RoseTTAFold-All-Atom/rf2aa/ffindex.py
2024-03-04 22:38:17 -08:00

92 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()