seqsearch.databases.string

  1#!/usr/bin/env python3
  2# -*- coding: utf-8 -*-
  3
  4"""
  5Written by Lucas Sinclair.
  6MIT Licensed.
  7Contact at www.sinclair.bio
  8"""
  9
 10# Built-in modules #
 11import urllib
 12from collections import OrderedDict
 13
 14# Internal modules #
 15from seqsearch.databases import base_directory
 16
 17# First party modules #
 18from fasta import FASTA
 19from autopaths.auto_paths import AutoPaths
 20from autopaths.file_path import FilePath
 21
 22###############################################################################
 23class String(object):
 24    """
 25    The STRING database. See:
 26    http://string.embl.de/newstring_cgi/show_download_page.pl
 27    """
 28
 29    base_url = "http://string.embl.de/newstring_download/"
 30    short_name = "string"
 31
 32    all_paths = """
 33    /raw/all_proteins.fasta.gz
 34    /raw/cog_mappings.tsv.gz
 35    /unzipped/all_proteins.fasta
 36    /unzipped/cog_mappings.tsv
 37    /blast_db/all_proteins.fasta
 38    /blast_db/all_proteins.fasta.00.pin
 39    /blast_db/logfile.txt
 40    /blast_db/out.txt
 41    """
 42
 43    def __init__(self, seq_type='prot'):
 44        self.seq_type = seq_type
 45        self.base_dir = base_directory + self.short_name
 46        self.p        = AutoPaths(self.base_dir, self.all_paths)
 47
 48    @property
 49    def files_to_retrieve(self):
 50        """The files we want to download with their destinations."""
 51        result = OrderedDict()
 52        result[self.base_url + "protein.sequences.v9.1.fa.gz"] = FilePath(self.p.raw_proteins)
 53        result[self.base_url + "COG.mappings.v9.1.txt.gz"]     = FilePath(self.p.raw_mappings)
 54        return result
 55
 56    @property
 57    def files_remaining(self):
 58        """The files we haven't downloaded yet based on size checks."""
 59        get_size_http = lambda url: urllib.urlopen(url).info().getheaders("Content-Length")[0]
 60        return OrderedDict((source, dest) for source, dest in self.files_to_retrieve.items()
 61                           if dest.count_bytes != get_size_http(source))
 62
 63    def download(self):
 64        """Retrieve all files from the website"""
 65        for source, dest in self.files_remaining.items():
 66            dest.remove()
 67            urllib.urlretrieve(source, dest)
 68            dest.permissions.only_readable()
 69
 70    @property
 71    def raw_files(self):
 72        """The files we have downloaded."""
 73        return map(FilePath, self.p.raw_dir.contents)
 74
 75    def unzip(self):
 76        """Unzip them"""
 77        for f in self.raw_files: f.ungzip_to(self.p.unzipped_dir + f.prefix)
 78
 79    @property
 80    def all_proteins(self):
 81        """The main fasta file."""
 82        return FASTA(self.p.unzipped_proteins)
 83
 84    @property
 85    def mappings(self):
 86        """The cog mappings."""
 87        return FilePath(self.p.unzipped_mappings)
 88
 89    @property
 90    def blast_db(self):
 91        """A BLASTable version of the sequences."""
 92        if not self.p.blast_fasta.exists:
 93            self.p.unzipped_proteins.link_to(self.p.blast_fasta, safe=True)
 94        from seqsearch.search.blast import BLASTdb
 95        blast_db = BLASTdb(self.p.blast_fasta, 'prot')
 96        if not self.p.pin.exists:
 97            blast_db.makeblastdb(logfile=self.p.logfile, out=self.p.out)
 98        return blast_db
 99
100###############################################################################
101string = String()