def _adjust_aa_seq(fraglist):
"""Transforms three-letter amino acid codes into one-letters in the
given HSPFragments."""
hsp_hstart = fraglist[0].hit_start
hsp_qstart = fraglist[0].query_start
for frag in fraglist:
assert frag.query_strand == 0 or frag.hit_strand == 0
# fragment should have a length that is a multiple of 3
assert len(frag) % 3 == 0
# hit step may be -1 as we're aligning to DNA
hstep = 1 if frag.hit_strand >= 0 else -1
# get one letter codes
# and replace gap codon markers and termination characters
custom_map = {'***': '*', '<->': '-'}
hseq1 = seq1(str(frag.hit.seq), custom_map=custom_map)
hstart = hsp_hstart
hend = hstart + len(hseq1.replace('-', '')) * hstep
qseq1 = seq1(str(frag.query.seq), custom_map=custom_map)
qstart = hsp_qstart
qend = qstart + len(qseq1.replace('-', ''))
# replace the old frag sequences with the new ones
frag.hit = None
frag.query = None
frag.hit = hseq1
frag.query = qseq1
# set coordinates for the protein sequence
if frag.query_strand == 0:
frag.query_start, frag.query_end = qstart, qend
elif frag.hit_strand == 0:
frag.hit_start, frag.hit_end = hstart, hend
# update alignment annotation
# by turning them into list of triplets
for annot, annotseq in frag.aln_annotation.items():
frag.aln_annotation[annot] = _make_triplets(annotseq)
# update values for next iteration
hsp_hstart, hsp_qstart = hend, qend
return fraglist
def _adjust_aa_seq(fraglist):
"""Transforms three-letter amino acid codes into one-letters in the
given HSPFragments."""
hsp_hstart = fraglist[0].hit_start
hsp_qstart = fraglist[0].query_start
for frag in fraglist:
assert frag.query_strand == 0 or frag.hit_strand == 0
# fragment should have a length that is a multiple of 3
assert len(frag) % 3 == 0
# hit step may be -1 as we're aligning to DNA
hstep = 1 if frag.hit_strand >= 0 else -1
# get one letter codes
# and replace gap codon markers and termination characters
custom_map = {'***': '*', '<->': '-'}
hseq1 = seq1(str(frag.hit.seq), custom_map=custom_map)
hstart = hsp_hstart
hend = hstart + len(hseq1.replace('-', '')) * hstep
qseq1 = seq1(str(frag.query.seq), custom_map=custom_map)
qstart = hsp_qstart
qend = qstart + len(qseq1.replace('-', ''))
# replace the old frag sequences with the new ones
frag.hit = None
frag.query = None
frag.hit = hseq1
frag.query = qseq1
# set coordinates for the protein sequence
if frag.query_strand == 0:
frag.query_start, frag.query_end = qstart, qend
elif frag.hit_strand == 0:
frag.hit_start, frag.hit_end = hstart, hend
# update alignment annotation
# by turning them into list of triplets
for annot, annotseq in frag.aln_annotation.items():
frag.aln_annotation[annot] = _make_triplets(annotseq)
# update values for next iteration
hsp_hstart, hsp_qstart = hend, qend
return fraglist
def restype(residue):
"""Return a residue's type as a one-letter code.
Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
"""
return seq1(residue.resname, custom_map=protein_letters_3to1)
def PdbSeqresIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file.
The sequences are derived from the SEQRES lines in the
PDB file header, not the atoms of the 3D structure.
Specifically, these PDB records are handled: DBREF, SEQADV, SEQRES, MODRES
See: http://www.wwpdb.org/documentation/format23/sect3.html
"""
# Late-binding import to avoid circular dependency on SeqIO in Bio.SeqUtils
from SAP.Bio.SeqUtils import seq1
chains = collections.defaultdict(list)
metadata = collections.defaultdict(list)
for line in handle:
rec_name = line[0:6].strip()
if rec_name == 'SEQRES':
# NB: We only actually need chain ID and the residues here;
# commented bits are placeholders from the wwPDB spec.
# Serial number of the SEQRES record for the current chain.
# Starts at 1 and increments by one each line.
# Reset to 1 for each chain.
# ser_num = int(line[8:10])
# Chain identifier. This may be any single legal character,
# including a blank which is used if there is only one chain.
chn_id = line[11]
# Number of residues in the chain (repeated on every record)
# num_res = int(line[13:17])
residues = [
seq1(res, custom_map=protein_letters_3to1)
for res in line[19:].split()
]
chains[chn_id].extend(residues)
elif rec_name == 'DBREF':
# ID code of this entry (PDB ID)
pdb_id = line[7:11]
# Chain identifier.
chn_id = line[12]
# Initial sequence number of the PDB sequence segment.
# seq_begin = int(line[14:18])
# Initial insertion code of the PDB sequence segment.
# icode_begin = line[18]
# Ending sequence number of the PDB sequence segment.
# seq_end = int(line[20:24])
# Ending insertion code of the PDB sequence segment.
# icode_end = line[24]
# Sequence database name.
database = line[26:32].strip()
# Sequence database accession code.
db_acc = line[33:41].strip()
# Sequence database identification code.
db_id_code = line[42:54].strip()
# Initial sequence number of the database seqment.
# db_seq_begin = int(line[55:60])
# Insertion code of initial residue of the segment, if PDB is the
# reference.
# db_icode_begin = line[60]
# Ending sequence number of the database segment.
# db_seq_end = int(line[62:67])
# Insertion code of the ending residue of the segment, if PDB is the
# reference.
# db_icode_end = line[67]
metadata[chn_id].append({
'pdb_id': pdb_id,
'database': database,
'db_acc': db_acc,
'db_id_code': db_id_code
})
# ENH: 'SEQADV' 'MODRES'
for chn_id, residues in sorted(chains.items()):
record = SeqRecord(Seq(''.join(residues), generic_protein))
record.annotations = {"chain": chn_id}
if chn_id in metadata:
m = metadata[chn_id][0]
record.id = record.name = "%s:%s" % (m['pdb_id'], chn_id)
record.description = (
"%s:%s %s" % (m['database'], m['db_acc'], m['db_id_code']))
for melem in metadata[chn_id]:
record.dbxrefs.extend([
"%s:%s" % (melem['database'], melem['db_acc']),
"%s:%s" % (melem['database'], melem['db_id_code'])
])
else:
record.id = chn_id
yield record
def PdbAtomIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file
The sequences are derived from the 3D structure (ATOM records), not the
SEQRES lines in the PDB file header.
Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries
are converted to "X" in the sequence.
In addition to information from the PDB header (which is the same for all
records), the following chain specific information is placed in the
annotation:
record.annotations["residues"] = List of residue ID strings
record.annotations["chain"] = Chain ID (typically A, B ,...)
record.annotations["model"] = Model ID (typically zero)
Where amino acids are missing from the structure, as indicated by residue
numbering, the sequence is filled in with 'X' characters to match the size
of the missing region, and None is included as the corresponding entry in
the list record.annotations["residues"].
This function uses the Bio.PDB module to do most of the hard work. The
annotation information could be improved but this extra parsing should be
done in parse_pdb_header, not this module.
"""
# Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
from SAP.Bio.PDB import PDBParser
from SAP.Bio.SeqUtils import seq1
def restype(residue):
"""Return a residue's type as a one-letter code.
Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
"""
return seq1(residue.resname, custom_map=protein_letters_3to1)
# Deduce the PDB ID from the PDB header
# ENH: or filename?
from SAP.Bio.File import UndoHandle
undo_handle = UndoHandle(handle)
firstline = undo_handle.peekline()
if firstline.startswith("HEADER"):
pdb_id = firstline[62:66]
else:
warnings.warn("First line is not a 'HEADER'; can't determine PDB ID")
pdb_id = '????'
struct = PDBParser().get_structure(pdb_id, undo_handle)
model = struct[0]
for chn_id, chain in sorted(model.child_dict.items()):
# HETATM mod. res. policy: remove mod if in sequence, else discard
residues = [
res for res in chain.get_unpacked_list()
if seq1(res.get_resname().upper(), custom_map=protein_letters_3to1)
!= "X"
]
if not residues:
continue
# Identify missing residues in the structure
# (fill the sequence with 'X' residues in these regions)
gaps = []
rnumbers = [r.id[1] for r in residues]
for i, rnum in enumerate(rnumbers[:-1]):
if rnumbers[i + 1] != rnum + 1:
# It's a gap!
gaps.append((i + 1, rnum, rnumbers[i + 1]))
if gaps:
res_out = []
prev_idx = 0
for i, pregap, postgap in gaps:
if postgap > pregap:
gapsize = postgap - pregap - 1
res_out.extend(restype(x) for x in residues[prev_idx:i])
prev_idx = i
res_out.append('X' * gapsize)
else:
warnings.warn("Ignoring out-of-order residues after a gap",
UserWarning)
# Keep the normal part, drop the out-of-order segment
# (presumably modified or hetatm residues, e.g. 3BEG)
res_out.extend(restype(x) for x in residues[prev_idx:i])
break
else:
# Last segment
res_out.extend(restype(x) for x in residues[prev_idx:])
else:
# No gaps
res_out = [restype(x) for x in residues]
record_id = "%s:%s" % (pdb_id, chn_id)
# ENH - model number in SeqRecord id if multiple models?
# id = "Chain%s" % str(chain.id)
# if len(structure) > 1 :
# id = ("Model%s|" % str(model.id)) + id
record = SeqRecord(
Seq(''.join(res_out), generic_protein),
id=record_id,
description=record_id,
)
# The PDB header was loaded as a dictionary, so let's reuse it all
record.annotations = struct.header.copy()
# Plus some chain specifics:
record.annotations["model"] = model.id
record.annotations["chain"] = chain.id
# Start & end
record.annotations["start"] = int(rnumbers[0])
record.annotations["end"] = int(rnumbers[-1])
# ENH - add letter annotations -- per-residue info, e.g. numbers
yield record
def PdbAtomIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file
The sequences are derived from the 3D structure (ATOM records), not the
SEQRES lines in the PDB file header.
Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries
are converted to "X" in the sequence.
In addition to information from the PDB header (which is the same for all
records), the following chain specific information is placed in the
annotation:
record.annotations["residues"] = List of residue ID strings
record.annotations["chain"] = Chain ID (typically A, B ,...)
record.annotations["model"] = Model ID (typically zero)
Where amino acids are missing from the structure, as indicated by residue
numbering, the sequence is filled in with 'X' characters to match the size
of the missing region, and None is included as the corresponding entry in
the list record.annotations["residues"].
This function uses the Bio.PDB module to do most of the hard work. The
annotation information could be improved but this extra parsing should be
done in parse_pdb_header, not this module.
"""
# Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
from SAP.Bio.PDB import PDBParser
from SAP.Bio.SeqUtils import seq1
def restype(residue):
"""Return a residue's type as a one-letter code.
Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
"""
return seq1(residue.resname, custom_map=protein_letters_3to1)
# Deduce the PDB ID from the PDB header
# ENH: or filename?
from SAP.Bio.File import UndoHandle
undo_handle = UndoHandle(handle)
firstline = undo_handle.peekline()
if firstline.startswith("HEADER"):
pdb_id = firstline[62:66]
else:
warnings.warn("First line is not a 'HEADER'; can't determine PDB ID")
pdb_id = '????'
struct = PDBParser().get_structure(pdb_id, undo_handle)
model = struct[0]
for chn_id, chain in sorted(model.child_dict.items()):
# HETATM mod. res. policy: remove mod if in sequence, else discard
residues = [res for res in chain.get_unpacked_list()
if seq1(res.get_resname().upper(),
custom_map=protein_letters_3to1) != "X"]
if not residues:
continue
# Identify missing residues in the structure
# (fill the sequence with 'X' residues in these regions)
gaps = []
rnumbers = [r.id[1] for r in residues]
for i, rnum in enumerate(rnumbers[:-1]):
if rnumbers[i+1] != rnum + 1:
# It's a gap!
gaps.append((i+1, rnum, rnumbers[i+1]))
if gaps:
res_out = []
prev_idx = 0
for i, pregap, postgap in gaps:
if postgap > pregap:
gapsize = postgap - pregap - 1
res_out.extend(restype(x) for x in residues[prev_idx:i])
prev_idx = i
res_out.append('X'*gapsize)
else:
warnings.warn("Ignoring out-of-order residues after a gap",
UserWarning)
# Keep the normal part, drop the out-of-order segment
# (presumably modified or hetatm residues, e.g. 3BEG)
res_out.extend(restype(x) for x in residues[prev_idx:i])
break
else:
# Last segment
res_out.extend(restype(x) for x in residues[prev_idx:])
else:
# No gaps
res_out = [restype(x) for x in residues]
record_id = "%s:%s" % (pdb_id, chn_id)
# ENH - model number in SeqRecord id if multiple models?
# id = "Chain%s" % str(chain.id)
# if len(structure) > 1 :
# id = ("Model%s|" % str(model.id)) + id
record = SeqRecord(Seq(''.join(res_out), generic_protein),
id=record_id,
description=record_id,
)
# The PDB header was loaded as a dictionary, so let's reuse it all
record.annotations = struct.header.copy()
# Plus some chain specifics:
record.annotations["model"] = model.id
record.annotations["chain"] = chain.id
# Start & end
record.annotations["start"] = int(rnumbers[0])
record.annotations["end"] = int(rnumbers[-1])
# ENH - add letter annotations -- per-residue info, e.g. numbers
yield record
def PdbSeqresIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file.
The sequences are derived from the SEQRES lines in the
PDB file header, not the atoms of the 3D structure.
Specifically, these PDB records are handled: DBREF, SEQADV, SEQRES, MODRES
See: http://www.wwpdb.org/documentation/format23/sect3.html
"""
# Late-binding import to avoid circular dependency on SeqIO in Bio.SeqUtils
from SAP.Bio.SeqUtils import seq1
chains = collections.defaultdict(list)
metadata = collections.defaultdict(list)
for line in handle:
rec_name = line[0:6].strip()
if rec_name == 'SEQRES':
# NB: We only actually need chain ID and the residues here;
# commented bits are placeholders from the wwPDB spec.
# Serial number of the SEQRES record for the current chain.
# Starts at 1 and increments by one each line.
# Reset to 1 for each chain.
# ser_num = int(line[8:10])
# Chain identifier. This may be any single legal character,
# including a blank which is used if there is only one chain.
chn_id = line[11]
# Number of residues in the chain (repeated on every record)
# num_res = int(line[13:17])
residues = [seq1(res, custom_map=protein_letters_3to1) for res in line[19:].split()]
chains[chn_id].extend(residues)
elif rec_name == 'DBREF':
# ID code of this entry (PDB ID)
pdb_id = line[7:11]
# Chain identifier.
chn_id = line[12]
# Initial sequence number of the PDB sequence segment.
# seq_begin = int(line[14:18])
# Initial insertion code of the PDB sequence segment.
# icode_begin = line[18]
# Ending sequence number of the PDB sequence segment.
# seq_end = int(line[20:24])
# Ending insertion code of the PDB sequence segment.
# icode_end = line[24]
# Sequence database name.
database = line[26:32].strip()
# Sequence database accession code.
db_acc = line[33:41].strip()
# Sequence database identification code.
db_id_code = line[42:54].strip()
# Initial sequence number of the database seqment.
# db_seq_begin = int(line[55:60])
# Insertion code of initial residue of the segment, if PDB is the
# reference.
# db_icode_begin = line[60]
# Ending sequence number of the database segment.
# db_seq_end = int(line[62:67])
# Insertion code of the ending residue of the segment, if PDB is the
# reference.
# db_icode_end = line[67]
metadata[chn_id].append({'pdb_id': pdb_id, 'database': database,
'db_acc': db_acc, 'db_id_code': db_id_code})
# ENH: 'SEQADV' 'MODRES'
for chn_id, residues in sorted(chains.items()):
record = SeqRecord(Seq(''.join(residues), generic_protein))
record.annotations = {"chain": chn_id}
if chn_id in metadata:
m = metadata[chn_id][0]
record.id = record.name = "%s:%s" % (m['pdb_id'], chn_id)
record.description = ("%s:%s %s" % (m['database'],
m['db_acc'],
m['db_id_code']))
for melem in metadata[chn_id]:
record.dbxrefs.extend([
"%s:%s" % (melem['database'], melem['db_acc']),
"%s:%s" % (melem['database'], melem['db_id_code'])])
else:
record.id = chn_id
yield record
def restype(residue):
"""Return a residue's type as a one-letter code.
Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
"""
return seq1(residue.resname, custom_map=protein_letters_3to1)
