def download_genome_seq(genome,
output_dir):
"""
Download genome sequence files from UCSC.
"""
print "Downloading genome sequence files for %s" %(genome)
print " - Output dir: %s" %(output_dir)
output_dir = os.path.join(output_dir, "genome")
if os.path.isdir(output_dir):
dir_files = os.listdir(output_dir)
if len(dir_files) >= 1:
print "Directory %s exists and contains files; skipping download of genome..." \
%(output_dir)
return None
utils.make_dir(output_dir)
# Change to output directory
os.chdir(output_dir)
##
## Download the genome sequence files
##
genome_url = "%s/%s/chromosomes/" %(UCSC_GOLDENPATH_FTP,
genome)
# Fetch all chromosome sequence files
download_utils.wget(os.path.join(genome_url, "*"))
# Download only chrom17 / chr13 random
#download_utils.wget(os.path.join(genome_url, "chr17.fa.gz"))
#download_utils.wget(os.path.join(genome_url, "chr13_random.fa.gz"))
# Remove random chromosome contigs
for fname in glob.glob(os.path.join(output_dir, "*.fa.gz")):
if "_" in os.path.basename(fname):
print "Deleting: %s" %(fname)
os.remove(fname)
##
## Uncompress the files
##
print "Uncompressing files..."
uncompress_cmd = "gunzip %s/*.gz" %(output_dir)
t1 = time.time()
os.system(uncompress_cmd)
t2 = time.time()
print "Uncompressing took %.2f minutes" %((t2 - t1)/60.)
def download_genome_seq(genome,
output_dir):
"""
Download genome sequence files from UCSC.
"""
print "Downloading genome sequence files for %s" %(genome)
print " - Output dir: %s" %(output_dir)
output_dir = utils.pathify(os.path.join(output_dir, "genome"))
utils.make_dir(output_dir)
dir_files = os.listdir(output_dir)
# Change to output directory
os.chdir(output_dir)
##
## Download the genome sequence files
##
genome_url = "%s/%s/chromosomes/" %(UCSC_GOLDENPATH_FTP,
genome)
# Fetch all chromosome sequence files
if len(dir_files) >= 1:
print "Directory %s exists and contains files; " \
"skipping download of genome..." \
%(output_dir)
else:
download_utils.wget(os.path.join(genome_url, "*"))
# Remove random chromosome contigs
for fname in glob.glob(os.path.join(output_dir, "*.fa.gz")):
if "_" in os.path.basename(fname):
print "Deleting: %s" %(fname)
os.remove(fname)
##
## Uncompress the files
##
print "Uncompressing files..."
uncompress_cmd = "gunzip %s/*.gz" %(output_dir)
print " - Uncompress cmd: %s" %(uncompress_cmd)
t1 = time.time()
ret_val = os.system(uncompress_cmd)
if ret_val != 0:
print "Error: Cannot uncompress files in %s" %(output_dir)
sys.exit(1)
t2 = time.time()
print "Uncompressing took %.2f minutes" %((t2 - t1)/60.)
# Create a single genome FASTA file by concatenating the
# chromosomes together
genome_output_fname = \
os.path.join(output_dir, "%s.fa" %(genome))
if not os.path.isfile(genome_output_fname):
print "Concatenating genome chromosomes into one file..."
print " - Output file: %s" %(genome_output_fname)
t1 = time.time()
concat_chrom_cmd = "cat %s/*.fa > %s" %(output_dir,
genome_output_fname)
print " - Concat cmd: %s" %(concat_chrom_cmd)
ret_val = os.system(concat_chrom_cmd)
if ret_val != 0:
print "Error: Could not concatenate genome chromosomes."
sys.exit(1)
# Create an index for resulting genome file
print "Indexing genome file..."
samtools_index_cmd = "samtools faidx %s" %(genome_output_fname)
print " - Index cmd: %s" %(samtools_index_cmd)
ret_val = os.system(samtools_index_cmd)
if ret_val != 0:
print "Error: Could not index genome file."
sys.exit(1)
t2 = time.time()
print "Concatenation and indexing took %.2f minutes" \
%((t2 - t1)/60.)
