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# Copyright (c) 2014. Mount Sinai School of Medicine
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from datacache import fetch_file
import gzip
URL = "".join([
'ftp://ftp.ensembl.org/pub/release-75',
'/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75',
'.dna_rm.chromosome.MT.fa.gz',
])
def fetch_fasta_dict(path_or_url):
path = fetch_file(path_or_url)
d = {}
value_buffer = []
key = None
if path.endswith(".gz") or path.endswith(".gzip"):
f = gzip.open(path, "r")
else:
f = open(path, "r")
for line in f.readlines():
if type(line) is bytes:
line = line.decode("ascii")
if line.startswith(">"):
if key is not None:
d[key] = "".join(value_buffer)
value_buffer = []
key = line.split()[0][1:]
else:
value_buffer.append(line.strip())
if key and value_buffer:
d[key] = "".join(value_buffer)
f.close()
return d
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