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comparison orf_tool.py @ 3:0095bf758b19 draft

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author nedias
date Wed, 12 Oct 2016 00:03:53 -0400
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2:c56b8a6bd02e 3:0095bf758b19
1 """
2 Actual function class of open reading frame searching tool
3 Served as a bridge between util class and entry.
4
5 Author Nedias Sept, 2016
6 """
7 from Bio import SeqIO
8 from Bio.SeqRecord import SeqRecord
9 import ORFFinder
10 import os
11 import GTranslator
12
13
14 # Get command and parameter from entry and call corresponding function
15 def exec_tool(options):
16 # If format is fasta
17 if options.format and options.format == "fasta":
18 exec_fasta(options.input, options.outputa, options.outputd, options.length)
19 # TODO: If format is fastq
20 elif options.format and options.format == "fastq":
21 print("Process Fastq File(TODO:Not Implemented)")
22 # TODO: If format is sam
23 elif options.format and options.format == "sam":
24 print("Process Sam File(TODO:Not Implemented)")
25 # TODO: If format is bam
26 elif options.format and options.format == "bam":
27 print("Process Bam File(TODO:Not Implemented)")
28
29
30 # Read the input fasta file find all open reading frames(ORFs)
31 # input: 1.in_file: input file in fasta format
32 # 2.outputa: all ORFs found are saved in this file
33 # 3.outputd: all ORFs longer than designated length are saved in this file
34 # 4.length: filter all ORFs if less than percentage of the length of the longest ORF found
35 # return: execute status code
36 # TODO: Seq and Rev_seq need to be process in the same time
37 def exec_fasta(in_file, output_all, output_dest, length):
38
39 # Open input file(read only)
40 input_file = open(in_file, "rU")
41 # Open all match file(create or override)
42 all_mth_file = open(output_all, "w+")
43 # Open all match file(create or override)
44 desi_file = open(output_dest, "w+")
45
46 # Scan through all Sequenced data in input file
47 for record in SeqIO.parse(input_file, "fasta"):
48
49 # for each sequence, use function in ORFFinder to abstract all ORFs
50 seq = record.seq
51 # Get all start and end positions in +strand
52 result = ORFFinder.get_all_orf(str(seq), False)
53 # Get all start-end pairs in +strand
54 pairs = ORFFinder.find_all_orf(result)
55
56 # Reverse the sequenced data
57 rev_seq = seq[::-1]
58 # Get all start and end positions in -strand
59 rev_result = ORFFinder.get_all_orf(str(rev_seq), True)
60 # Get all start-end pairs in -strand
61 rev_pairs = ORFFinder.find_all_orf(rev_result)
62
63 # Get longest start-end pair of both strands
64 longest_match = ORFFinder.get_longest_pair(pairs, rev_pairs)
65
66 # Calculate the designated length
67 match_length = int(longest_match * int(length) / 100)
68
69 # All ORFs
70 all_frags = []
71 # All designated ORFs
72 desi_frags = []
73
74 # TODO: considering make the result in dictionary and make this four for-loop into 2 or 1 loop
75 # For each pair in the +strand
76 for pair in pairs[:-1]:
77 # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
78 # into polypeptide sequence
79 frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(record.seq[pair[0]:pair[1]], False), record.id + "|"
80 + str(pair[0]) + "-" + str(pair[1]),
81 '', '')
82 all_frags.append(frag)
83
84 # For each pair in the -strand
85 for pair2 in rev_pairs[:-1]:
86 # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
87 # into polypeptide sequence
88 frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(rev_seq[pair2[0]:pair2[1]], True),
89 record.id + "|" + str(len(rev_seq) - pair2[0]) + "-" + str(len(rev_seq) - pair2[1]),
90 '', '')
91 all_frags.append(frag)
92
93 desi_pairs = ORFFinder.get_desi_pairs(pairs, match_length)
94 rev_desi_pairs = ORFFinder.get_desi_pairs(rev_pairs, match_length)
95
96 # For each designated pair in the +strand
97 for pair in desi_pairs:
98 # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
99 # into polypeptide sequence
100 frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(seq[pair[0]:pair[1]], False),
101 record.id + "|" + str(pair[0]) + "-" + str(pair[1]), '', '')
102 desi_frags.append(frag)
103
104 # For each designated pair in the strand
105 for pair in rev_desi_pairs:
106 # Intercept ORF from the original sequence using the start-end pair, and than translate the sequence
107 # into polypeptide sequence
108 frag = SeqRecord(GTranslator.nucleotide_to_polypeptide(rev_seq[pair[0]:pair[1]], True),
109 record.id + "|" + str(len(rev_seq) - pair[0]) + "-" + str(len(rev_seq) - pair[1]),
110 '', '')
111 desi_frags.append(frag)
112
113 # Write the result to output file
114 SeqIO.write(all_frags, all_mth_file, "fasta")
115 SeqIO.write(desi_frags, desi_file, "fasta")
116
117 # Close file entry
118 input_file.close()
119 all_mth_file.close()
120 desi_file.close()
121
122 return 0