#!/usr/bin/env python
"""
    Usage: extract.py <refdir> <filename>
"""

import sys
import os
import re
import string
import subprocess
import tempfile
import getopt

"""
"""
def getFromReference(refID, offset, length):
    reffile = ReferenceFastaFile(refID)
    seq = reffile.getSequence(offset, length)
    reffile.close()
    return seq

class ReferenceFastaFile:
    def __init__(self, refID):
        self.filename = ReferenceFastaFile.getFilename(refID) 
        self.fd = open(self.filename, "r")
        self.start = 0
        self.lineLength = 0
        self.getInfo()

    def getFilename(refID):
        global refFilename, refDirectory
        if refDirectory:
            filename = "%s/chr%s.fa" % (refDirectory, refID)
        else:
            filename = refFilename
        return filename
    getFilename = staticmethod(getFilename)

    def getInfo(self):
        """
            determines offset in file of first byte of sequence data (by skipping the comment line)
            determines length of data lines
            returns both
        """
        self.fd.seek(0, 0)
        line = self.fd.readline();
        self.start = self.fd.tell();
        line = self.fd.readline();
        line = line.rstrip("\n");
        self.lineLength = len(line);

    def getSequence(self, offset, length):
        start = offset + int(offset / self.lineLength) + self.start
        self.fd.seek(start, 0)

        got = 0
        result = []
        while got < length:
            ch = self.fd.read(1)
            if (ch == '\n'):
                continue
            result.append(ch)       
            got += 1
        return ''.join(result) 

    def close(self):
        self.fd.close()

    

refFilename =  refDirectory = None
def main(argv=None):
    if argv is None:
        argv = sys.argv

    global refFilename, refDirectory

    options, remainder = getopt.getopt(argv[1:], "h")
    for opt, arg in options:
        if opt in ("-h"):
            print __doc__ 
            return 0
    if len(remainder) != 2:
        print __doc__
        return 1
    refDirectory = remainder[0]
    coordFilename = remainder[1]
    coordFile = open(coordFilename)

    for line in coordFile:
        line.strip()
        field = line.split()
        seq = getFromReference(field[0], int(field[1]), int(field[2]))
        print seq
            
if __name__ == "__main__":
    sys.exit(main())