def convertMali2Alignlib(mali):
"""convert a multiple alignment into an alignlib multiple alignment object."""
import alignlib
m = alignlib.makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib.makeAlignatumFromString(mali[identifier])
m.add(a)
return m
def convertMali2Alignlib( mali ):
"""convert a multiple alignment into an alignlib multiple alignment object."""
import alignlib
m = alignlib.makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib.makeAlignatumFromString( mali[identifier] )
m.add( a )
return m
def convertMali2Mali( mali ):
"""convert a mali to a profile."""
new_mali = alignlib.makeMultipleAlignment()
for id in mali.getIdentifiers():
s = alignlib.makeAlignatumFromString( mali[id] )
s.thisown = 0
new_mali.addAlignatum( s )
return new_mali
def readPicasso( infile ):
"""read alignment in the non-defined picasso format.
"""
mali = alignlib.makeMultipleAlignment()
while 1:
line = infile.readline()
if not line: break
x = re.search( "\d+\s+([A-Z\-\.]*)\s+\d+", line)
if x:
s = x.groups()[0]
a = alignlib.makeAlignatumFromString(s)
a.thisown = 0
mali.addAlignatum( a )
return mali
map_mali2seq = alignlib.makeAlignataVector()
sequence = alignlib.makeSequence( cur_record.sequence )
profile = alignlib.makeProfileFromMali( new_mali )
if options.loglevel >= 4:
options.stdlog.write(profile.Write())
alignator.Align( profile, sequence, map_mali2seq )
if options.loglevel >= 3:
options.stdlog.write( map_mali2seq.Write() )
## add sequence to mali
a = alignlib.makeAlignatumFromString( cur_record.sequence )
a.thisown = 0
new_mali.addAlignatum( a, map_mali2seq, 1, 1, 1, 1, 1 )
id = cur_record.title
mali.mIdentifiers.append( id )
mali.mMali[id] = Mali.AlignedString( id, 0, len(cur_record.sequence), new_mali.getRow( new_mali.getWidth() - 1 ).getString() )
# substitute
for x in range(old_length):
mali.mMali[mali.mIdentifiers[x]].mString = new_mali.getRow( x ).getString()
mali.writeToFile( sys.stdout, format = options.output_format )
E.Stop()
try:
(query_nid, sbjct_nid, score, query_from, query_to, query_ali, sbjct_from, sbjct_to, sbjct_ali) = line
except ValueError:
continue
## first time: add query
if not query_sequence:
## if alignment is to a sequence, add query sequence at top (without gaps)
if query_nid and query_nid != "0":
if param_sequences:
if param_sequences.has_key( query_nid ):
query_sequence = param_sequences[query_nid]
else:
print "# sequence %s not found" % sbjct_nid
continue
query_alignatum = alignlib.makeAlignatumFromString( query_sequence )
identifiers.append( query_nid )
else:
query_sequence, query_nid = GetSequence( tbl_nrdb, query_nid )
(identifier, description ) = tbl_nrdb.GetAnnotationFromNid(query_nid)
query_alignatum = pairsdblib.makeAlignatumNeighbour( query_sequence, identifier, description, query_nid)
query_alignatum.thisown = 0
mali.addAlignatum( query_alignatum )
else:
query_sequence = 1
mali.setLength( max_mali_length )
## discard self-alignments
if query_nid == sbjct_nid: continue
