def loadSequence(self, sequence, seqtype="na"):
"""load sequence properties from a sequence."""
SequencePropertiesLength.loadSequence(self, sequence, seqtype)
if len(sequence) % 3:
raise ValueError(
'''sequence length is not a multiple of 3 (length=%i)''' %
(len(sequence)))
# uppercase all letters
sequence = sequence.upper()
self.mNStopCodons = 0
# setup counting arrays
# nucleotide counts for each position (is not a sum of the counts
# per degenerate site, as the codon might be intelligible, e.g. GNN).
self.mCounts = [{
'A': 0,
'C': 0,
'G': 0,
'T': 0,
'X': 0,
'N': 0
}, {
'A': 0,
'C': 0,
'G': 0,
'T': 0,
'X': 0,
'N': 0
}, {
'A': 0,
'C': 0,
'G': 0,
'T': 0,
'X': 0,
'N': 0
}]
# nucleotide counts for each position per degeneracy
self.mCountsDegeneracy = []
for x in (0, 1, 2):
xx = []
for y in range(5):
yy = {}
for z in Bio.Alphabet.IUPAC.extended_dna.letters:
yy[z] = 0
xx.append(yy)
self.mCountsDegeneracy.append(xx)
# use generator rather than list to save memory
for codon in (sequence[x:x + 3] for x in range(0, len(sequence), 3)):
for x in (0, 1, 2):
self.mCounts[x][codon[x]] += 1
if Genomics.IsStopCodon(codon):
self.mNStopCodons += 1
continue
try:
aa, deg1, deg2, deg3 = Genomics.GetDegeneracy(codon)
degrees = (deg1, deg2, deg3)
for x in range(len(degrees)):
self.mCountsDegeneracy[x][degrees[x]][codon[x]] += 1
except KeyError:
pass
def main(argv=None):
parser = E.ArgumentParser(description=__doc__)
parser.add_argument("--version", action='version', version="1.0")
parser.add_argument(
"-w",
"--weights-tsv-file",
dest="filename_weights",
type=str,
help="filename with codon frequencies. Multiple filenames "
"can be separated by comma.")
parser.add_argument("-s",
"--section",
dest="sections",
nargs="*",
type=str,
choices=("length", "sequence", "hid", "na", "aa",
"cpg", "dn", "degeneracy", "gaps", "codons",
"codon-usage", "codon-translator",
"codon-bias"),
help="which sections to output ")
parser.add_argument(
"-t",
"--sequence-type",
dest="seqtype",
type=str,
choices=("na", "aa"),
help="type of sequence: na=nucleotides, aa=amino acids .")
parser.add_argument(
"-e",
"--regex-identifier",
dest="regex_identifier",
type=str,
help="regular expression to extract identifier from fasta "
"description line.")
parser.add_argument(
"--split-fasta-identifier",
dest="split_id",
action="store_true",
help="split fasta description line (starting >) and use "
"only text before first space")
parser.add_argument(
"--add-total",
dest="add_total",
action="store_true",
help="add a row with column totals at the end of the table")
parser.set_defaults(
filename_weights=None,
pseudocounts=1,
sections=[],
regex_identifier="(.+)",
seqtype="na",
gap_chars='xXnN',
split_id=False,
add_total=False,
)
(args) = E.start(parser, argv=argv)
rx = re.compile(args.regex_identifier)
reference_codons = []
if args.filename_weights:
args.filename_weights = args.filename_weights.split(",")
for filename in args.filename_weights:
if filename == "uniform":
reference_codons.append(Genomics.GetUniformCodonUsage())
else:
reference_codons.append(
iotools.ReadMap(iotools.open_file(filename, "r"),
has_header=True,
map_functions=(str, float)))
# print codon table differences
args.stdlog.write(
"# Difference between supplied codon usage preferences.\n")
for x in range(0, len(reference_codons)):
for y in range(0, len(reference_codons)):
if x == y:
continue
# calculate KL distance
a = reference_codons[x]
b = reference_codons[y]
d = 0
for codon, p in list(a.items()):
if Genomics.IsStopCodon(codon):
continue
d += b[codon] * math.log(b[codon] / p)
args.stdlog.write(
"# tablediff\t%s\t%s\t%f\n" %
(args.filename_weights[x], args.filename_weights[y], d))
iterator = FastaIterator.FastaIterator(args.stdin)
def getCounter(section):
if args.seqtype == "na":
if section == "length":
s = SequenceProperties.SequencePropertiesLength()
elif section == "sequence":
s = SequenceProperties.SequencePropertiesSequence()
elif section == "hid":
s = SequenceProperties.SequencePropertiesHid()
elif section == "na":
s = SequenceProperties.SequencePropertiesNA()
elif section == "gaps":
s = SequenceProperties.SequencePropertiesGaps(args.gap_chars)
elif section == "cpg":
s = SequenceProperties.SequencePropertiesCpg()
elif section == "dn":
s = SequenceProperties.SequencePropertiesDN()
# these sections requires sequence length to be a multiple of 3
elif section == "aa":
s = SequenceProperties.SequencePropertiesAA()
elif section == "degeneracy":
s = SequenceProperties.SequencePropertiesDegeneracy()
elif section == "codon-bias":
s = SequenceProperties.SequencePropertiesBias(reference_codons)
elif section == "codons":
s = SequenceProperties.SequencePropertiesCodons()
elif section == "codon-usage":
s = SequenceProperties.SequencePropertiesCodonUsage()
elif section == "codon-translator":
s = SequenceProperties.SequencePropertiesCodonTranslator()
else:
raise ValueError("unknown section %s" % section)
elif args.seqtype == "aa":
if section == "length":
s = SequenceProperties.SequencePropertiesLength()
elif section == "sequence":
s = SequenceProperties.SequencePropertiesSequence()
elif section == "hid":
s = SequenceProperties.SequencePropertiesHid()
elif section == "aa":
s = SequenceProperties.SequencePropertiesAminoAcids()
else:
raise ValueError("unknown section %s" % section)
return s
# setup totals
totals = {}
for section in args.sections:
totals[section] = getCounter(section)
args.stdout.write("id")
for section in args.sections:
args.stdout.write("\t" + "\t".join(totals[section].getHeaders()))
args.stdout.write("\n")
args.stdout.flush()
s = getCounter("hid")
s.loadSequence("AAAAAAAAA", "na")
for cur_record in iterator:
sequence = re.sub(" ", "", cur_record.sequence).upper()
if len(sequence) == 0:
raise ValueError("empty sequence %s" % cur_record.title)
id = rx.search(cur_record.title).groups()[0]
if args.split_id is True:
args.stdout.write("%s" % id.split()[0])
else:
args.stdout.write("%s" % id)
args.stdout.flush()
for section in args.sections:
s = getCounter(section)
s.loadSequence(sequence, args.seqtype)
totals[section].addProperties(s)
args.stdout.write("\t" + "\t".join(s.getFields()))
args.stdout.write("\n")
if args.add_total:
args.stdout.write("total")
for section in args.sections:
args.stdout.write("\t" + "\t".join(totals[section].getFields()))
args.stdout.write("\n")
E.stop()
def main(argv=None):
if argv is None:
argv = sys.argv
parser = E.ArgumentParser(description=__doc__)
parser.add_argument("--version", action='version', version="1.0")
parser.add_argument(
"-m",
"--method",
dest="methods",
type=str,
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",
"map-identifier", "nop", "remove-stops", "upper", "lower",
"reverse-complement", "sample", "shuffle"),
help="method to apply to sequences.")
parser.add_argument("-p",
"--parameters",
dest="parameters",
type=str,
help="parameter stack for methods that require one ")
parser.add_argument("-x",
"--ignore-errors",
dest="ignore_errors",
action="store_true",
help="ignore errors.")
parser.add_argument("--sample-proportion",
dest="sample_proportion",
type=float,
help="sample proportion.")
parser.add_argument(
"--exclude-pattern",
dest="exclude_pattern",
type=str,
help="exclude all sequences with ids matching pattern ")
parser.add_argument(
"--include-pattern",
dest="include_pattern",
type=str,
help="include only sequences with ids matching pattern ")
parser.add_argument("--filter-method",
dest="filter_methods",
type=str,
action="append",
help="filtering methods to apply ")
parser.add_argument(
"-t",
"--sequence-type",
dest="type",
type=str,
choices=("aa", "na"),
help="sequence type (aa or na) . This option determines "
"which characters to use for masking.")
parser.add_argument(
"-l",
"--template-identifier",
dest="template_identifier",
type=str,
help="template for numerical identifier"
"for the operation --build-map. A %i is replaced by the position "
"of the sequence in the file.")
parser.add_argument(
"--map-tsv-file",
dest="map_tsv_file",
type=str,
help=
"input filename with map for identifiers. The first row is a header")
parser.add_argument("--fold-width",
dest="fold_width",
type=int,
help="fold width for sequence output. 0 is unfolded ")
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=[],
input_filename_fasta="-",
input_filename_map=None,
fold_width=80)
(args, unknown) = E.start(parser, unknowns=True)
if len(unknown) > 0:
args.input_filename_fasta = unknown[0]
args.parameters = args.parameters.split(",")
rx_include, rx_exclude = None, None
if args.include_pattern:
rx_include = re.compile(args.include_pattern)
if args.exclude_pattern:
rx_exclude = re.compile(args.exclude_pattern)
iterator = FastaIterator.FastaIterator(args.stdin)
nseq = 0
map_seq2nid = {}
map_identifier = ("apply-map" in args.methods
or "map-identifier" in args.methods)
if map_identifier:
if args.input_filename_map is None:
raise ValueError("for method=map-identifier use --map-tsv-file")
with iotools.open_file(args.input_filename_map) as infile:
map_identifier = iotools.read_map(infile, has_header=True)
if args.type == "na":
mask_chars = args.na_mask_chars
mask_char = args.na_mask_char
else:
mask_chars = args.aa_mask_chars
mask_char = args.aa_mask_char
if "map-codons" in args.methods:
map_codon2code = iotools.ReadMap(open(args.parameters[0], "r"))
del args.parameters[0]
if "mask-soft" in args.methods:
f = args.parameters[0]
del args.parameters[0]
hard_masked_iterator = FastaIterator.FastaIterator(open(f, "r"))
if "mask-codons" in args.methods or "back-translate" in args.methods:
# open a second stream to read sequences from
f = args.parameters[0]
del args.parameters[0]
other_iterator = FastaIterator.FastaIterator(open(f, "r"))
if "sample" in args.methods:
if not args.sample_proportion:
raise ValueError("specify a sample proportion")
sample_proportion = args.sample_proportion
else:
sample_proportion = None
filter_min_sequence_length = None
filter_max_sequence_length = None
filter_id_list = None
for f in args.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.open_file(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))
iterator = pysam.FastxFile(args.input_filename_fasta)
c = E.Counter()
fold_width = args.fold_width
def fold(s, w):
return "\n".join([s[x:x + w] for x in range(0, len(s), w)])
for record in iterator:
c.nseq += 1
c.input += 1
sequence = re.sub(" ", "", record.sequence)
l = len(sequence)
if rx_include and not rx_include.search(record.name):
c.skipped += 1
continue
if rx_exclude and rx_exclude.search(record.name):
c.skipped += 1
continue
if sample_proportion:
if random.random() > sample_proportion:
continue
if not (filter_id_list is None or record.name in filter_id_list):
c.skipped += 1
continue
for method in args.methods:
if method == "translate":
# translate such that gaps are preserved
seq = []
ls = len(re.sub('[%s]' % args.gap_chars, sequence, ""))
if ls % 3 != 0:
msg = "length of sequence %s (%i) not divisible by 3" % (
record.name, ls)
c.errors += 1
if args.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 record.name != other_record.title:
raise "sequence titles don't match: %s %s" % (
record.name, other_record.title)
other_sequence = re.sub("[ %s]" % args.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]" % args.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 args.gap_chars:
c = args.gap_char * 3
else:
c = other_sequence[x:x + 3]
x += 3
seq.append(c)
sequence = "".join(seq)
elif method == "pseudo-codons":
raiseIfNotCodon(l, record.name)
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 = sequence.translate(
str.maketrans("ACGTacgt", "TGCAtgca"))[::-1]
elif method in ("mask-stops", "remove-stops"):
c = []
codon = []
new_sequence = []
if method == "mask-stops":
char = args.na_mask_char
elif method == "remove-stops":
char = args.gap_char
for x in sequence:
if x not in args.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 args.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" % (record.name))
# 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, record.name)
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, record.name)
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 args.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, record.name)
seq = []
sequence = " ".join(
[sequence[x:x + 3] for x in range(0, l, 3)])
elif method == "apply-map":
id = re.match("^(\S+)", record.name).groups()[0]
if id in map_seq2nid:
rest = record.name[len(id):]
record.name = map_seq2nid[id] + rest
elif method == "build-map":
# build a map of identifiers
id = re.match("^(\S+)", record.name).groups()[0]
new_id = args.template_identifier % nseq
if id in map_seq2nid:
raise "duplicate fasta entries - can't map those: %s" % id
map_seq2nid[id] = new_id
record.name = 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 record.name != other_record.title:
raise ValueError("sequence titles don't match: %s %s" %
(record.name, 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"
%
(record.name, len(other_sequence) * 3, len(sequence)))
seq = list(sequence)
c = 0
for x in other_sequence:
if x in args.aa_mask_chars:
if x.isupper():
seq[c:c + 3] = [args.na_mask_char.upper()] * 3
else:
seq[c:c + 3] = [args.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:
c.skipped += 1
if filter_max_sequence_length is not None and \
l > filter_max_sequence_length:
c.skipped += 1
continue
record.sequence = sequence
if fold_width >= 0:
if record.comment:
args.stdout.write(">{} {}\n{}\n".format(
record.name, record.comment,
fold(record.sequence, fold_width)))
else:
args.stdout.write(">{}\n{}\n".format(
record.name, fold(record.sequence, fold_width)))
else:
args.stdout.write(str(record) + "\n")
c.output += 1
if "build-map" in args.methods:
p = args.parameters[0]
if p:
outfile = iotools.open_file(p, "w")
else:
outfile = args.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(c)
E.stop()
