Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

rf2aa/ffindex.py

@@ -0,0 +1,91 @@
+#!/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()