def maskMali(mali, method="seg"):
"""mask multiple alignment according to an external masker.
"""
if method == "seg":
masker = Masker.MaskerSeg()
elif method == "bias":
masker = Masker.MaskerBias()
elif method == "random":
masker = Masker.MaskerRandom()
if mali.getAlphabet() == "na" and method in ("seg", "bias"):
for id, s in mali.items():
ss = Genomics.TranslateDNA2Protein(s.mString)
mss = masker(ss)
columns = []
for x in range(0, len(mss)):
if mss[x] in ("X", "x"):
columns += range(x, x + 3)
mali.getEntry(id).maskColumns(columns)
else:
for id, s in mali.items():
mali[id].mString = masker(s.mString)
def main(argv=None):
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version",
usage=globals()["__doc__"])
parser.add_option(
"-m",
"--method",
dest="methods",
type="choice",
action="append",
choices=("translate", "translate-to-stop", "truncate-at-stop",
"back-translate", "mark-codons", "apply-map", "build-map",
"pseudo-codons", "filter", "interleaved-codons", "map-codons",
"remove-gaps", "mask-seg", "mask-bias", "mask-codons",
"mask-incomplete-codons", "mask-stops", "mask-soft",
"remove-stops", "upper", "lower", "reverse-complement",
"sample", "shuffle"),
help="method to apply to sequences.")
parser.add_option("-p",
"--parameters",
dest="parameters",
type="string",
help="parameter stack for methods that require one "
"[default=%default].")
parser.add_option("-x",
"--ignore-errors",
dest="ignore_errors",
action="store_true",
help="ignore errors [default = %default].")
parser.add_option("--sample-proportion",
dest="sample_proportion",
type="float",
help="sample proportion [default = %default].")
parser.add_option("--exclude-pattern",
dest="exclude_pattern",
type="string",
help="exclude all sequences with ids matching pattern "
"[default = %default].")
parser.add_option("--include-pattern",
dest="include_pattern",
type="string",
help="include only sequences with ids matching pattern "
"[default = %default].")
parser.add_option("--filter-method",
dest="filter_methods",
type="string",
action="append",
help="filtering methods to apply "
"[default = %default].")
parser.add_option(
"-t",
"--sequence-type",
dest="type",
type="choice",
choices=("aa", "na"),
help="sequence type (aa or na) [%default]. This option determines "
"which characters to use for masking [default = %default].")
parser.add_option(
"-l",
"--template-identifier",
dest="template_identifier",
type="string",
help="template for numerical identifier [default = %default] "
"for the operation --build-map. A %i is replaced by the position "
"of the sequence in the file.")
parser.set_defaults(
methods=[],
parameters="",
type="na",
aa_mask_chars="xX",
aa_mask_char="x",
na_mask_chars="nN",
na_mask_char="n",
gap_chars="-.",
gap_char="-",
template_identifier="ID%06i",
ignore_errors=False,
exclude_pattern=None,
include_pattern=None,
sample_proportion=None,
filter_methods=[],
)
(options, args) = E.Start(parser)
options.parameters = options.parameters.split(",")
rx_include, rx_exclude = None, None
if options.include_pattern:
rx_include = re.compile(options.include_pattern)
if options.exclude_pattern:
rx_exclude = re.compile(options.exclude_pattern)
iterator = FastaIterator.FastaIterator(options.stdin)
nseq = 0
map_seq2nid = {}
if "apply-map" in options.methods:
map_seq2nid = IOTools.ReadMap(open(options.parameters[0], "r"))
del options.parameters[0]
if options.type == "na":
mask_chars = options.na_mask_chars
mask_char = options.na_mask_char
else:
mask_chars = options.aa_mask_chars
mask_char = options.aa_mask_char
if "map-codons" in options.methods:
map_codon2code = IOTools.ReadMap(open(options.parameters[0], "r"))
del options.parameters[0]
if "mask-soft" in options.methods:
f = options.parameters[0]
del options.parameters[0]
hard_masked_iterator = FastaIterator.FastaIterator(open(f, "r"))
if "mask-codons" in options.methods or "back-translate" in options.methods:
# open a second stream to read sequences from
f = options.parameters[0]
del options.parameters[0]
other_iterator = FastaIterator.FastaIterator(open(f, "r"))
ninput, noutput, nerrors, nskipped = 0, 0, 0, 0
if "sample" in options.methods:
if not options.sample_proportion:
raise ValueError("specify a sample proportion")
sample_proportion = options.sample_proportion
else:
sample_proportion = None
filter_min_sequence_length = None
filter_max_sequence_length = None
filter_id_list = None
for f in options.filter_methods:
if f.startswith("min-length"):
filter_min_sequence_length = int(f.split("=")[1])
elif f.startswith("max-length"):
filter_max_sequence_length = int(f.split("=")[1])
elif f.startswith("id-file"):
filter_id_list = [
line[:-1] for line in IOTools.openFile(f.split("=")[1])
]
def raiseIfNotCodon(l, title):
'''raise ValueError if sequence length l is not divisible by
3'''
if l % 3 != 0:
raise ValueError("length of sequence %s not divisible by 3" %
(title))
while 1:
try:
cur_record = next(iterator)
except StopIteration:
break
if cur_record is None:
break
nseq += 1
ninput += 1
sequence = re.sub(" ", "", cur_record.sequence)
l = len(sequence)
if rx_include and not rx_include.search(cur_record.title):
nskipped += 1
continue
if rx_exclude and rx_exclude.search(cur_record.title):
nskipped += 1
continue
if sample_proportion:
if random.random() > sample_proportion:
continue
if not (filter_id_list is None or cur_record.title in filter_id_list):
nskipped += 1
continue
for method in options.methods:
if method == "translate":
# translate such that gaps are preserved
seq = []
ls = len(re.sub('[%s]' % options.gap_chars, sequence, ""))
if ls % 3 != 0:
msg = "length of sequence %s (%i) not divisible by 3" % (
cur_record.title, ls)
nerrors += 1
if options.ignore_errors:
E.warn(msg)
continue
else:
raise ValueError(msg)
for codon in [sequence[x:x + 3] for x in range(0, l, 3)]:
aa = Genomics.MapCodon2AA(codon)
seq.append(aa)
sequence = "".join(seq)
elif method == "back-translate":
# translate from an amino acid alignment to codon alignment
seq = []
try:
other_record = next(other_iterator)
except StopIteration:
raise ValueError("run out of sequences")
if cur_record.title != other_record.title:
raise "sequence titles don't match: %s %s" % (
cur_record.title, other_record.title)
other_sequence = re.sub("[ %s]" % options.gap_chars, "",
other_record.sequence)
if len(other_sequence) % 3 != 0:
raise ValueError(
"length of sequence %s not divisible by 3" %
(other_record.title))
r = re.sub("[%s]" % options.gap_chars, "", sequence)
if len(other_sequence) != len(r) * 3:
raise ValueError(
"length of sequences do not match: %i vs %i" %
(len(other_sequence), len(r)))
x = 0
for aa in sequence:
if aa in options.gap_chars:
c = options.gap_char * 3
else:
c = other_sequence[x:x + 3]
x += 3
seq.append(c)
sequence = "".join(seq)
elif method == "pseudo-codons":
raiseIfNotCodon(l, cur_record.title)
seq = []
for codon in [sequence[x:x + 3] for x in range(0, l, 3)]:
aa = Genomics.MapCodon2AA(codon)
seq.append(aa)
sequence = " ".join(seq)
elif method == "reverse-complement":
sequence = string.translate(
sequence, string.maketrans("ACGTacgt", "TGCAtgca"))[::-1]
elif method in ("mask-stops", "remove-stops"):
c = []
codon = []
new_sequence = []
if method == "mask-stops":
char = options.na_mask_char
elif method == "remove-stops":
char = options.gap_char
for x in sequence:
if x not in options.gap_chars:
codon.append(x.upper())
c.append(x)
if len(codon) == 3:
codon = "".join(codon).upper()
# mask all non-gaps
if Genomics.IsStopCodon(codon):
for x in c:
if x in options.gap_chars:
new_sequence.append(x)
else:
new_sequence.append(char)
else:
new_sequence += c
c = []
codon = []
new_sequence += c
sequence = "".join(new_sequence)
elif method == "mask-soft":
# Get next hard masked record and extract sequence and length
try:
cur_hm_record = next(hard_masked_iterator)
except StopIteration:
break
hm_sequence = re.sub(" ", "", cur_hm_record.sequence)
lhm = len(hm_sequence)
new_sequence = []
# Check lengths of unmasked and soft masked sequences the same
if l != lhm:
raise ValueError(
"length of unmasked and hard masked sequences not "
"identical for record %s" % (cur_record.title))
# Check if hard masked seq contains repeat (N), if so replace N
# with lowercase sequence from unmasked version
if sequence == hm_sequence:
pass
else:
for x, y in zip_longest(sequence, hm_sequence):
if y == "N":
new_sequence += x.lower()
else:
new_sequence += x.upper()
sequence = "".join(new_sequence)
elif method == "map-codons":
raiseIfNotCodon(l, cur_record.title)
seq = []
for codon in (sequence[x:x + 3].upper()
for x in range(0, l, 3)):
if codon not in map_codon2code:
aa = "X"
else:
aa = map_codon2code[codon]
seq.append(aa)
sequence = "".join(seq)
elif method == "interleaved-codons":
raiseIfNotCodon(l, cur_record.title)
seq = []
for codon in [sequence[x:x + 3] for x in range(0, l, 3)]:
aa = Genomics.MapCodon2AA(codon)
seq.append("%s:%s" % (aa, codon))
sequence = " ".join(seq)
elif method == "translate-to-stop":
seq = []
for codon in [sequence[x:x + 3] for x in range(0, l, 3)]:
if Genomics.IsStopCodon(codon):
break
aa = Genomics.MapCodon2AA(codon)
seq.append(aa)
sequence = "".join(seq)
elif method == "truncate-at-stop":
seq = []
for codon in [sequence[x:x + 3] for x in range(0, l, 3)]:
if Genomics.IsStopCodon(codon):
break
seq.append(codon)
sequence = "".join(seq)
elif method == "remove-gaps":
seq = []
for s in sequence:
if s in options.gap_chars:
continue
seq.append(s)
sequence = "".join(seq)
elif method == "upper":
sequence = sequence.upper()
elif method == "lower":
sequence = sequence.lower()
elif method == "mark-codons":
raiseIfNotCodon(l, cur_record.title)
seq = []
sequence = " ".join(
[sequence[x:x + 3] for x in range(0, l, 3)])
elif method == "apply-map":
id = re.match("^(\S+)", cur_record.title).groups()[0]
if id in map_seq2nid:
rest = cur_record.title[len(id):]
cur_record.title = map_seq2nid[id] + rest
elif method == "build-map":
# build a map of identifiers
id = re.match("^(\S+)", cur_record.title).groups()[0]
new_id = options.template_identifier % nseq
if id in map_seq2nid:
raise "duplicate fasta entries - can't map those: %s" % id
map_seq2nid[id] = new_id
cur_record.title = new_id
elif method == "mask-bias":
masker = Masker.MaskerBias()
sequence = masker(sequence)
elif method == "mask-seg":
masker = Masker.MaskerSeg()
sequence = masker(sequence)
elif method == "shuffle":
s = list(sequence)
random.shuffle(s)
sequence = "".join(s)
elif method == "mask-incomplete-codons":
seq = list(sequence)
for x in range(0, l, 3):
nm = len([x for x in seq[x:x + 3] if x in mask_chars])
if 0 < nm < 3:
seq[x:x + 3] = [mask_char] * 3
sequence = "".join(seq)
elif method == "mask-codons":
# mask codons based on amino acids given as reference
# sequences.
other_record = next(other_iterator)
if other_record is None:
raise ValueError("run out of sequences.")
if cur_record.title != other_record.title:
raise ValueError("sequence titles don't match: %s %s" %
(cur_record.title, other_record.title))
other_sequence = re.sub(" ", "", other_record.sequence)
if len(other_sequence) * 3 != len(sequence):
raise ValueError(
"sequences for %s don't have matching lengths %i - %i"
% (cur_record.title, len(other_sequence) * 3,
len(sequence)))
seq = list(sequence)
c = 0
for x in other_sequence:
if x in options.aa_mask_chars:
if x.isupper():
seq[c:c + 3] = [options.na_mask_char.upper()] * 3
else:
seq[c:c + 3] = [options.na_mask_char.lower()] * 3
c += 3
sequence = "".join(seq)
l = len(sequence)
if filter_min_sequence_length is not None and \
l < filter_min_sequence_length:
nskipped += 1
if filter_max_sequence_length is not None and \
l > filter_max_sequence_length:
nskipped += 1
continue
options.stdout.write(">%s\n%s\n" % (cur_record.title, sequence))
noutput += 1
if "build-map" in options.methods:
p = options.parameters[0]
if p:
outfile = IOTools.openFile(p, "w")
else:
outfile = options.stdout
outfile.write("old\tnew\n")
for old_id, new_id in list(map_seq2nid.items()):
outfile.write("%s\t%s\n" % (old_id, new_id))
if p:
outfile.close()
E.info("ninput=%i, noutput=%i, nskipped=%i, nerrors=%i" %
(ninput, noutput, nskipped, nerrors))
E.Stop()
