mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-11-04 22:25:42 +00:00
91 lines
2.1 KiB
Python
91 lines
2.1 KiB
Python
#!/usr/bin/env python
|
|
# https://raw.githubusercontent.com/ahcm/ffindex/master/python/ffindex.py
|
|
|
|
'''
|
|
Created on Apr 30, 2014
|
|
|
|
@author: meiermark
|
|
'''
|
|
|
|
|
|
import sys
|
|
import mmap
|
|
from collections import namedtuple
|
|
|
|
FFindexEntry = namedtuple("FFindexEntry", "name, offset, length")
|
|
|
|
|
|
def read_index(ffindex_filename):
|
|
entries = []
|
|
|
|
fh = open(ffindex_filename, "r")
|
|
for line in fh:
|
|
tokens = line.split("\t")
|
|
entries.append(FFindexEntry(tokens[0], int(tokens[1]), int(tokens[2])))
|
|
fh.close()
|
|
|
|
return entries
|
|
|
|
|
|
def read_data(ffdata_filename):
|
|
fh = open(ffdata_filename, "rb")
|
|
data = mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ)
|
|
fh.close()
|
|
return data
|
|
|
|
|
|
def get_entry_by_name(name, index):
|
|
#TODO: bsearch
|
|
for entry in index:
|
|
if(name == entry.name):
|
|
return entry
|
|
return None
|
|
|
|
|
|
def read_entry_lines(entry, data):
|
|
lines = data[entry.offset:entry.offset + entry.length - 1].decode("utf-8").split("\n")
|
|
return lines
|
|
|
|
|
|
def read_entry_data(entry, data):
|
|
return data[entry.offset:entry.offset + entry.length - 1]
|
|
|
|
|
|
def write_entry(entries, data_fh, entry_name, offset, data):
|
|
data_fh.write(data[:-1])
|
|
data_fh.write(bytearray(1))
|
|
|
|
entry = FFindexEntry(entry_name, offset, len(data))
|
|
entries.append(entry)
|
|
|
|
return offset + len(data)
|
|
|
|
|
|
def write_entry_with_file(entries, data_fh, entry_name, offset, file_name):
|
|
with open(file_name, "rb") as fh:
|
|
data = bytearray(fh.read())
|
|
return write_entry(entries, data_fh, entry_name, offset, data)
|
|
|
|
|
|
def finish_db(entries, ffindex_filename, data_fh):
|
|
data_fh.close()
|
|
write_entries_to_db(entries, ffindex_filename)
|
|
|
|
|
|
def write_entries_to_db(entries, ffindex_filename):
|
|
sorted(entries, key=lambda x: x.name)
|
|
index_fh = open(ffindex_filename, "w")
|
|
|
|
for entry in entries:
|
|
index_fh.write("{name:.64}\t{offset}\t{length}\n".format(name=entry.name, offset=entry.offset, length=entry.length))
|
|
|
|
index_fh.close()
|
|
|
|
|
|
def write_entry_to_file(entry, data, file):
|
|
lines = read_lines(entry, data)
|
|
|
|
fh = open(file, "w")
|
|
for line in lines:
|
|
fh.write(line+"\n")
|
|
fh.close()
|