repmatch_gff3: repmatch_gff3

annotate repmatch_gff3_util.py @ 8:64c87be9dbd8 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit b50166c05f3484b0d0171cd668653efb54cf0545"

author	iuc
date	Mon, 16 Dec 2019 20:44:52 +0000
parents	367f700059fd
children

rev	line source
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	1 import bisect
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	2 import csv
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	3 import os
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	4 import shutil
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	5 import sys
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	6 import tempfile
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	7
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	8 import matplotlib
2 86876dfc75d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e7c1b37cf73425c6637b4e196fdeb290e042bc1 iuc parents: 1 diff changeset	9 matplotlib.use('Agg')
6 367f700059fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c iuc parents: 5 diff changeset	10 from matplotlib import pyplot # noqa: I202,E402
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	11
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	12 # Graph settings
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	13 Y_LABEL = 'Counts'
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	14 X_LABEL = 'Number of matched replicates'
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	15 TICK_WIDTH = 3
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	16 # Amount to shift the graph to make labels fit, [left, right, top, bottom]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	17 ADJUST = [0.180, 0.9, 0.9, 0.1]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	18 # Length of tick marks, use TICK_WIDTH for width
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	19 pyplot.rc('xtick.major', size=10.00)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	20 pyplot.rc('ytick.major', size=10.00)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	21 pyplot.rc('lines', linewidth=4.00)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	22 pyplot.rc('axes', linewidth=3.00)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	23 pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	24
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	25 COLORS = 'krb'
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	26 ISPY2 = sys.version_info[0] == 2
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	27
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	28
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	29 class Replicate(object):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	30
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	31 def __init__(self, id, dataset_path):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	32 self.id = id
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	33 self.dataset_path = dataset_path
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	34 if ISPY2:
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	35 fh = open(dataset_path, 'rb')
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	36 else:
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	37 fh = open(dataset_path, 'r', newline='')
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	38 self.parse(csv.reader(fh, delimiter='\t'))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	39
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	40 def parse(self, reader):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	41 self.chromosomes = {}
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	42 for line in reader:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	43 if line[0].startswith("#") or line[0].startswith('"'):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	44 continue
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	45 cname, junk, junk, mid, midplus, value, strand, junk, attrs = line
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	46 attrs = parse_gff_attrs(attrs)
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	47 distance = int(attrs['cw_distance'])
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	48 mid = int(mid)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	49 midplus = int(midplus)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	50 value = float(value)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	51 if cname not in self.chromosomes:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	52 self.chromosomes[cname] = Chromosome(cname)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	53 chrom = self.chromosomes[cname]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	54 chrom.add_peak(Peak(cname, mid, value, distance, self))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	55 for chrom in self.chromosomes.values():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	56 chrom.sort_by_index()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	57
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	58 def filter(self, up_limit, low_limit):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	59 for chrom in self.chromosomes.values():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	60 chrom.filter(up_limit, low_limit)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	61
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	62 def size(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	63 return sum([len(c.peaks) for c in self.chromosomes.values()])
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	64
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	65
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	66 class Chromosome(object):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	67
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	68 def __init__(self, name):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	69 self.name = name
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	70 self.peaks = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	71
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	72 def add_peak(self, peak):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	73 self.peaks.append(peak)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	74
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	75 def sort_by_index(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	76 self.peaks.sort(key=lambda peak: peak.midpoint)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	77 self.keys = make_keys(self.peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	78
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	79 def remove_peak(self, peak):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	80 i = bisect.bisect_left(self.keys, peak.midpoint)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	81 # If the peak was actually found
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	82 if i < len(self.peaks) and self.peaks[i].midpoint == peak.midpoint:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	83 del self.keys[i]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	84 del self.peaks[i]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	85
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	86 def filter(self, up_limit, low_limit):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	87 self.peaks = [p for p in self.peaks if low_limit <= p.distance <= up_limit]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	88 self.keys = make_keys(self.peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	89
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	90
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	91 class Peak(object):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	92
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	93 def __init__(self, chrom, midpoint, value, distance, replicate):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	94 self.chrom = chrom
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	95 self.value = value
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	96 self.midpoint = midpoint
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	97 self.distance = distance
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	98 self.replicate = replicate
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	99
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	100 def normalized_value(self, med):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	101 return self.value * med / self.replicate.median
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	102
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	103
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	104 class PeakGroup(object):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	105
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	106 def __init__(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	107 self.peaks = {}
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	108
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	109 def add_peak(self, repid, peak):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	110 self.peaks[repid] = peak
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	111
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	112 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	113 def chrom(self):
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	114 return list(self.peaks.values())[0].chrom
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	115
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	116 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	117 def midpoint(self):
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	118 return int(median([peak.midpoint for peak in self.peaks.values()]))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	119
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	120 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	121 def num_replicates(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	122 return len(self.peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	123
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	124 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	125 def median_distance(self):
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	126 return int(median([peak.distance for peak in self.peaks.values()]))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	127
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	128 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	129 def value_sum(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	130 return sum([peak.value for peak in self.peaks.values()])
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	131
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	132 def normalized_value(self, med):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	133 values = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	134 for peak in self.peaks.values():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	135 values.append(peak.normalized_value(med))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	136 return median(values)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	137
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	138 @property
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	139 def peakpeak_distance(self):
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	140 keys = list(self.peaks.keys())
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	141 return abs(self.peaks[keys[0]].midpoint - self.peaks[keys[1]].midpoint)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	142
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	143
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	144 class FrequencyDistribution(object):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	145
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	146 def __init__(self, d=None):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	147 self.dist = d or {}
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	148
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	149 def add(self, x):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	150 self.dist[x] = self.dist.get(x, 0) + 1
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	151
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	152 def graph_series(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	153 x = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	154 y = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	155 for key, val in self.dist.items():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	156 x.append(key)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	157 y.append(val)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	158 return x, y
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	159
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	160 def mode(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	161 return max(self.dist.items(), key=lambda data: data[1])[0]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	162
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	163 def size(self):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	164 return sum(self.dist.values())
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	165
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	166
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	167 def stop_err(msg):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	168 sys.stderr.write(msg)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	169 sys.exit(1)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	170
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	171
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	172 def median(data):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	173 """
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	174 Find the integer median of the data set.
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	175 """
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	176 if not data:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	177 return 0
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	178 sdata = sorted(data)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	179 if len(data) % 2 == 0:
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	180 return (sdata[len(data) // 2] + sdata[len(data) // 2 - 1]) / 2
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	181 else:
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	182 return sdata[len(data) // 2]
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	183
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	184
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	185 def make_keys(peaks):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	186 return [data.midpoint for data in peaks]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	187
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	188
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	189 def get_window(chromosome, target_peaks, distance):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	190 """
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	191 Returns a window of all peaks from a replicate within a certain distance of
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	192 a peak from another replicate.
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	193 """
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	194 lower = list(target_peaks)[0].midpoint
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	195 upper = list(target_peaks)[0].midpoint
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	196 for peak in target_peaks:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	197 lower = min(lower, peak.midpoint - distance)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	198 upper = max(upper, peak.midpoint + distance)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	199 start_index = bisect.bisect_left(chromosome.keys, lower)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	200 end_index = bisect.bisect_right(chromosome.keys, upper)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	201 return (chromosome.peaks[start_index: end_index], chromosome.name)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	202
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	203
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	204 def match_largest(window, peak, chrum):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	205 if not window:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	206 return None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	207 if peak.chrom != chrum:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	208 return None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	209 return max(window, key=lambda cpeak: cpeak.value)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	210
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	211
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	212 def match_closest(window, peak, chrum):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	213 if not window:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	214 return None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	215 if peak.chrom != chrum:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	216 return None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	217 return min(window, key=lambda match: abs(match.midpoint - peak.midpoint))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	218
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	219
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	220 def frequency_histogram(freqs, dataset_path, labels=[], title=''):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	221 pyplot.clf()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	222 pyplot.figure(figsize=(10, 10))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	223 for i, freq in enumerate(freqs):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	224 xvals, yvals = freq.graph_series()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	225 # Go from high to low
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	226 xvals.reverse()
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	227 pyplot.bar([x - 0.4 + 0.8 / len(freqs) * i for x in xvals], yvals, width=0.8 / len(freqs), color=COLORS[i])
28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	228 pyplot.xticks(range(min(xvals), max(xvals) + 1), map(str, reversed(range(min(xvals), max(xvals) + 1))))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	229 pyplot.xlabel(X_LABEL)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	230 pyplot.ylabel(Y_LABEL)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	231 pyplot.subplots_adjust(left=ADJUST[0], right=ADJUST[1], top=ADJUST[2], bottom=ADJUST[3])
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	232 ax = pyplot.gca()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	233 for l in ax.get_xticklines() + ax.get_yticklines():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	234 l.set_markeredgewidth(TICK_WIDTH)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	235 pyplot.savefig(dataset_path)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	236
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	237
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	238 METHODS = {'closest': match_closest, 'largest': match_largest}
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	239
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	240
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	241 def gff_attrs(l):
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	242 if len(l) == 0:
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	243 return '.'
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	244 return ';'.join('%s=%s' % (tup[0], tup[1]) for tup in l)
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	245
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	246
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	247 def parse_gff_attrs(s):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	248 d = {}
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	249 if s == '.':
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	250 return d
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	251 for item in s.split(';'):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	252 key, val = item.split('=')
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	253 d[key] = val
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	254 return d
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	255
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	256
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	257 def gff_row(cname, start, end, score, source, stype='.', strand='.', phase='.', attrs=None):
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	258 return (cname, source, stype, start, end, score, strand, phase, gff_attrs(attrs or []))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	259
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	260
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	261 def get_temporary_plot_path():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	262 """
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	263 Return the path to a temporary file with a valid image format
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	264 file extension that can be used with bioformats.
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	265 """
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	266 tmp_dir = tempfile.mkdtemp(prefix='tmp-repmatch-')
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	267 fd, name = tempfile.mkstemp(suffix='.pdf', dir=tmp_dir)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	268 os.close(fd)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	269 return name
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	270
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	271
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	272 def process_files(dataset_paths, galaxy_hids, method, distance, step, replicates, up_limit, low_limit, output_files,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	273 output_matched_peaks, output_unmatched_peaks, output_detail, output_statistics_table, output_statistics_histogram):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	274 output_statistics_histogram_file = output_files in ["all"] and method in ["all"]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	275 if len(dataset_paths) < 2:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	276 return
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	277 if method == 'all':
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	278 match_methods = METHODS.keys()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	279 else:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	280 match_methods = [method]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	281 for match_method in match_methods:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	282 statistics = perform_process(dataset_paths,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	283 galaxy_hids,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	284 match_method,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	285 distance,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	286 step,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	287 replicates,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	288 up_limit,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	289 low_limit,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	290 output_files,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	291 output_matched_peaks,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	292 output_unmatched_peaks,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	293 output_detail,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	294 output_statistics_table,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	295 output_statistics_histogram)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	296 if output_statistics_histogram_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	297 tmp_statistics_histogram_path = get_temporary_plot_path()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	298 frequency_histogram([stat['distribution'] for stat in [statistics]],
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	299 tmp_statistics_histogram_path,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	300 METHODS.keys())
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	301 shutil.move(tmp_statistics_histogram_path, output_statistics_histogram)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	302
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	303
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	304 def perform_process(dataset_paths, galaxy_hids, method, distance, step, num_required, up_limit, low_limit, output_files,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	305 output_matched_peaks, output_unmatched_peaks, output_detail, output_statistics_table, output_statistics_histogram):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	306 output_detail_file = output_files in ["all"] and output_detail is not None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	307 output_statistics_table_file = output_files in ["all"] and output_statistics_table is not None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	308 output_unmatched_peaks_file = output_files in ["all", "matched_peaks_unmatched_peaks"] and output_unmatched_peaks is not None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	309 output_statistics_histogram_file = output_files in ["all"] and output_statistics_histogram is not None
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	310 replicates = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	311 for i, dataset_path in enumerate(dataset_paths):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	312 try:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	313 galaxy_hid = galaxy_hids[i]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	314 r = Replicate(galaxy_hid, dataset_path)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	315 replicates.append(r)
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	316 except Exception as e:
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	317 stop_err('Unable to parse file "%s", exception: %s' % (dataset_path, str(e)))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	318 attrs = 'd%sr%s' % (distance, num_required)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	319 if up_limit != 1000:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	320 attrs += 'u%d' % up_limit
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	321 if low_limit != -1000:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	322 attrs += 'l%d' % low_limit
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	323 if step != 0:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	324 attrs += 's%d' % step
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	325
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	326 def td_writer(file_path):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	327 # Returns a tab-delimited writer for a certain output
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	328 if ISPY2:
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	329 fh = open(file_path, 'wb')
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	330 return csv.writer(fh, delimiter='\t')
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	331 else:
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	332 fh = open(file_path, 'w', newline='')
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	333 return csv.writer(fh, delimiter='\t', quoting=csv.QUOTE_NONE)
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	334
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	335 labels = ('chrom',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	336 'median midpoint',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	337 'median midpoint+1',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	338 'median normalized reads',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	339 'replicates',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	340 'median c-w distance',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	341 'reads sum')
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	342 for replicate in replicates:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	343 labels += ('chrom',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	344 'median midpoint',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	345 'median midpoint+1',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	346 'c-w sum',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	347 'c-w distance',
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	348 'replicate id')
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	349 matched_peaks_output = td_writer(output_matched_peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	350 if output_statistics_table_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	351 statistics_table_output = td_writer(output_statistics_table)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	352 statistics_table_output.writerow(('data', 'median read count'))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	353 if output_detail_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	354 detail_output = td_writer(output_detail)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	355 detail_output.writerow(labels)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	356 if output_unmatched_peaks_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	357 unmatched_peaks_output = td_writer(output_unmatched_peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	358 unmatched_peaks_output.writerow(('chrom', 'midpoint', 'midpoint+1', 'c-w sum', 'c-w distance', 'replicate id'))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	359 # Perform filtering
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	360 if up_limit < 1000 or low_limit > -1000:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	361 for replicate in replicates:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	362 replicate.filter(up_limit, low_limit)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	363 # Actually merge the peaks
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	364 peak_groups = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	365 unmatched_peaks = []
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	366 freq = FrequencyDistribution()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	367
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	368 def do_match(reps, distance):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	369 # Copy list because we will mutate it, but keep replicate references.
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	370 reps = reps[:]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	371 while len(reps) > 1:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	372 # Iterate over each replicate as "main"
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	373 main = reps[0]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	374 reps.remove(main)
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	375 for chromosome in list(main.chromosomes.values()):
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	376 peaks_by_value = chromosome.peaks[:]
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	377 # Sort main replicate by value
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	378 peaks_by_value.sort(key=lambda peak: -peak.value)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	379
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	380 def search_for_matches(group):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	381 # Here we use multiple passes, expanding the window to be
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	382 # +- distance from any previously matched peak.
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	383 while True:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	384 new_match = False
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	385 for replicate in reps:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	386 if replicate.id in group.peaks:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	387 # Stop if match already found for this replicate
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	388 continue
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	389 try:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	390 # Lines changed to remove a major bug by Rohit Reja.
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	391 window, chrum = get_window(replicate.chromosomes[chromosome.name], list(group.peaks.values()), distance)
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	392 match = METHODS[method](window, peak, chrum)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	393 except KeyError:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	394 continue
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	395 if match:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	396 group.add_peak(replicate.id, match)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	397 new_match = True
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	398 if not new_match:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	399 break
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	400 # Attempt to enlarge existing peak groups
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	401 for group in peak_groups:
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	402 old_peaks = list(group.peaks.values())
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	403 search_for_matches(group)
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	404 for peak in list(group.peaks.values()):
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	405 if peak not in old_peaks:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	406 peak.replicate.chromosomes[chromosome.name].remove_peak(peak)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	407 # Attempt to find new peaks groups. For each peak in the
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	408 # main replicate, search for matches in the other replicates
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	409 for peak in peaks_by_value:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	410 matches = PeakGroup()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	411 matches.add_peak(main.id, peak)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	412 search_for_matches(matches)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	413 # Were enough replicates matched?
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	414 if matches.num_replicates >= num_required:
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	415 for peak in list(matches.peaks.values()):
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	416 peak.replicate.chromosomes[chromosome.name].remove_peak(peak)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	417 peak_groups.append(matches)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	418 # Zero or less = no stepping
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	419 if step <= 0:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	420 do_match(replicates, distance)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	421 else:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	422 for d in range(0, distance, step):
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	423 do_match(replicates, d)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	424 for group in peak_groups:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	425 freq.add(group.num_replicates)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	426 # Collect together the remaining unmatched_peaks
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	427 for replicate in replicates:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	428 for chromosome in replicate.chromosomes.values():
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	429 for peak in chromosome.peaks:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	430 freq.add(1)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	431 unmatched_peaks.append(peak)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	432 # Average the unmatched_peaks count in the graph by # replicates
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	433 med = median([peak.value for group in peak_groups for peak in group.peaks.values()])
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	434 for replicate in replicates:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	435 replicate.median = median([peak.value for group in peak_groups for peak in group.peaks.values() if peak.replicate == replicate])
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	436 statistics_table_output.writerow((replicate.id, replicate.median))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	437 for group in peak_groups:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	438 # Output matched_peaks (matched pairs).
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	439 matched_peaks_output.writerow(gff_row(cname=group.chrom,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	440 start=group.midpoint,
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	441 end=group.midpoint + 1,
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	442 score=group.normalized_value(med),
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	443 source='repmatch',
5 095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	444 stype='.',
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	445 strand='.',
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	446 phase='.',
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	447 attrs=[('median_distance', group.median_distance),
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	448 ('value_sum', group.value_sum),
095437917d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 315c3ddcdbf38a27d43753aae3b6d379306be5a9 iuc parents: 2 diff changeset	449 ('replicates', group.num_replicates)]))
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	450 if output_detail_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	451 matched_peaks = (group.chrom,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	452 group.midpoint,
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	453 group.midpoint + 1,
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	454 group.normalized_value(med),
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	455 group.num_replicates,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	456 group.median_distance,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	457 group.value_sum)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	458 for peak in group.peaks.values():
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	459 matched_peaks += (peak.chrom, peak.midpoint, peak.midpoint + 1, peak.value, peak.distance, peak.replicate.id)
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	460 detail_output.writerow(matched_peaks)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	461 if output_unmatched_peaks_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	462 for unmatched_peak in unmatched_peaks:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	463 unmatched_peaks_output.writerow((unmatched_peak.chrom,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	464 unmatched_peak.midpoint,
1 28171ec04890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit ea49259a702be2cc2b70166770d09177019bb210 iuc parents: 0 diff changeset	465 unmatched_peak.midpoint + 1,
0 d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	466 unmatched_peak.value,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	467 unmatched_peak.distance,
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	468 unmatched_peak.replicate.id))
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	469 if output_statistics_histogram_file:
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	470 tmp_statistics_histogram_path = get_temporary_plot_path()
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	471 frequency_histogram([freq], tmp_statistics_histogram_path)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	472 shutil.move(tmp_statistics_histogram_path, output_statistics_histogram)
d437f7b3cc9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 iuc parents: diff changeset	473 return {'distribution': freq}

Mercurial > repos > iuc > repmatch_gff3

annotate repmatch_gff3_util.py @ 8:64c87be9dbd8 draft default tip