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from Bio import SeqIO
import os
import csv
import sys
import collections
import hashlib
import collections
import csv
def version_from_init(init_file):
version=None
with open(init_file, "r") as fr:
for l in fr:
if l.startswith("__version__"):
l = l.rstrip("\n")
version = l.split('=')[1]
version = version.replace('"',"").replace(" ","")
break
return version
def get_pango_version(pango_path):
version =""
for r,d,f in os.walk(pango_path):
for fn in f:
if fn == "__init__.py":
version = version_from_init(os.path.join(r, fn))
if not version:
continue
print("Pango version is:", version)
if not version:
sys.sterr.write("No version found at pango path")
sys.exit(-1)
else:
return version
def get_hash_string(record):
seq = str(record.seq).upper().encode()
hash_object = hashlib.md5(seq)
hash_string = hash_object.hexdigest()
return hash_string
def get_dict(in_csv,name_column,data_column):
this_dict = {}
with open(in_csv,"r") as f:
reader = csv.DictReader(f)
for row in reader:
this_dict[row[name_column]] = row[data_column]
return this_dict
def add_to_hash(seq_file):
hash_map = {}
seq_hash = {}
for record in SeqIO.parse(seq_file, "fasta"):
seq = str(record.seq).upper().encode()
hash_object = hashlib.md5(seq)
hash_map[hash_object.hexdigest()] = record.id
seq_hash[str(record.seq)] = record.id
return hash_map,seq_hash
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