - should be aligned!',printerror=False)
raise ValueError
if (block_align[otherseq][r] or len(badres) == 3):
conx += self._saqCon(a, otherseq.info['Sequence'][r])
#if seq == query and r > 590:
# print seq.shortName(),r,conx,'vs',self.stat['SAQCon'],
if conx >= self.stat['SAQCon']:
res_align[seq][r] = True
#if seq == query and r > 590:
# print r, res_align[seq][r]
## <SAQ2b> ## Marked regions of well-aligned residues for each sequence
_stage = '<2b> Mark Regions'
## <i> ## Clear first
_stage = '<2b-i> Mark Regions'
for r in range(seq.seqLen()):
block_align[seq][r] = False
## <ii> ## Recalculate
_stage = '<2b-ii> Mark Regions'
for r in range(seq.seqLen()):
_stage = '<2b-ii> Blocks'
if res_align[seq][r]: # Start of potential block
blen = 0 # Block length (SAQBlock) = AAs
win = 0 # Window length = all sequence
matchx = 1 # Good residues in window (first residue must be good!) (SAQMatch)
while blen < self.stat['SAQBlock'] and matchx < self.stat['SAQMatch']:
win += 1
if (r + win) >= seq.seqLen() or seq.info['Sequence'][r+win] == 'X': # Hit Bad Region: Abort
break
else: # Better region
if gap_align[seq][r+win]: # Decent gap
continue
else:
blen += 1 # Increase Block
if res_align[seq][r+win]: # Good residue
matchx += 1
#if seq == query and r > 590:
# print seq.shortName(),r,matchx,'vs',self.stat['SAQMatch'],
if matchx >= self.stat['SAQMatch']:
for w in range((win+1)):
block_align[seq][r+w] = True
#if seq == query and r > 590:
# print r, block_align[seq][r]
## <iii> ## Update bad residue count
for r in range(seq.seqLen()):
_stage = '<2b-iii> Mark Regions'
#print seq.shortName(), r, seq.seqLen(), block_align[seq][r], res_gap[seq][r], badres[-1] # Bad residue
if not block_align[seq][r] and not res_gap[seq][r]: # Bad residue
badres[-1] += 1
if not res_gap[seq][r]:
total_res += 1
myinfo = '%s 100.0%%' % infotxt
myinfo += ' => %s bad of %s total residues' % (rje.integerString(badres[-1]),rje.integerString(total_res))
self.log.printLog('\r#SAQ',myinfo)
#self.verbose(0,3,'\r%45s' % myinfo,0)
if badres[-1] == total_res:
self.log.errorLog('All residues marked as bad in SAQ!',printerror=False,quitchoice=True)
# Now have all residues in all sequences marked as good (block_align=True) or bad (block_align=False)
### <SAQ3> ### X out badly-aligned blocks
_stage = '<3> X-Out'
self.log.printLog('#SAQ','SAQ%d-%d: Masking "bad" residues ...' % (self.stat['SAQCyc'],len(badres)-2),log=False,newline=False)
#self.verbose(0,3,'SAQ%d-%d: Masking "bad" residues ...' % (self.stat['SAQCyc'],len(badres)-2),0)
for seq in haqlist.seq:
newseq = ''
for r in range(seq.seqLen()):
if block_align[seq][r] or seq.info['Sequence'][r] == '-': #!# Was backwards? res_gap[seq][r] == False:
newseq += seq.info['Sequence'][r]
else: # Bad residue
newseq += 'X'
seq.info['Sequence'] = newseq[0:]
seq.info['SAQX'] = newseq[0:] # Stores Xd sequences for individuals for use in PAQ
#!# Add saving of data in 'datafull' option
### <SAQ4> ### Remove sequences and/or badly-aligned regions
_stage = '<4> Removal'
self.log.printLog('\r#SAQ','SAQ%d-%d: Removing bad sequences and/or dodgy regions...' % (self.stat['SAQCyc'],len(badres)-2),log=False,newline=False)
#self.verbose(0,3,'\rSAQ%d-%d: Removing bad sequences and/or dodgy regions...' % (self.stat['SAQCyc'],len(badres)-2),0)
## <SAQ4a> ## Process Query first - only interested in good regions within query
_stage = '<4a> Query Removal'
if self.opt['NoQuery'] or query == None: # No preprocessing of Query
self.verbose(0,4,'no Master Query processing...',0)
else:
haqlist.mapX(query, qtrim=True, focus=focus) # Replaces other sequence ends and query X columns with Xs
self.verbose(0,4,'Query (%s) processed...' % query.shortName(),0)
self.verbose(0,3,'',1)
if self.opt['ManSAQ']:
haqlist.saveFasta(seqfile='%s.mansaq.fas' % haqlist.info['Basefile'])
## <SAQ4b> ## Cycle through other sequences (worst first) until no more good residues or sequences are lost
_stage = '<4b> Seq Removal'
goodres = [0, self._getGood(haqlist.seq)] # List of number of 'good' residues
goodseq = [0, haqlist.seqNum()]
while goodres[-1] != goodres[-2] or goodseq[-1] != goodseq[-2]:
colgood = [0] * haqlist.seq[0].seqLen() # Good residues per column
for r in range(haqlist.seq[0].seqLen()):
for seq in haqlist.seq:
if seq.info['Sequence'][r] != '-' and seq.info['Sequence'][r] != 'X':
colgood[r] += 1
## <i> ## Compare relative loss of masking and losing each sequence
keepx = {} # Dictionary of seq:number of lost residues if seq kept
losex = {} # Dictionary of seq:number of lost residues if seq lost
badkx = -1 # Biggest loss if kept
badlx = -1 # Biggest loss if lost
bads = None # Worst sequence
for seq in haqlist.seq:
if seq == query and self.opt['NoQuery'] == False:
continue # Next sequence
# Calculate keepx and losex
keepx[seq] = 0
for r in range(seq.seqLen()):
if seq.info['Sequence'][r] == 'X':
keepx[seq] += colgood[r]
losex[seq] = self._getGood([seq])
# Update bads if worse
if keepx[seq] > badkx:
badkx = keepx[seq]
badlx = losex[seq]
bads = seq
elif keepx[seq] == badkx and losex[seq] < badlx:
badlx = losex[seq]
bads = seq
## <ii> ## Remove bad sequences and/or regions
if badkx > 0:
if self.opt['ManSAQ']:
default = 'N'
if badkx * self.stat['SAQKeepLen'] > badlx * self.stat['SAQKeepSeq']: # Lose sequence!
default = 'Y'
if rje.yesNo('%s worst: -%s aa if kept vs -%s aa if lost. Remove?' % (bads.shortName(),rje.integerString(badkx),rje.integerString(badlx)),default):
seqlist.removeSeq(text='SAQ%d: -%s aa if kept vs -%s aa if lost. (Manual decision.)' % (self.stat['SAQCyc'],rje.integerString(badkx),rje.integerString(badlx)),seq=bads)
else: # X out
haqlist.mapX(bads)
else:
self.verbose(1,3,'%s worst: -%s aa if kept vs -%s aa if lost.' % (bads.shortName(),rje.integerString(badkx),rje.integerString(badlx)),1)
#!# Add option for upweighting certain sequence type? (e.g. vs fragment or hypothetical?)
if badkx * self.stat['SAQKeepLen'] > badlx * self.stat['SAQKeepSeq']: # Lose sequence!
haqlist.removeSeq(text='SAQ%d: -%s aa if kept vs -%s aa if lost.' % (self.stat['SAQCyc'],rje.integerString(badkx),rje.integerString(badlx)),seq=bads)
else: # X out
haqlist.mapX(bads)
### <iii> ### Recalculate goodres
goodres.append(self._getGood(haqlist.seq))
goodseq.append(haqlist.seqNum())
#X#self.verbose(1,3,'%d -> %d "good" aa' % (goodres[-2],goodres[-1]),1)
### <SAQ5> ### Reinstate UnX'd sequence:
_stage = '<4b> Seq Removal'
for seq in haqlist.seq:
#print seq.info
[seq.info['SAQ'],seq.info['Sequence']] = [seq.info['Sequence'],seq.info['SAQ']]
if self.opt['ManSAQ'] and rje.checkForFile('%s.mansaq.fas' % haqlist.info['Basefile']):
os.unlink('%s.mansaq.fas' % haqlist.info['Basefile'])
except:
self.log.errorLog('Problem with singleSeqAQ() %s.' % _stage, quitchoice=True)
def buildPam(self): ### Builds PAM Matrix in memory
'''Builds PAM matrix in memory.'''
try:
### Check for Alternative PAM Matrix ###
if self.info['AltPam'].lower() not in ['', 'none']:
self.altPAM()
self.verbose(0, 3,
"Reading PAM1 matrix from %s" % self.info['Name'], 2)
### <a> ### Open file & Read Lines
pamfiles = [
self.info['Name'],
rje.makePath(self.info['Path']) + self.info['Name'],
rje.makePath(self.info['Path']) + rje.makePath('../data/') +
self.info['Name']
]
self.info['Name'] = None
for pfile in pamfiles:
if rje.checkForFile(pfile):
file_lines = open(pfile, 'r').readlines()
self.info['Name'] = pfile
break
if not self.info['Name']:
for pfile in pamfiles:
self.printLog('#ERR', 'File "%s" not found' % pfile)
self.printLog('#ERR', 'No PAM file found!')
raise ValueError
### <b> ### Read in alphabet
self.verbose(0, 3, file_lines[0], 1)
if file_lines[0].upper().find('X') >= 0:
self.opt['X-Value'] = False
if file_lines[0].find('-') >= 0:
self.opt['GapValue'] = False
self.alphabet = file_lines[0].split()
### <c> ### Make PAM0
## <i> ## Clear dics
zeropamp = {}
for r in self.alphabet:
for c in self.alphabet:
zeropamp[r + c] = 0
zeropamp[r + r] = 1
if self.opt['X-Value']:
zeropamp['X' + r] = 1
zeropamp[r + 'X'] = 1
if self.opt['GapValue']:
zeropamp['-' + r] = 1
zeropamp[r + '-'] = 1
if self.opt['X-Value']:
zeropamp['XX'] = 1
if self.opt['GapValue']:
zeropamp['--'] = 1
if self.opt['X-Value'] and self.opt['GapValue']:
zeropamp['-X'] = 1
zeropamp['X-'] = 1
## <ii> ## New Matrix
newmatrix = PAM(pam=0, rawpamp=zeropamp, alpha=self.alphabet)
self.matrix.append(newmatrix)
## <d> ## Read in PAM1
rawpamp = {}
line = 1
for r in self.alphabet:
pamline = file_lines[line].split()
if len(pamline) != (len(self.alphabet) + 1):
self.log.errorLog(
"%s has wrong format! Does not match %s" %
(pamline, self.alphabet),
printerror=False,
quitchoice=True)
raise
for c in range(int(len(self.alphabet))):
prob = float(pamline[c + 1])
rawpamp[r + self.alphabet[c]] = prob
if self.opt['X-Value']:
rawpamp['X' + r] = 1
rawpamp[r + 'X'] = 1
if self.opt['GapValue']:
rawpamp['-' + r] = 1
rawpamp[r + '-'] = 1
line += 1
if self.opt['X-Value']:
rawpamp['XX'] = 1
if self.opt['GapValue']:
rawpamp['--'] = 1
if self.opt['X-Value'] and self.opt['GapValue']:
rawpamp['-X'] = 1
rawpamp['X-'] = 1
newmatrix = PAM(pam=1, rawpamp=rawpamp, alpha=self.alphabet)
self.matrix.append(newmatrix)
## <e> ## Raise to pammax
self.log.printLog('\r#PAM',
'Building PAM Matrices <= %d: ' %
self.stat['PamMax'],
log=False,
newline=False)
self.pamUp()
self.log.printLog(
'\r#PAM',
'Building PAM Matrices <= %d: Complete.' % self.stat['PamMax'])
except:
self.log.errorLog('Fatal Error in PamCtrl.buildPam().')
raise
def badasp(out,mainlog,cmd_list,tree=None): ### Main BADASP Method
'''
Main BADASP Method. Automated run if interactive < 1
<1> Load Sequences and Tree
<2> Define Subfamilies
<3> GASP Ancestral Sequence Prediction
<4> Peform Functional Specificity and Sequence Conservation Calculations
<5> Output Results
'''
try: ### <0> ### Setup
_seqfile = None
_treefile = None
append_file = None
basefile = None
for cmd in cmd_list:
if cmd.find('seqin=') == 0:
_seqfile = cmd[len('seqin='):]
if _seqfile[-4] == '.':
_seqfile = _seqfile[:-4]
if cmd.find('useanc=') == 0:
_seqfile = cmd[len('useanc='):]
if _seqfile[-8:] == '.anc.fas':
_seqfile = _seqfile[:-8]
if cmd.find('nsfin=') == 0:
_treefile = cmd[len('nsfin='):]
if cmd.find('append=') == 0:
append_file = cmd[len('append='):]
if cmd.find('basefile=') == 0:
basefile = cmd[len('basefile='):]
if _seqfile and os.path.exists('%s.grp' % _seqfile):
cmd_list.append('group=%s.grp' % _seqfile)
if _seqfile and _treefile == None:
if rje.checkForFile('%s.nwk' % _seqfile): _treefile = '%s.nwk' % _seqfile
else: _treefile = '%s.nsf' % _seqfile
out.verbose(0,2,'Looking for treefile %s.' % _treefile,1)
if rje.checkForFile(_treefile):
cmd_list.append('nsfin=%s' % _treefile)
if tree == None:
mainlog.verbose(0,1,'Tree: %s' % cmd_list,2)
tree = rje_tree.Tree(log=mainlog,cmd_list=cmd_list)
#tree._setupFromCmd()
if tree.stat['MinFamNum'] < 2:
tree.stat['MinFamNum'] = 2
### <1> ### Load Sequences and Tree
while out.stat['Interactive'] > 0 or tree.obj['SeqList'] == None:
tree = rje_tree.treeMenu(out,mainlog,['root=yes']+cmd_list,tree)
if tree.obj['SeqList'] and tree.opt['Rooted']:
break
else:
print '\n ** Must have loaded sequences and a rooted tree. ** \n'
if out.stat['Interactive'] < 0 or rje.yesNo('Quit BADASP?',default='N'):
sys.exit()
basename = tree.obj['SeqList'].info['Name']
if basename[-4:] == '.fas':
basename = basename[:-4]
if basename[-4:] == '.anc':
basename = basename[:-4]
if basefile:
basename = basefile
except SystemExit:
raise
except:
mainlog.errorLog('Major Error in badasp loading sequences and tree',True)
try: ### <2> ### Define Subfamilies
while out.stat['Interactive'] > 0 or tree.groupNum() < 2:
tree.treeGroup(callmenu=True)
if tree.groupNum() >= 2:
break
else:
mainlog.errorLog('Must have at least two subfamilies for specificity analyses.',printerror=False)
if out.stat['Interactive'] < 0 or rje.yesNo('Continue without specificity analyses?'):
cmd_list.append('funcspec=')
break
elif rje.yesNo('Abort BADASP?'):
sys.exit()
except SystemExit:
raise
except:
mainlog.errorLog('Major Error in BADASP subfamilies',True)
try: ### <3> ### GASP Ancestral Sequence Prediction
if tree.node[-1].obj['Sequence'] == None: # No ancseq loaded
while out.stat['Interactive'] > 0 and rje.yesNo('Use %s for output filenames?' % basename) == False:
basename = rje.choice('FILEname (FILE.anc.fas, FILE.anc.nsf, FILE.txt)?: ', default=basename)
mygasp = rje_ancseq.Gasp(tree=tree,ancfile=basename,cmd_list=cmd_list,log=mainlog)
out.verbose(0,2,'%s' % mygasp.details(),1)
if out.stat['Interactive'] > 0:
if rje.yesNo('Use these parameters?') == False:
mygasp.edit()
mygasp.gasp()
except:
mainlog.errorLog('Major Error in BADASP GASP',True)
try: ### <4> ### Peform Functional Specificity and Sequence Conservation Calculations
_stage = '<4> Specificity/Conservation Analyses'
aaprop = rje_aaprop.AAPropMatrix(log=mainlog,cmd_list=cmd_list)
query = tree.obj['SeqList'].obj['QuerySeq']
## <a> ## Chosen Methods
_stage = '<4a> Specificity/Conservation Analyses - Chosen Methods'
funcspec = rje_specificity.methodlist # ['BAD','BADN','BADX']
seqcon = rje_conseq.methodlist # ['info']
for cmd in cmd_list:
if cmd.find('funcspec=') == 0:
funcspec = cmd[9:].split(',')
if cmd.find('seqcon=') == 0:
seqcon = cmd[len('seqcon='):].split(',')
if 'all' in funcspec:
funcspec = rje_specificity.methodlist
if 'all' in seqcon:
seqcon = rje_conseq.methodlist
for method in ['BADX','BADN','QPCon_Mean','QPCon_Abs','QPCon_Mean_All']:
while method in funcspec and query == None:
if rje.yesNo('Method %s needs query but none given. Drop %s from specificity methods?' % (method,method)):
funcspec.remove(method)
break
for seq in tree.obj['SeqList'].seq:
if rje.yesNo('Method %s needs query but none given. Use sequence 1 (%s)?' % (method,seq.shortName()),default='N'):
query = seq
tree.obj['SeqList'].obj['Query'] = seq
break
while method in seqcon and query == None:
if rje.yesNo('Method %s needs query but none given. Drop %s from conservation methods?' % (method,method)):
seqcon.remove(method)
break
for seq in tree.obj['SeqList'].seq:
if rje.yesNo('Method %s needs query but none given. Use sequence 1 (%s)?' % (method,seq.shortName()),default='N'):
query = seq
tree.obj['SeqList'].obj['Query'] = seq
break
qname = query
if query:
qname = query.info['Name']
out.verbose(0,3,'\nQuery = %s' % qname,2)
## <b> ## Spec Calculations
_stage = '<4b> Specificity Calculations'
specmatrix = rje_specificity.FuncSpec(log=mainlog,cmd_list=cmd_list,tree=tree,aaprop=aaprop)
specmatrix.calcScore(query=query,methods=funcspec)
## <c> ## Conservation Calculations
_stage = '<4c> Specificity/Conservation Analyses - Conservation Calculations'
conseq = rje_conseq.SeqStat(log=mainlog,cmd_list=cmd_list,tree=tree,aaprop=aaprop)
conseq.calcScore(query=query,methods=seqcon) ### Sends appropriate seqlist to self.calcScore()
## <d> ## Special Case: QPCon vs All seqs
_stage = '<4d> Specificity/Conservation Analyses - QPCon vs All'
qpconall = []
#if 'QPCon_Abs_All' in seqcon and query:
# qpconall.append('QPCon_Abs')
if 'QPCon_Mean_All' in seqcon and query:
qpconall.append('QPCon_Mean')
for qp in qpconall:
conseq.score['%s_All' % qp] = conseq.score[qp]
if conseq.alnwin.has_key(qp):
conseq.alnwin['%s_All' % qp] = conseq.alnwin[qp]
if conseq.qrywin.has_key(qp):
conseq.qrywin['%s_All' % qp] = conseq.qrywin[qp]
if conseq.rank.has_key(qp):
conseq.rank['%s_All' % qp] = conseq.rank[qp]
if conseq.alnrankwin.has_key(qp):
conseq.alnrankwin['%s_All' % qp] = conseq.alnrankwin[qp]
if conseq.qryrankwin.has_key(qp):
conseq.qryrankwin['%s_All' % qp] = conseq.qryrankwin[qp]
_stage = '<4d> Specificity/Conservation Analyses - FamQP'
famqp = []
if 'QPCon_Mean' in seqcon:
famqp.append('QPCon_Mean')
if 'QPCon_Abs' in seqcon:
famqp.append('QPCon_Abs')
if len(famqp) > 0 and query: #!# And subfam option?
qseq = []
for fam in tree.subfam:
for node in tree._nodeClade(fam):
if query == node.obj['Sequence']:
for qnode in tree._nodeClade(fam):
qseq.append(qnode.obj['Sequence'])
conseq.calcScore(query=query,seqlist=qseq,methods=famqp) ### Sends appropriate seqlist to self.calcScore()
except:
mainlog.errorLog('Major Error in BADASP Specificity Analysis (%s):' % _stage,True)
try: ### <5> ### Full Output Results
_stage = '<5> Full Output'
# This output is in a tab- or comma-delimited file for easy manipulation or viewing with other programs.
# (1) statistics for a given residue;
# (2) statistics for a given window size across
# - (a) the whole alignment, (node=None)
# - (b) the Query protein of interest (if given) and (node=QueryNode)
# - (c) the ancestral sequence of each subfamily; (node=ancnode)
# (3) Predicted ancestral sequences at
# - (a) the root and
# - (b) the ancestor of each subfamily.
delimit = rje.getDelimit(cmd_list)
## <a> ## Setup
_stage = '<5a> Output - Setup'
rankout = specmatrix.opt['Rank']
#tree._regenerateSeqList(tree.obj['SeqList'],tree.node)
root = tree.node[-1].obj['Sequence'] #!# At some point, make sure this is the most ancient duplication!
out.verbose(0,3,'\nBADASP Results Output (%s.badasp) ...' % basename,0)
## <b> ## Header
_stage = '<5b> Output - Header'
_header = True
if append_file:
if rje.checkForFile(append_file):
_header = False
BADASP = open(append_file, 'a')
else:
BADASP = open('%s.badasp' % basename, 'w')
BADASP.write("BADASP Output: %s\n" % (time.asctime(time.localtime(time.time()))))
BADASP.write('%s\n\n' % cmd_list)
header = ['aln_pos','anc_aa'] # Aln Pos and AA
alnlen = 0
statlist = funcspec + seqcon
_stage = '<5b-i> Output - Header Query'
if query:
header += ['qry_pos','qry_aa'] # Qry Pos and AA
_stage = '<5b-ii> Output - Header Subfam'
for f in range(len(tree.subfam)):
header += ['fam%d_pos' % (f+1),'fam%d_aa' % (f+1)] # Subfam Pos and AA
for func in statlist:
_stage = '<5b-iii> Output - Header %s' % func
statobj = statObj(method=func,objlist=[specmatrix,conseq])
fs = func.lower()
alnlen = len(statobj.score[func])
header.append(fs) # Score
if rankout:
header.append('%s_rank' % fs) # Rank
if statobj.stat['WinSize'] > 1:
header.append('%s_alnwin' % fs) # Full align window
if rankout:
header.append('%s_alnrankwin' % fs) # Rank
if query:
header.append('%s_qrywin' % fs) # Qry window
if rankout:
header.append('%s_qryrankwin' % fs) # Rank
if func in funcspec:
for f in range(len(tree.subfam)):
header.append('%s_fam%d_win' % (fs,f+1)) # Subfam windows
if rankout:
header.append('%s_fam%d_rankwin' % (fs,f+1)) # Subfam windows
#if _header:
BADASP.write('%s\n' % string.join(header, delimit))
out.verbose(1,3,'%s...' % string.join(header, delimit),0)
## <c> ## Stats
_stage = '<5c> Stats'
qr = 0 # Qry pos
fr = [0] * len(tree.subfam) # List of subfam positions
aa = '' # Root aa
qa = '' # Qry aa
fa = [''] * len(tree.subfam) # List of subfam aas
for r in range(alnlen):
# <i> # Positions and aas
_stage = '<5c-i> Output - Stats, positions & aas'
aa = root.info['Sequence'][r]
if query:
qa = query.info['Sequence'][r]
if qa != '-':
qr += 1
for f in range(len(tree.subfam)):
fa[f] = tree.subfam[f].obj['Sequence'].info['Sequence'][r]
if fa[f] != '-':
fr[f] += 1
# <ii> # Positions and AAs ii
_stage = '<5c-ii> Output - Pos & AA ii'
line = ['%d' % (r+1), aa] # Aln Pos and AA
if query:
if qa == '-':
line += ['-',qa] # Qry Pos and AA
else:
line += ['%d' % qr,qa] # Qry Pos and AA
for f in range(len(tree.subfam)):
if fa[f] == '-':
line += ['-',fa[f]] # Subfam Pos and AA
else:
line += ['%d' % fr[f],fa[f]] # Subfam Pos and AA
# <iii> # Stats
_stage = '<5c-iii> Output - Stats'
for func in statlist:
statobj = statObj(method=func,objlist=[specmatrix,conseq])
fs = func.lower()
line.append(str(statobj.score[func][r])) # Score
if rankout:
line.append(str(statobj.rank[func][r])) # Rank
if specmatrix.stat['WinSize'] > 1:
line.append(str(statobj.alnwin[func][r])) # Full align window
if rankout:
line.append(str(statobj.alnrankwin[func][r])) # Rank
if query:
line.append(str(statobj.qrywin[func][r])) # Qry window
if rankout:
line.append(str(statobj.qryrankwin[func][r])) # Rank
if func in funcspec:
for f in range(len(tree.subfam)):
line.append(str(statobj.famwin[func][tree.subfam[f]][r])) # Subfam windows
if rankout:
line.append(str(statobj.famrankwin[func][tree.subfam[f]][r])) # Subfam windows
# <iv> # Writing
_stage = '<5c-iv> Output - Writing'
BADASP.write('%s\n' % string.join(line, delimit))
BADASP.close()
out.verbose(0,2,'Done!',2)
except:
mainlog.errorLog('Fatal Error in BADASP Full output (%s):' % _stage,True)
BADASP.write('%s\n' % string.join(line, delimit))
BADASP.close()
try: ### <6> ### Partial Results Output
_stage = '<6> Partial Output'
## <a> ## Setup
_stage = '<6a> Output - Setup'
# statlist & alnlen from above
_part_append = False
if out.stat['Interactive'] > 0 and rje.yesNo('Output additional, filtered results?',default='N'):
partfile = rje.choice('Name for partial results file?:','%s.partial.badasp' % basename,confirm=True)
if rje.checkForFile(partfile) and rje.yesNo('File %s exists. Append file without headers?' % partfile):
_part_append = True
else:
return
if rje.yesNo('Filter output columns?',default='N'):
if rje.yesNo('Output query details (pos,aa & win)?') == False:
query = None
f = 1
for fam in tree.subfam[0:]:
if rje.yesNo('Output subfam %d (%s) details (pos,aa & win)?' % (f,fam.info['CladeName'])) == False:
tree.subfam.remove(fam)
f += 1
for func in statlist[0:]:
if rje.yesNo('Output %s results?' % func) == False:
statlist.remove(func)
alnout = [True] * alnlen
if rje.yesNo('Filter Rows by Results VALUES?'):
out.verbose(0,0,'Initial Defaults are minmum values. Accept intital default for no filtering of given Stat.',1)
for stat in statlist:
### Filter by value? ###
statobj = statObj(method=stat,objlist=[specmatrix,conseq])
scores = statobj.score[stat][0:]
scores.sort()
cutoff = rje.getFloat('Min. value for %s?:' % stat,default='%f' % scores[0],confirm=True)
for r in range(alnlen):
if statobj.score[stat][r] < cutoff:
alnout[r] = False
if rankout and rje.yesNo('Filter Rows by Results RANKS?'):
out.verbose(0,0,'Ranks range from 0 (low) to 1 (high).',1)
for stat in statlist:
### Filter by Rank? ###
statobj = statObj(method=stat,objlist=[specmatrix,conseq])
cutoff = rje.getFloat('Min. rank for %s?:' % stat,default='0.0',confirm=True)
for r in range(alnlen):
if statobj.rank[stat][r] < cutoff:
alnout[r] = False
out.verbose(0,3,'\nBADASP Partial Results Output (%s) ...' % partfile,0)
## <b> ## Header
_stage = '<6b> Partial Output - Header'
if _part_append:
BADASP = open(partfile, 'a')
else:
BADASP = open(partfile, 'w')
BADASP.write("Partial BADASP Output: %s\n" % (time.asctime(time.localtime(time.time()))))
BADASP.write('%s\n\n' % cmd_list)
header = ['aln_pos','anc_aa'] # Aln Pos and AA
_stage = '<6b-i> Partial Output - Header Query'
if query:
header += ['qry_pos','qry_aa'] # Qry Pos and AA
_stage = '<6b-ii> Partial Output - Header Subfam'
for f in range(len(tree.subfam)):
header += ['fam%d_pos' % (f+1),'fam%d_aa' % (f+1)] # Subfam Pos and AA
for func in statlist:
_stage = '<6b-iii> Partial Output - Header %s' % func
statobj = statObj(method=func,objlist=[specmatrix,conseq])
fs = func.lower()
header.append(fs) # Score
if rankout:
header.append('%s_rank' % fs) # Rank
if statobj.stat['WinSize'] > 1:
header.append('%s_alnwin' % fs) # Full align window
if rankout:
header.append('%s_alnrankwin' % fs) # Rank
if query:
header.append('%s_qrywin' % fs) # Qry window
if rankout:
header.append('%s_qryrankwin' % fs) # Rank
if func in funcspec:
for f in range(len(tree.subfam)):
header.append('%s_fam%d_win' % (fs,f+1)) # Subfam windows
if rankout:
header.append('%s_fam%d_rankwin' % (fs,f+1)) # Subfam windows
#if not _part_append:
BADASP.write('%s\n' % string.join(header, delimit))
out.verbose(1,3,'%s...' % string.join(header, delimit),0)
## <c> ## Stats
_stage = '<6c> Stats'
qr = 0 # Qry pos
fr = [0] * len(tree.subfam) # List of subfam positions
aa = '' # Root aa
qa = '' # Qry aa
fa = [''] * len(tree.subfam) # List of subfam aas
for r in range(alnlen):
if alnout[r] == False:
continue
# <i> # Positions and aas
_stage = '<6c-i> Partial Output - Stats, positions & aas'
aa = root.info['Sequence'][r]
if query:
qa = query.info['Sequence'][r]
if qa != '-':
qr += 1
for f in range(len(tree.subfam)):
fa[f] = tree.subfam[f].obj['Sequence'].info['Sequence'][r]
if fa[f] != '-':
fr[f] += 1
# <ii> # Positions and AAs ii
_stage = '<6c-ii> Partial Output - Pos & AA ii'
line = ['%d' % (r+1), aa] # Aln Pos and AA
if query:
if qa == '-':
line += ['-',qa] # Qry Pos and AA
else:
line += ['%d' % qr,qa] # Qry Pos and AA
for f in range(len(tree.subfam)):
if fa[f] == '-':
line += ['-',fa[f]] # Subfam Pos and AA
else:
line += ['%d' % fr[f],fa[f]] # Subfam Pos and AA
# <iii> # Stats
_stage = '<6c-iii> Partial Output - Stats'
for func in statlist:
statobj = statObj(method=func,objlist=[specmatrix,conseq])
fs = func.lower()
line.append(str(statobj.score[func][r])) # Score
if rankout:
line.append(str(statobj.rank[func][r])) # Rank
if specmatrix.stat['WinSize'] > 1:
line.append(str(statobj.alnwin[func][r])) # Full align window
if rankout:
line.append(str(statobj.alnrankwin[func][r])) # Rank
if query:
line.append(str(statobj.qrywin[func][r])) # Qry window
if rankout:
line.append(str(statobj.qryrankwin[func][r])) # Rank
if func in funcspec:
for f in range(len(tree.subfam)):
line.append(str(statobj.famwin[func][tree.subfam[f]][r])) # Subfam windows
if rankout:
line.append(str(statobj.famrankwin[func][tree.subfam[f]][r])) # Subfam windows
# <iv> # Writing
_stage = '<6c-iv> Partial Output - Writing'
BADASP.write('%s\n' % string.join(line, delimit))
BADASP.close()
out.verbose(0,2,'Done!',2)
except:
mainlog.errorLog('Fatal Error in BADASP Partial output (%s):' % _stage,True)
BADASP.write('%s\n' % string.join(line, delimit))
BADASP.close()