Mercurial > repos > iuc > cwpair2

comparison cwpair2_util.py @ 5:71188f3f4b76 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
author iuc
date Mon, 06 Nov 2017 23:19:50 -0500
parents 436dc65bd902
children c4b926c9831c
comparison
equal deleted inserted replaced
4:d843468aeb8f 5:71188f3f4b76
4 import sys 4 import sys
5 import traceback 5 import traceback
6 6
7 import matplotlib 7 import matplotlib
8 matplotlib.use('Agg') 8 matplotlib.use('Agg')
9 from matplotlib import pyplot # noqa: E402 9 from matplotlib import pyplot # noqa: I202,E402
10 10
11 # Data outputs 11 # Data outputs
12 DETAILS = 'D' 12 DETAILS = 'D'
13 MATCHED_PAIRS = 'MP' 13 MATCHED_PAIRS = 'MP'
14 ORPHANS = 'O' 14 ORPHANS = 'O'
90 90
91 91
92 def parse_chromosomes(reader): 92 def parse_chromosomes(reader):
93 # This version of cwpair2 accepts only gff format as input. 93 # This version of cwpair2 accepts only gff format as input.
94 chromosomes = {} 94 chromosomes = {}
95 reader.next() 95 next(reader)
96 for line in reader: 96 for line in reader:
97 cname, junk, junk, start, end, value, strand, junk, junk = line 97 cname, junk, junk, start, end, value, strand, junk, junk = line
98 start = int(start) 98 start = int(start)
99 end = int(end) 99 end = int(end)
100 value = float(value) 100 value = float(value)
243 output_files) 243 output_files)
244 statistics.append(stats) 244 statistics.append(stats)
245 if output_files == 'all' and method == 'all': 245 if output_files == 'all' and method == 'all':
246 frequency_plot([s['dist'] for s in statistics], 246 frequency_plot([s['dist'] for s in statistics],
247 statistics[0]['graph_path'], 247 statistics[0]['graph_path'],
248 labels=METHODS.keys()) 248 labels=list(METHODS.keys()))
249 return statistics 249 return statistics
250 250
251 251
252 def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance, 252 def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
253 down_distance, binsize, output_files): 253 down_distance, binsize, output_files):