Mercurial > repos > bebatut > extract_min_max_lines

comparison extract_min_max_lines.py @ 0:90fc00b34716 draft default tip

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/extract_min_max_lines commit 718c006213709b631862b8d6d655fafc92e79ef7-dirty
author bebatut
date Fri, 15 Apr 2016 07:59:28 -0400
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-1:000000000000 0:90fc00b34716
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3
4 import sys
5 import os
6 import argparse
7 import re
8 import time
9
10 def extract_lines(input_content, column_id, extraction_type, extraction_nb):
11 conserved_lines = []
12 for line in input_content:
13 split_line = line[:-1].split('\t')
14 value = float(split_line[column_id])
15
16 if len(conserved_lines) < extraction_nb:
17 conserved_lines.append(split_line)
18 else:
19 best_pos = None
20 #print value
21 #print conserved_lines
22 for i in range(len(conserved_lines)-1,-1,-1):
23 compared_value = float(conserved_lines[i][column_id])
24 if extraction_type(value, compared_value) == value:
25 print value, compared_value, extraction_type(value, compared_value)
26 best_pos = i
27 else:
28 break
29 if best_pos != None:
30 print best_pos
31 tmp_conserved_lines = conserved_lines
32 conserved_lines = tmp_conserved_lines[:best_pos]
33 conserved_lines += [split_line]
34 conserved_lines += tmp_conserved_lines[best_pos:-1]
35 print conserved_lines
36 print
37 return conserved_lines
38
39 def extract_min_max_lines(args):
40 if args.extraction_type == 'max':
41 extraction_type = max
42 elif args.extraction_type == 'min':
43 extraction_type = min
44
45 with open(args.input_file, 'r') as input_file:
46 input_content = input_file.readlines()
47 conserved_lines = extract_lines(input_content, args.column_id - 1,
48 extraction_type, args.extraction_nb)
49
50 with open(args.output_file, 'w') as output_file:
51 for line in conserved_lines:
52 output_file.write('\t'.join(line) + "\n")
53
54 if __name__ == '__main__':
55 parser = argparse.ArgumentParser()
56 parser.add_argument('--input_file', required=True)
57 parser.add_argument('--output_file', required=True)
58 parser.add_argument('--column_id', required=True, type=int)
59 parser.add_argument('--extraction_type', required=True, choices = ['min','max'])
60 parser.add_argument('--extraction_nb', required=True, type=int)
61 args = parser.parse_args()
62
63 extract_min_max_lines(args)