def PrintAlignedSequences( sequence1, sequence2, chain = None, format="modeller" ):
## align sequences by identity
seq_row = alignlib.makeSequence( sequence1 )
seq_col = alignlib.makeSequence( sequence2 )
alignator = alignlib.makeAlignatorFullDP( -0.0, -0.0 )
map_row2col = alignlib.makeAlignataVector()
alignator.Align( seq_row, seq_col, map_row2col )
lines = string.split(alignlib.writePairAlignment( seq_row, seq_col, map_row2col ), "\n")
if format == "modeller":
first_res, sequence, last_res = string.split( lines[0], "\t" )
print ">P1;structure"
print "structureX: %s : %s : %s : %s : %s : : : : " % ("structure", first_res, "" , last_res, "" )
print "%s*" % sequence
first_res, sequence, last_res = string.split( lines[1], "\t" )
print ">P1;sequence"
print "sequence:%s : %s : %s : %s : %s : : : : " % ("sequence" , first_res, "", last_res, "")
print "%s*" % sequence
else:
print lines
def PrintAlignedSequences(sequence1, sequence2, chain=None, format="modeller"):
## align sequences by identity
seq_row = alignlib.makeSequence(sequence1)
seq_col = alignlib.makeSequence(sequence2)
alignator = alignlib.makeAlignatorFullDP(-0.0, -0.0)
map_row2col = alignlib.makeAlignataVector()
alignator.Align(seq_row, seq_col, map_row2col)
lines = string.split(
alignlib.writePairAlignment(seq_row, seq_col, map_row2col), "\n")
if format == "modeller":
first_res, sequence, last_res = string.split(lines[0], "\t")
print ">P1;structure"
print "structureX: %s : %s : %s : %s : %s : : : : " % (
"structure", first_res, "", last_res, "")
print "%s*" % sequence
first_res, sequence, last_res = string.split(lines[1], "\t")
print ">P1;sequence"
print "sequence:%s : %s : %s : %s : %s : : : : " % (
"sequence", first_res, "", last_res, "")
print "%s*" % sequence
else:
print lines
if map_query2sbjct.getRowTo() > len(cds_fragment):
print "# ERROR: length mismatch: cds fragment (%i) shorter than last aligned residue (%i)" %\
(len(cds_fragment), map_query2sbjct.getRowTo())
print "#", line
print "# cds"
print "#", cds_fragment
print "# genomic"
print "#",genomic_fragment
continue
cds_seq = alignlib.makeSequence( cds_fragment )
genomic_seq = alignlib.makeSequence( genomic_fragment )
data = map( lambda x: string.split(x, "\t"),
string.split( alignlib.writePairAlignment( cds_seq,
genomic_seq,
map_query2sbjct ), "\n" ))
row_ali, col_ali = Genomics.RemoveFrameShiftsFromAlignment(data[0][1], data[1][1])
row_ali = Genomics.MaskStopCodons( row_ali )
col_ali = Genomics.MaskStopCodons( col_ali )
if len(row_ali) != len(col_ali):
print "# ERROR: wrong alignment lengths."
sys.exit(1)
if len(row_ali) % 3 or len(col_ali) % 3:
print line
print row_ali
def buildMapPdb2Sequence( sequence, filename_pdb, options, pdb_chain = ""):
"""build a map for residue numbers in pdb file to residue numbers on
a sequence.
returns the following maps:
map_structure2seq: mapping of residue numbers between structure and
sequence. These are mappings that will work if you "renumber" the
structure.
map_pdb2seq, map_seq2pdb: mapping according to residue numbers in pdb file.
"""
if not os.path.exists( filename_pdb ):
return None, None
structure = Scientific.IO.PDB.Structure( filename_pdb )
map_pdb2seq = {}
map_seq2pdb = {}
for chain in structure.peptide_chains:
if chain.chain_id == pdb_chain:
## align pdb sequence to sequence
map_structure2seq = alignlib.makeAlignataVector()
alignator = alignlib.makeFullDP( -10.0, -2.0 )
## build sequence of pdb file
structure = ""
for residue in chain.sequence():
structure += AMINOACIDS[residue]
## align reference sequence to sequence of pdb file
row = alignlib.makeSequence( structure )
col = alignlib.makeSequence( sequence )
alignator.Align(row, col, map_structure2seq)
if options.loglevel >= 3:
options.stdlog.write( "structure: %s\n" % structure )
options.stdlog.write( "sequence : %s\n" % sequence )
options.stdlog.write( "alignment of structure to sequence:\n" )
options.stdlog.write( alignlib.writePairAlignment( row, col, map_structure2seq ) + "\n" )
# print alignlib.writeAlignataTable(map_structure2seq)
residue_number = 0
for residue in chain.residues:
residue_number += 1
mapped_residue = map_structure2seq.mapRowToCol(residue_number)
if not mapped_residue:
if options.loglevel >= 3:
options.stdlog.write( "# skipped residue %s=%s %i\n" % (str(residue.number), residue.name, residue_number))
continue
r = str(residue.number)
map_pdb2seq[r] = mapped_residue
map_seq2pdb[mapped_residue] = r
return map_structure2seq, map_pdb2seq, map_seq2pdb, residue_number-1, str(chain.residues[0].number), str(chain.residues[-1].number), structure
for line in sys.stdin:
if line[0] == "#": continue
link.Read( line )
ninput += 1
if link.mQueryToken not in sequences or link.mSbjctToken not in sequences:
nskipped += 1
continue
ali.Clear()
alignlib.fillAlignataCompressed( ali, link.mQueryFrom, link.mQueryAli, link.mSbjctFrom, link.mSbjctAli )
result = alignlib.writePairAlignment( sequences[link.mQueryToken], sequences[link.mSbjctToken], ali ).split("\n")
if len(result) != 3:
nfailed += 1
if options.format == "fasta":
print ">%s %i-%i\n%s\n>%s %i-%i\n%s\n" %\
(link.mQueryToken, link.mQueryFrom, link.mQueryTo, result[0].split("\t")[1],
link.mSbjctToken, link.mSbjctFrom, link.mSbjctTo, result[1].split("\t")[1] )
noutput += 1
print "# ninput=%i, noutput=%i, nskipped=%i, nfailed=%i" % (ninput, noutput, nskipped, nfailed)
E.Stop()
