Mercurial > repos > iuc > resize_coordinate_window

comparison resize_coordinate_window.py @ 4:4eb3cc1f8466 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
author iuc
date Wed, 11 Dec 2019 18:06:42 -0500
parents 9ba78e8985dc
children
comparison
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3:9ba78e8985dc 4:4eb3cc1f8466
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1 import argparse 3 import argparse
2 import fileinput 4 import fileinput
3 import sys 5 import sys
4 6
5 # Maximum value of a signed 32 bit integer (2**31 - 1). 7 # Maximum value of a signed 32 bit integer (2**31 - 1).
6 MAX_CHROM_LEN = 2147483647 8 MAX_CHROM_LEN = 2147483647
7 9
8 10
9 def stop_err(msg): 11 def stop_err(msg):
10 sys.stderr.write(msg) 12 sys.exit(msg)
11 sys.exit(1)
12 13
13 14
14 parser = argparse.ArgumentParser() 15 parser = argparse.ArgumentParser()
15 parser.add_argument('--input', dest='input', help="Input dataset") 16 parser.add_argument('--input', dest='input', help="Input dataset")
16 parser.add_argument('--start_coordinate', dest='start_coordinate', type=int, help='Chromosome start coordinate, either 0 or 1.') 17 parser.add_argument('--start_coordinate', dest='start_coordinate', type=int, help='Chromosome start coordinate, either 0 or 1.')
21 parser.add_argument('--region_boundaries', dest='region_boundaries', help="Option for handling region boundaries") 22 parser.add_argument('--region_boundaries', dest='region_boundaries', help="Option for handling region boundaries")
22 parser.add_argument('--output', dest='output', help="Output dataset") 23 parser.add_argument('--output', dest='output', help="Output dataset")
23 args = parser.parse_args() 24 args = parser.parse_args()
24 25
25 extend_existing = args.extend_existing == 'existing' 26 extend_existing = args.extend_existing == 'existing'
26 out = open(args.output, 'wb') 27 out = open(args.output, 'w')
27 28
28 chrom_start = int(args.start_coordinate) 29 chrom_start = int(args.start_coordinate)
29 chrom_lens = dict() 30 chrom_lens = dict()
30 # Determine the length of each chromosome and add it to the chrom_lens dictionary. 31 # Determine the length of each chromosome and add it to the chrom_lens dictionary.
31 len_file_missing = False 32 len_file_missing = False
82 new_line = '\t'.join([chrom, items[1], items[2], str(new_start), str(new_end), items[5], items[6], items[7], items[8]]) 83 new_line = '\t'.join([chrom, items[1], items[2], str(new_start), str(new_end), items[5], items[6], items[7], items[8]])
83 out.write(new_line) 84 out.write(new_line)
84 out.close() 85 out.close()
85 86
86 if len_file_error is not None: 87 if len_file_error is not None:
87 print "All chrom lengths set to %d, error in chrom len file: %s" % (MAX_CHROM_LEN, len_file_error) 88 print("All chrom lengths set to %d, error in chrom len file: %s" % (MAX_CHROM_LEN, len_file_error))
88 if len_file_missing: 89 if len_file_missing:
89 print "All chrom lengths set to %d, chrom len files are not installed." % MAX_CHROM_LEN 90 print("All chrom lengths set to %d, chrom len files are not installed." % MAX_CHROM_LEN)