def Alignment2CDNA(alignment,
query_from=0,
sbjct_from=0,
genome=None,
remove_frameshifts=0):
"""build cDNA sequence from genomic fragment and
return alignment of query to it.
"""
fragments = []
sbjct_pos = 0
map_query2sbjct = alignlib_lite.py_makeAlignmentVector()
# count in nucleotides for query
query_pos = query_from * 3
sbjct_pos = sbjct_from
# position in cDNA
cdna_pos = 0
for state, l_query, l_sbjct in alignment:
# count as nucleotides
l_query *= 3
keep = False
if state == "M":
keep = True
elif state == "S":
l_query = l_sbjct
keep = True
elif state == "F" and not remove_frameshifts:
keep = True
elif state == "G":
if l_sbjct > 0:
keep = True
elif state == "P":
keep = False
if keep:
if genome:
fragments.append(genome[sbjct_pos:sbjct_pos + l_sbjct])
if l_query > 0 and l_sbjct > 0:
alignlib_lite.py_addDiagonal2Alignment(map_query2sbjct,
query_pos,
query_pos + l_query,
cdna_pos - query_pos)
cdna_pos += l_sbjct
query_pos += l_query
sbjct_pos += l_sbjct
return map_query2sbjct, fragments.join("")
def Alignment2CDNA(alignment,
query_from=0,
sbjct_from=0,
genome=None,
remove_frameshifts=0):
"""build cDNA sequence from genomic fragment and
return alignment of query to it.
"""
fragments = []
sbjct_pos = 0
map_query2sbjct = alignlib_lite.py_makeAlignmentVector()
# count in nucleotides for query
query_pos = query_from * 3
sbjct_pos = sbjct_from
# position in cDNA
cdna_pos = 0
for state, l_query, l_sbjct in alignment:
# count as nucleotides
l_query *= 3
keep = False
if state == "M":
keep = True
elif state == "S":
l_query = l_sbjct
keep = True
elif state == "F" and not remove_frameshifts:
keep = True
elif state == "G":
if l_sbjct > 0:
keep = True
elif state == "P":
keep = False
if keep:
if genome:
fragments.append(genome[sbjct_pos:sbjct_pos + l_sbjct])
if l_query > 0 and l_sbjct > 0:
alignlib_lite.py_addDiagonal2Alignment(map_query2sbjct,
query_pos,
query_pos + l_query,
cdna_pos - query_pos)
cdna_pos += l_sbjct
query_pos += l_query
sbjct_pos += l_sbjct
return map_query2sbjct, fragments.join("")
def Alignment2PeptideAlignment(alignment,
query_from=0,
sbjct_from=0,
genomic_sequence=None):
"""convert a Peptide2DNA aligment to a Peptide2Peptide alignment.
How to handle frameshifts?
"""
map_query2sbjct = alignlib_lite.py_makeAlignmentVector()
query_pos = query_from
sbjct_pos = 0
sbjct_genome_pos = sbjct_from
sbjct_residues = []
codon = ""
for state, l_query, l_sbjct in alignment:
query_increment = 0
sbjct_increment = 0
if state == "M":
query_increment = l_query
sbjct_increment = l_sbjct / 3
if genomic_sequence:
codon = genomic_sequence[sbjct_genome_pos:sbjct_genome_pos +
l_sbjct]
elif state == "S":
if l_query:
sbjct_increment = 1
query_increment = 1
if genomic_sequence:
codon += genomic_sequence[sbjct_genome_pos:sbjct_genome_pos +
l_sbjct]
elif state == "G":
query_increment = l_query
sbjct_increment = l_sbjct / 3
if genomic_sequence:
codon += genomic_sequence[sbjct_genome_pos:sbjct_genome_pos +
l_sbjct]
elif state == "P":
# only increment query, sbjct does not advance.
query_increment = l_query
if query_increment and sbjct_increment:
alignlib_lite.py_addDiagonal2Alignment(map_query2sbjct, query_pos,
query_pos + query_increment,
sbjct_pos - query_pos)
if sbjct_increment and genomic_sequence:
for x in range(0, len(codon), 3):
sbjct_residues.append(MapCodon2AA(codon[x:x + 3]))
codon = ""
query_pos += query_increment
sbjct_pos += sbjct_increment
sbjct_genome_pos += l_sbjct
return map_query2sbjct, "".join(sbjct_residues)
def Alignment2PeptideAlignment(alignment,
query_from=0,
sbjct_from=0,
genomic_sequence=None):
"""convert a Peptide2DNA aligment to a Peptide2Peptide alignment.
How to handle frameshifts?
"""
map_query2sbjct = alignlib_lite.py_makeAlignmentVector()
query_pos = query_from
sbjct_pos = 0
sbjct_genome_pos = sbjct_from
sbjct_residues = []
codon = ""
for state, l_query, l_sbjct in alignment:
query_increment = 0
sbjct_increment = 0
if state == "M":
query_increment = l_query
sbjct_increment = l_sbjct / 3
if genomic_sequence:
codon = genomic_sequence[
sbjct_genome_pos:sbjct_genome_pos + l_sbjct]
elif state == "S":
if l_query:
sbjct_increment = 1
query_increment = 1
if genomic_sequence:
codon += genomic_sequence[sbjct_genome_pos:
sbjct_genome_pos + l_sbjct]
elif state == "G":
query_increment = l_query
sbjct_increment = l_sbjct / 3
if genomic_sequence:
codon += genomic_sequence[sbjct_genome_pos:
sbjct_genome_pos + l_sbjct]
elif state == "P":
# only increment query, sbjct does not advance.
query_increment = l_query
if query_increment and sbjct_increment:
alignlib_lite.py_addDiagonal2Alignment(map_query2sbjct,
query_pos, query_pos +
query_increment,
sbjct_pos - query_pos)
if sbjct_increment and genomic_sequence:
for x in range(0, len(codon), 3):
sbjct_residues.append(MapCodon2AA(codon[x:x + 3]))
codon = ""
query_pos += query_increment
sbjct_pos += sbjct_increment
sbjct_genome_pos += l_sbjct
return map_query2sbjct, "".join(sbjct_residues)