Source code for valerius.utilities

"""Utility functions for reading in data."""

import builtins
import re
import requests
from .sequences import Sequence, DnaSequence, RnaSequence, PeptideSequence

[docs]def open(path): """Opens a sequence file and returns a processed :py:class:`.Sequence`. If the file is a FASTA file this will be detected and parsed accordingly. :param str path: the location of the sequence file. :rtype: ``Sequence``""" with as f: blocks = split_string( sequences = [from_string(block) for block in blocks] return sequences[0] if len(sequences) == 1 else sequences
[docs]def split_string(string): """Takes a raw string and splits it into individual raw sequences. :param str string: the string to split. :rtype: ``list``""" string = string.replace("\n>", "\n\n>") while "\n\n\n" in string: string = string.replace("\n\n\n", "\n\n") return string.split("\n\n")
[docs]def get_sequence_class(string): """Looks at a string sequence and tries to guess what kind of sequence it is before returning the appropriate class. :param str string: the string sequence to inspect. :rtype: ``class``""" if re.compile(r"^[GCATgcat]+$").match(string): return DnaSequence elif re.compile(r"^[GCAUgcau]+$").match(string): return RnaSequence else: return PeptideSequence
[docs]def from_string(string): """Takes a filestring and turns it into a :py:class:`.Sequence`, parsing from FASTA if required. :param str string: the string to convert. :rtype: ``Sequence``""" lines = string.splitlines() label = lines.pop(0)[1:] if is_fasta(string) else "" string = " ".join([ line for line in lines if line.strip() ]).replace(" ", "") return get_sequence_class(string)(string, label=label)
[docs]def is_fasta(filestring): """Checks whether a filestring is FASTA formatted. :param str filestring: the filestring to check. :rtype: ``bool``""" return re.match(r"^>(.+?)\n", filestring)
[docs]def fetch(accession, db="uniprot"): """Fetches a sequence from UNIPROT by accession code. :param str accession: the UNIPROT accession ID. :param str db: an alternative database, such as NCBI. :rtype: ``Sequence``""" url = { "uniprot": "{}.fasta", "ncbi": "" "efetch.fcgi?db=nucleotide&id={}&rettype=fasta" } response = requests.get(url[db].format(accession)) if response.status_code == 200: return from_string(response.text)