def download_ucsc_tables(genome,
output_dir):
"""
Download all relevant UCSC tables for a given genome.
"""
tables_outdir = os.path.join(output_dir, "ucsc")
utils.make_dir(tables_outdir)
print "Download UCSC tables..."
print " - Output dir: %s" %(tables_outdir)
ucsc_tables = get_ucsc_tables_urls(genome)
for table_label, table_url in ucsc_tables:
print "Downloading %s" %(table_label)
# If the table exists in uncompressed form, don't download it
table_filename = os.path.join(tables_outdir, table_label)
unzipped_table_fname = table_filename[0:-3]
if os.path.isfile(unzipped_table_fname):
print "Got %s already. Skipping download.." \
%(unzipped_table_fname)
continue
# Download table
download_status = download_utils.download_url(table_url,
tables_outdir)
if download_status is None:
print "Failed to get %s, skipping.." %(table_label)
continue
# Uncompress table
utils.gunzip_file(table_filename, tables_outdir)
def download_ncbi_fasta(access_id, output_dir):
"""
Download NCBI FASTA file by accession number and
label them as access.fasta in the given output directory.
"""
ncbi_url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text" \
%(access_id)
url_filename = download_utils.download_url(ncbi_url,
output_dir,
basename="%s.fa" %(access_id),
binary=False)
return url_filename