annotate orf_tool.py @ 7:0eda2c588bcd draft

Deleted selected files

"""
 Actual function class of open reading frame searching tool
 Served as a bridge between util class and entry.

 Author Nedias Sept, 2016
"""
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import ORFFinder
import os
import GTranslator


# Get command and parameter from entry and call corresponding function
def exec_tool(options):
    # If format is fasta
    if options.format and options.format == "fasta":
        exec_fasta(options.input, options.outputa, options.outputd, options.length)
    # TODO: If format is fastq
    elif options.format and options.format == "fastq":
        print("Process Fastq File(TODO:Not Implemented)")
    # TODO: If format is sam
    elif options.format and options.format == "sam":
        print("Process Sam File(TODO:Not Implemented)")
    # TODO: If format is bam
    elif options.format and options.format == "bam":
        print("Process Bam File(TODO:Not Implemented)")


# Read the input fasta file find all open reading frames(ORFs)
# input: 1.in_file: input file in fasta format
#        2.outputa: all ORFs found are saved in this file
#        3.outputd: all ORFs longer than designated length are saved in this file
#        4.length: filter all ORFs if less than percentage of the length of the longest ORF found
# return: execute status code
# TODO: Seq and Rev_seq need to be process in the same time
def exec_fasta(in_file, output_all, output_dest, length):

    # Open input file(read only)
    input_file = open(in_file, "rU")
    # Open all match file(create or override)
    all_mth_file = open(output_all, "w+")
    # Open all match file(create or override)
    desi_file = open(output_dest, "w+")

    # Scan through all Sequenced data in input file
    for record in SeqIO.parse(input_file, "fasta"):

        # for each sequence, use function in ORFFinder to abstract all ORFs
        seq = record.seq
        # Get all start and end positions in +strand
        result = ORFFinder.get_all_orf(str(seq), False)
        # Get all start-end pairs in +strand
        pairs = ORFFinder.find_all_orf(result)

        # Reverse the sequenced data
        rev_seq = seq[::-1]
        # Get all start and end positions in -strand
        rev_result = ORFFinder.get_all_orf(str(rev_seq), True)
        # Get all start-end pairs in -strand
        rev_pairs = ORFFinder.find_all_orf(rev_result)

        # Get longest start-end pair of both strands
        longest_match = ORFFinder.get_longest_pair(pairs, rev_pairs)

        # Calculate the designated length
        match_length = int(longest_match * int(length) / 100)

        # All ORFs
        all_frags = []
        # All designated ORFs
        desi_frags = []

        # TODO: considering make the result in dictionary and make this four for-loop into 2 or 1 loop
        # For each pair in the +strand
        for pair in pairs[:-1]:
            # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
            # into polypeptide sequence
            frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(record.seq[pair[0]:pair[1]], False), record.id + "|"
                             + str(pair[0]) + "-" + str(pair[1]),
                             '', '')
            all_frags.append(frag)

        # For each pair in the -strand
        for pair2 in rev_pairs[:-1]:
            # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
            # into polypeptide sequence
            frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(rev_seq[pair2[0]:pair2[1]], True),
                             record.id + "|" + str(len(rev_seq) - pair2[0]) + "-" + str(len(rev_seq) - pair2[1]),
                             '', '')
            all_frags.append(frag)

        desi_pairs = ORFFinder.get_desi_pairs(pairs, match_length)
        rev_desi_pairs = ORFFinder.get_desi_pairs(rev_pairs, match_length)

        # For each designated pair in the +strand
        for pair in desi_pairs:
            # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
            # into polypeptide sequence
            frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(seq[pair[0]:pair[1]], False),
                             record.id + "|" + str(pair[0]) + "-" + str(pair[1]), '', '')
            desi_frags.append(frag)

        # For each designated pair in the strand
        for pair in rev_desi_pairs:
            # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
            # into polypeptide sequence
            frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(rev_seq[pair[0]:pair[1]], True),
                             record.id + "|" + str(len(rev_seq) - pair[0]) + "-" + str(len(rev_seq) - pair[1]),
                             '', '')
            desi_frags.append(frag)

        # Write the result to output file
        SeqIO.write(all_frags, all_mth_file, "fasta")
        SeqIO.write(desi_frags, desi_file, "fasta")

    # Close file entry
    input_file.close()
    all_mth_file.close()
    desi_file.close()

    return 0