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#!/usr/bin/python3
"""
Note: This would look so much better replaced by XML or at least JSON. But
is not worth to do it for now.
"""
import os
import gzip
import urllib.request, urllib.error, urllib.parse
import logging
class LargeTestsData(object):
"""
Large index tests use quite big datasets. Make sure these
are present before starting the time consuming tests.
"""
def __init__(self,bt2_path=''):
self.data_dir = 'big_data'
curr_path = os.path.realpath(bt2_path)
curr_path = os.path.join(curr_path,'scripts')
curr_path = os.path.join(curr_path,'test')
self.data_dir_path = os.path.join(curr_path,self.data_dir)
self.reads_dir_path = os.path.join(curr_path,'reads')
try:
os.stat(self.data_dir_path)
except:
logging.error("Cannot find the working datadir %s!" % self.data_dir_path)
raise
self.genomes = dict()
self.genomes['human'] = dict()
hm = self.genomes['human']
hm['link'] = "ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/"
hm['ref_name'] = 'human.fa'
hm['chromosomes'] = []
chromosomes = hm['chromosomes']
for i in range(1,22):
chromosomes.append('chr%d' % i)
chromosomes.extend(['chrX', 'chrY', 'chrM'])
self.genomes['mouse'] = dict()
ms = self.genomes['mouse']
ms['link'] = "ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/chromosomes"
ms['ref_name'] = 'mouse.fa'
ms['chromosomes'] = []
chromosomes = ms['chromosomes']
for i in range(1,21):
chromosomes.append('chr%d' % i)
chromosomes.extend(['chrX', 'chrM'])
self.joint_genomes = dict()
self.joint_genomes['ms_hum'] = dict()
mh = self.joint_genomes['ms_hum']
mh['link'] = None
mh['ref_name'] = 'ms_hum.fa'
mh['genomes'] = ['human','mouse']
self.init_data()
def init_data(self):
""" Try and init the data we need.
"""
for genome,gdata in list(self.genomes.items()):
gn_path = os.path.join(self.data_dir_path,genome)
gn_fasta = os.path.join(gn_path,gdata['ref_name'])
if not os.path.exists(gn_fasta):
self._get_genome(genome)
self._build_genome(genome)
for genome,gdata in list(self.joint_genomes.items()):
gn_path = os.path.join(self.data_dir_path,genome)
gn_fasta = os.path.join(gn_path,gdata['ref_name'])
if not os.path.exists(gn_fasta):
self._build_joint_genome(genome)
def _get_genome(self,genome):
g = self.genomes[genome]
gn_path = os.path.join(self.data_dir_path,genome)
if not os.path.exists(gn_path):
os.mkdir(gn_path)
logging.info("Downloading genome: %s " % genome)
for chrs in g['chromosomes']:
chr_file = chrs + ".fa.gz"
fname = os.path.join(gn_path,chr_file)
if os.path.exists(fname):
logging.info("Skip %s (already present)" % chr_file)
continue
uri = g['link'] + r"/" + chr_file
logging.info("file: %s" % chr_file)
try:
f = open(fname,'wb')
u = urllib.request.urlopen(uri)
f.write(u.read())
except:
f.close()
os.remove(fname)
os.close(u.fileno())
raise
else:
os.close(u.fileno())
u.close()
f.close()
def _build_genome(self,genome):
g = self.genomes[genome]
gn_path = os.path.join(self.data_dir_path,genome)
gn_fasta = os.path.join(gn_path,g['ref_name'])
logging.info("Building fasta file for genome: %s" % genome)
f_gn = open(gn_fasta,'wb')
for chrs in g['chromosomes']:
chr_file = chrs + ".fa.gz"
fname = os.path.join(gn_path,chr_file)
try:
f_chr = gzip.open(fname,'rb')
f_gn.write(f_chr.read())
except:
f_chr_close()
f_gn.close()
os.remove(gn_fasta)
raise
else:
f_chr.close()
f_gn.close()
def _build_joint_genome(self,genome):
jg = self.joint_genomes[genome]
jgn_path = os.path.join(self.data_dir_path,genome)
jgn_fasta = os.path.join(jgn_path,jg['ref_name'])
if not os.path.exists(jgn_path):
os.mkdir(jgn_path)
logging.info("Building fasta file for genome: %s" % genome)
f_jg = open(jgn_fasta,'wb')
for g in jg['genomes']:
gn_path = os.path.join(self.data_dir_path,g)
fasta_file = os.path.join(gn_path,self.genomes[g]['ref_name'])
try:
fin = open(fasta_file,'rb')
f_jg.write(fin.read())
except:
fin.close()
f_jg.close()
os.remove(jgn_fasta)
raise
else:
fin.close()
f_jg.close()
class ExampleData(object):
""" The example data.
"""
def __init__(self,bt2_path=''):
curr_path = os.path.realpath(bt2_path)
curr_path = os.path.join(curr_path,'example')
self.index_dir_path = os.path.join(curr_path,'index')
self.reads_dir_path = os.path.join(curr_path,'reads')
self.ref_dir_path = os.path.join(curr_path,'reference')
try:
os.stat(curr_path)
except:
logging.error("Cannot find the example datadir %s!" % curr_path)
raise
|
