import os
import re
from copy import deepcopy
import numpy as np
from snapgene_reader import snapgene_file_to_seqrecord
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
try:
# Biopython <1.78
from Bio.Alphabet import DNAAlphabet
has_dna_alphabet = True
except ImportError:
# Biopython >=1.78
has_dna_alphabet = False
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio import SeqIO
complements_dict = {"A": "T", "T": "A", "C": "G", "G": "C"}
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def random_dna_sequence(length, probas=None, seed=None):
"""Return a random DNA sequence ("ATGGCGT...") with the specified length.
Parameters
----------
length
Length of the DNA sequence.
proba
Frequencies for the different nucleotides, for instance
``probas={"A":0.2, "T":0.3, "G":0.3, "C":0.2}``.
If not specified, all nucleotides are equiprobable (p=0.25).
seed
The seed to feed to the random number generator. When a seed is provided
the random results depend deterministically on the seed, thus enabling
reproducibility.
"""
if seed is not None:
np.random.seed(seed)
if probas is None:
sequence = np.random.choice(list("ATCG"), length)
else:
bases, probas = zip(*probas.items())
sequence = np.random.choice(bases, length, p=probas)
return "".join(sequence)
formats_dict = {".fa": "fasta", ".gb": "genbank", ".gbk": "genbank", ".dna": "snapgene"}
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def load_record(filename, linear=True, name="unnamed", capitalize=True):
no_extension, extension = os.path.splitext(filename)
fmt = formats_dict[extension]
if fmt == "snapgene":
record = snapgene_file_to_seqrecord(filename)
else:
record = SeqIO.read(filename, fmt)
if capitalize:
record.seq = record.seq.upper()
record.linear = linear
record.id = name
record.name = name.replace(" ", "_")[:20]
return record
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def load_records(path, capitalize=True):
if isinstance(path, (list, tuple)):
return [record for p in path for record in load_records(p)]
no_extension, extension = os.path.splitext(path)
fmt = formats_dict[extension]
if fmt == "snapgene":
records = [snapgene_file_to_seqrecord(path)]
else:
records = list(SeqIO.parse(path, fmt))
for i, record in enumerate(records):
if capitalize:
record.seq = record.seq.upper()
if str(record.id) in ["None", "", "<unknown id>", ".", " "]:
record.id = path.replace("/", "_").replace("\\", "_")
if len(records) > 1:
record.id += "_%04d" % i
return records
def complement(sequence):
return "".join(complements_dict[c] for c in sequence)
def reverse_complement(sequence):
return complement(sequence)[::-1]
def sequence_to_record(sequence, features=()):
if has_dna_alphabet:
seq = Seq(sequence, alphabet=DNAAlphabet())
else:
seq = Seq(sequence)
seqrecord = SeqRecord(seq, features=list(features))
seqrecord.annotations["molecule_type"] = "DNA"
return seqrecord
def annotate_record(
seqrecord, location="full", feature_type="feature", margin=0, **qualifiers
):
"""Add a feature to a Biopython SeqRecord.
Parameters
----------
seqrecord
The biopython seqrecord to be annotated.
location
Either (start, end) or (start, end, strand). (strand defaults to +1).
feature_type
The type associated with the feature.
margin
Number of extra bases added on each side of the given location.
qualifiers
Dictionary that will be the Biopython feature's `qualifiers` attribute.
"""
if location == "full":
location = (margin, len(seqrecord) - margin)
strand = location[2] if len(location) == 3 else 1
seqrecord.features.append(
SeqFeature(
FeatureLocation(location[0], location[1], strand),
qualifiers=qualifiers,
type=feature_type,
)
)
def sanitize_string(
string, max_length=15, replacements=(("'", "p"), ("*", "s"), ("-", "_"))
):
for old, new in replacements:
string = string.replace(old, new)
string = re.sub(r"[^a-zA-Z\d\S]", "_", string)
return string[:max_length]
def sanitize_and_uniquify(
strings, max_length, replacements=(("'", "p"), ("*", "s"), ("-", "_"))
):
dejavu = set()
table = {}
for string in strings:
newstring = sanitize_string(
string, max_length=max_length, replacements=replacements
)
i = 1
while newstring in dejavu:
i += 1
newstring = newstring[:-1] + str(i)
dejavu.add(newstring)
table[string] = newstring
return table
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def write_record(record, target, fmt="genbank"):
"""Write a record as genbank, fasta, etc. via Biopython, with fixes."""
record = deepcopy(record)
record.name = record.name[:20]
if has_dna_alphabet:
if str(record.seq.alphabet.__class__.__name__) != "DNAAlphabet":
record.seq.alphabet = DNAAlphabet()
record.annotations["molecule_type"] = "DNA"
if hasattr(target, "open"):
target = target.open("w")
SeqIO.write(record, target, fmt)