repmatch_gff3: repmatch_gff3

annotate repmatch_gff3_util.py @ 0:b26d50dd3226 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9

author	bgruening
date	Wed, 23 Dec 2015 09:24:35 -0500
parents
children

rev	line source
0 b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	1 import bisect
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	2 import csv
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	3 import os
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	4 import shutil
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	5 import sys
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	6 import tempfile
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	7 import matplotlib
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	8 matplotlib.use('Agg')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	9 from matplotlib import pyplot
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	10
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	11 # Graph settings
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	12 Y_LABEL = 'Counts'
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	13 X_LABEL = 'Number of matched replicates'
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	14 TICK_WIDTH = 3
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	15 # Amount to shift the graph to make labels fit, [left, right, top, bottom]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	16 ADJUST = [0.180, 0.9, 0.9, 0.1]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	17 # Length of tick marks, use TICK_WIDTH for width
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	18 pyplot.rc('xtick.major', size=10.00)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	19 pyplot.rc('ytick.major', size=10.00)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	20 pyplot.rc('lines', linewidth=4.00)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	21 pyplot.rc('axes', linewidth=3.00)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	22 pyplot.rc('font', family='Bitstream Vera Sans', size=32.0)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	23
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	24 COLORS = 'krb'
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	25
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	26
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	27 class Replicate(object):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	28
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	29 def __init__(self, id, dataset_path):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	30 self.id = id
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	31 self.dataset_path = dataset_path
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	32 self.parse(csv.reader(open(dataset_path, 'rt'), delimiter='\t'))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	33
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	34 def parse(self, reader):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	35 self.chromosomes = {}
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	36 for line in reader:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	37 if line[0].startswith("#") or line[0].startswith('"'):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	38 continue
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	39 cname, junk, junk, mid, midplus, value, strand, junk, attrs = line
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	40 attrs = parse_gff_attrs(attrs)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	41 distance = attrs['cw_distance']
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	42 mid = int(mid)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	43 midplus = int(midplus)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	44 value = float(value)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	45 distance = int(distance)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	46 if cname not in self.chromosomes:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	47 self.chromosomes[cname] = Chromosome(cname)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	48 chrom = self.chromosomes[cname]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	49 chrom.add_peak(Peak(cname, mid, value, distance, self))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	50 for chrom in self.chromosomes.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	51 chrom.sort_by_index()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	52
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	53 def filter(self, up_limit, low_limit):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	54 for chrom in self.chromosomes.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	55 chrom.filter(up_limit, low_limit)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	56
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	57 def size(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	58 return sum([len(c.peaks) for c in self.chromosomes.values()])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	59
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	60
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	61 class Chromosome(object):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	62
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	63 def __init__(self, name):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	64 self.name = name
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	65 self.peaks = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	66
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	67 def add_peak(self, peak):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	68 self.peaks.append(peak)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	69
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	70 def sort_by_index(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	71 self.peaks.sort(key=lambda peak: peak.midpoint)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	72 self.keys = make_keys(self.peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	73
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	74 def remove_peak(self, peak):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	75 i = bisect.bisect_left(self.keys, peak.midpoint)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	76 # If the peak was actually found
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	77 if i < len(self.peaks) and self.peaks[i].midpoint == peak.midpoint:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	78 del self.keys[i]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	79 del self.peaks[i]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	80
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	81 def filter(self, up_limit, low_limit):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	82 self.peaks = [p for p in self.peaks if low_limit <= p.distance <= up_limit]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	83 self.keys = make_keys(self.peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	84
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	85
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	86 class Peak(object):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	87
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	88 def __init__(self, chrom, midpoint, value, distance, replicate):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	89 self.chrom = chrom
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	90 self.value = value
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	91 self.midpoint = midpoint
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	92 self.distance = distance
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	93 self.replicate = replicate
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	94
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	95 def normalized_value(self, med):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	96 return self.value * med / self.replicate.median
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	97
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	98
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	99 class PeakGroup(object):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	100
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	101 def __init__(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	102 self.peaks = {}
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	103
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	104 def add_peak(self, repid, peak):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	105 self.peaks[repid] = peak
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	106
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	107 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	108 def chrom(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	109 return self.peaks.values()[0].chrom
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	110
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	111 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	112 def midpoint(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	113 return median([peak.midpoint for peak in self.peaks.values()])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	114
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	115 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	116 def num_replicates(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	117 return len(self.peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	118
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	119 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	120 def median_distance(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	121 return median([peak.distance for peak in self.peaks.values()])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	122
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	123 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	124 def value_sum(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	125 return sum([peak.value for peak in self.peaks.values()])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	126
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	127 def normalized_value(self, med):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	128 values = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	129 for peak in self.peaks.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	130 values.append(peak.normalized_value(med))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	131 return median(values)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	132
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	133 @property
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	134 def peakpeak_distance(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	135 keys = self.peaks.keys()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	136 return abs(self.peaks[keys[0]].midpoint - self.peaks[keys[1]].midpoint)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	137
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	138
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	139 class FrequencyDistribution(object):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	140
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	141 def __init__(self, d=None):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	142 self.dist = d or {}
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	143
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	144 def add(self, x):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	145 self.dist[x] = self.dist.get(x, 0) + 1
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	146
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	147 def graph_series(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	148 x = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	149 y = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	150 for key, val in self.dist.items():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	151 x.append(key)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	152 y.append(val)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	153 return x, y
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	154
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	155 def mode(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	156 return max(self.dist.items(), key=lambda data: data[1])[0]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	157
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	158 def size(self):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	159 return sum(self.dist.values())
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	160
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	161
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	162 def stop_err(msg):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	163 sys.stderr.write(msg)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	164 sys.exit(1)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	165
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	166
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	167 def median(data):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	168 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	169 Find the integer median of the data set.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	170 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	171 if not data:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	172 return 0
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	173 sdata = sorted(data)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	174 if len(data) % 2 == 0:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	175 return (sdata[len(data)//2] + sdata[len(data)//2-1]) / 2
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	176 else:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	177 return sdata[len(data)//2]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	178
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	179
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	180 def make_keys(peaks):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	181 return [data.midpoint for data in peaks]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	182
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	183
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	184 def get_window(chromosome, target_peaks, distance):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	185 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	186 Returns a window of all peaks from a replicate within a certain distance of
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	187 a peak from another replicate.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	188 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	189 lower = target_peaks[0].midpoint
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	190 upper = target_peaks[0].midpoint
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	191 for peak in target_peaks:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	192 lower = min(lower, peak.midpoint - distance)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	193 upper = max(upper, peak.midpoint + distance)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	194 start_index = bisect.bisect_left(chromosome.keys, lower)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	195 end_index = bisect.bisect_right(chromosome.keys, upper)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	196 return (chromosome.peaks[start_index: end_index], chromosome.name)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	197
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	198
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	199 def match_largest(window, peak, chrum):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	200 if not window:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	201 return None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	202 if peak.chrom != chrum:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	203 return None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	204 return max(window, key=lambda cpeak: cpeak.value)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	205
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	206
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	207 def match_closest(window, peak, chrum):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	208 if not window:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	209 return None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	210 if peak.chrom != chrum:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	211 return None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	212 return min(window, key=lambda match: abs(match.midpoint - peak.midpoint))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	213
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	214
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	215 def frequency_histogram(freqs, dataset_path, labels=[], title=''):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	216 pyplot.clf()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	217 pyplot.figure(figsize=(10, 10))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	218 for i, freq in enumerate(freqs):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	219 xvals, yvals = freq.graph_series()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	220 # Go from high to low
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	221 xvals.reverse()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	222 pyplot.bar([x-0.4 + 0.8/len(freqs)*i for x in xvals], yvals, width=0.8/len(freqs), color=COLORS[i])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	223 pyplot.xticks(range(min(xvals), max(xvals)+1), map(str, reversed(range(min(xvals), max(xvals)+1))))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	224 pyplot.xlabel(X_LABEL)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	225 pyplot.ylabel(Y_LABEL)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	226 pyplot.subplots_adjust(left=ADJUST[0], right=ADJUST[1], top=ADJUST[2], bottom=ADJUST[3])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	227 ax = pyplot.gca()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	228 for l in ax.get_xticklines() + ax.get_yticklines():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	229 l.set_markeredgewidth(TICK_WIDTH)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	230 pyplot.savefig(dataset_path)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	231
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	232
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	233 METHODS = {'closest': match_closest, 'largest': match_largest}
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	234
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	235
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	236 def gff_attrs(d):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	237 if not d:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	238 return '.'
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	239 return ';'.join('%s=%s' % item for item in d.items())
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	240
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	241
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	242 def parse_gff_attrs(s):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	243 d = {}
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	244 if s == '.':
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	245 return d
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	246 for item in s.split(';'):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	247 key, val = item.split('=')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	248 d[key] = val
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	249 return d
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	250
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	251
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	252 def gff_row(cname, start, end, score, source, type='.', strand='.', phase='.', attrs={}):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	253 return (cname, source, type, start, end, score, strand, phase, gff_attrs(attrs))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	254
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	255
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	256 def get_temporary_plot_path():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	257 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	258 Return the path to a temporary file with a valid image format
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	259 file extension that can be used with bioformats.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	260 """
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	261 tmp_dir = tempfile.mkdtemp(prefix='tmp-repmatch-')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	262 fd, name = tempfile.mkstemp(suffix='.pdf', dir=tmp_dir)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	263 os.close(fd)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	264 return name
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	265
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	266
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	267 def process_files(dataset_paths, galaxy_hids, method, distance, step, replicates, up_limit, low_limit, output_files,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	268 output_matched_peaks, output_unmatched_peaks, output_detail, output_statistics_table, output_statistics_histogram):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	269 output_statistics_histogram_file = output_files in ["all"] and method in ["all"]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	270 if len(dataset_paths) < 2:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	271 return
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	272 if method == 'all':
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	273 match_methods = METHODS.keys()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	274 else:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	275 match_methods = [method]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	276 for match_method in match_methods:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	277 statistics = perform_process(dataset_paths,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	278 galaxy_hids,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	279 match_method,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	280 distance,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	281 step,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	282 replicates,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	283 up_limit,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	284 low_limit,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	285 output_files,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	286 output_matched_peaks,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	287 output_unmatched_peaks,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	288 output_detail,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	289 output_statistics_table,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	290 output_statistics_histogram)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	291 if output_statistics_histogram_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	292 tmp_statistics_histogram_path = get_temporary_plot_path()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	293 frequency_histogram([stat['distribution'] for stat in [statistics]],
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	294 tmp_statistics_histogram_path,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	295 METHODS.keys())
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	296 shutil.move(tmp_statistics_histogram_path, output_statistics_histogram)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	297
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	298
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	299 def perform_process(dataset_paths, galaxy_hids, method, distance, step, num_required, up_limit, low_limit, output_files,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	300 output_matched_peaks, output_unmatched_peaks, output_detail, output_statistics_table, output_statistics_histogram):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	301 output_detail_file = output_files in ["all"] and output_detail is not None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	302 output_statistics_table_file = output_files in ["all"] and output_statistics_table is not None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	303 output_unmatched_peaks_file = output_files in ["all", "matched_peaks_unmatched_peaks"] and output_unmatched_peaks is not None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	304 output_statistics_histogram_file = output_files in ["all"] and output_statistics_histogram is not None
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	305 replicates = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	306 for i, dataset_path in enumerate(dataset_paths):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	307 try:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	308 galaxy_hid = galaxy_hids[i]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	309 r = Replicate(galaxy_hid, dataset_path)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	310 replicates.append(r)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	311 except Exception, e:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	312 stop_err('Unable to parse file "%s", exception: %s' % (dataset_path, str(e)))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	313 attrs = 'd%sr%s' % (distance, num_required)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	314 if up_limit != 1000:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	315 attrs += 'u%d' % up_limit
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	316 if low_limit != -1000:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	317 attrs += 'l%d' % low_limit
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	318 if step != 0:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	319 attrs += 's%d' % step
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	320
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	321 def td_writer(file_path):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	322 # Returns a tab-delimited writer for a certain output
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	323 return csv.writer(open(file_path, 'wt'), delimiter='\t')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	324
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	325 labels = ('chrom',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	326 'median midpoint',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	327 'median midpoint+1',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	328 'median normalized reads',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	329 'replicates',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	330 'median c-w distance',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	331 'reads sum')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	332 for replicate in replicates:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	333 labels += ('chrom',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	334 'median midpoint',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	335 'median midpoint+1',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	336 'c-w sum',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	337 'c-w distance',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	338 'replicate id')
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	339 matched_peaks_output = td_writer(output_matched_peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	340 if output_statistics_table_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	341 statistics_table_output = td_writer(output_statistics_table)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	342 statistics_table_output.writerow(('data', 'median read count'))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	343 if output_detail_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	344 detail_output = td_writer(output_detail)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	345 detail_output.writerow(labels)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	346 if output_unmatched_peaks_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	347 unmatched_peaks_output = td_writer(output_unmatched_peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	348 unmatched_peaks_output.writerow(('chrom', 'midpoint', 'midpoint+1', 'c-w sum', 'c-w distance', 'replicate id'))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	349 # Perform filtering
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	350 if up_limit < 1000 or low_limit > -1000:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	351 for replicate in replicates:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	352 replicate.filter(up_limit, low_limit)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	353 # Actually merge the peaks
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	354 peak_groups = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	355 unmatched_peaks = []
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	356 freq = FrequencyDistribution()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	357
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	358 def do_match(reps, distance):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	359 # Copy list because we will mutate it, but keep replicate references.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	360 reps = reps[:]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	361 while len(reps) > 1:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	362 # Iterate over each replicate as "main"
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	363 main = reps[0]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	364 reps.remove(main)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	365 for chromosome in main.chromosomes.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	366 peaks_by_value = chromosome.peaks[:]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	367 # Sort main replicate by value
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	368 peaks_by_value.sort(key=lambda peak: -peak.value)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	369
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	370 def search_for_matches(group):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	371 # Here we use multiple passes, expanding the window to be
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	372 # +- distance from any previously matched peak.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	373 while True:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	374 new_match = False
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	375 for replicate in reps:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	376 if replicate.id in group.peaks:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	377 # Stop if match already found for this replicate
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	378 continue
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	379 try:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	380 # Lines changed to remove a major bug by Rohit Reja.
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	381 window, chrum = get_window(replicate.chromosomes[chromosome.name],
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	382 group.peaks.values(),
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	383 distance)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	384 match = METHODS[method](window, peak, chrum)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	385 except KeyError:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	386 continue
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	387 if match:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	388 group.add_peak(replicate.id, match)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	389 new_match = True
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	390 if not new_match:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	391 break
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	392 # Attempt to enlarge existing peak groups
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	393 for group in peak_groups:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	394 old_peaks = group.peaks.values()[:]
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	395 search_for_matches(group)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	396 for peak in group.peaks.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	397 if peak not in old_peaks:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	398 peak.replicate.chromosomes[chromosome.name].remove_peak(peak)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	399 # Attempt to find new peaks groups. For each peak in the
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	400 # main replicate, search for matches in the other replicates
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	401 for peak in peaks_by_value:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	402 matches = PeakGroup()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	403 matches.add_peak(main.id, peak)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	404 search_for_matches(matches)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	405 # Were enough replicates matched?
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	406 if matches.num_replicates >= num_required:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	407 for peak in matches.peaks.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	408 peak.replicate.chromosomes[chromosome.name].remove_peak(peak)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	409 peak_groups.append(matches)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	410 # Zero or less = no stepping
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	411 if step <= 0:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	412 do_match(replicates, distance)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	413 else:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	414 for d in range(0, distance, step):
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	415 do_match(replicates, d)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	416 for group in peak_groups:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	417 freq.add(group.num_replicates)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	418 # Collect together the remaining unmatched_peaks
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	419 for replicate in replicates:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	420 for chromosome in replicate.chromosomes.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	421 for peak in chromosome.peaks:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	422 freq.add(1)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	423 unmatched_peaks.append(peak)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	424 # Average the unmatched_peaks count in the graph by # replicates
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	425 med = median([peak.value for group in peak_groups for peak in group.peaks.values()])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	426 for replicate in replicates:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	427 replicate.median = median([peak.value for group in peak_groups for peak in group.peaks.values() if peak.replicate == replicate])
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	428 statistics_table_output.writerow((replicate.id, replicate.median))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	429 for group in peak_groups:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	430 # Output matched_peaks (matched pairs).
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	431 matched_peaks_output.writerow(gff_row(cname=group.chrom,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	432 start=group.midpoint,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	433 end=group.midpoint+1,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	434 source='repmatch',
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	435 score=group.normalized_value(med),
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	436 attrs={'median_distance': group.median_distance,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	437 'replicates': group.num_replicates,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	438 'value_sum': group.value_sum}))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	439 if output_detail_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	440 matched_peaks = (group.chrom,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	441 group.midpoint,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	442 group.midpoint+1,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	443 group.normalized_value(med),
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	444 group.num_replicates,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	445 group.median_distance,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	446 group.value_sum)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	447 for peak in group.peaks.values():
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	448 matched_peaks += (peak.chrom, peak.midpoint, peak.midpoint+1, peak.value, peak.distance, peak.replicate.id)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	449 detail_output.writerow(matched_peaks)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	450 if output_unmatched_peaks_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	451 for unmatched_peak in unmatched_peaks:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	452 unmatched_peaks_output.writerow((unmatched_peak.chrom,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	453 unmatched_peak.midpoint,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	454 unmatched_peak.midpoint+1,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	455 unmatched_peak.value,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	456 unmatched_peak.distance,
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	457 unmatched_peak.replicate.id))
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	458 if output_statistics_histogram_file:
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	459 tmp_statistics_histogram_path = get_temporary_plot_path()
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	460 frequency_histogram([freq], tmp_statistics_histogram_path)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	461 shutil.move(tmp_statistics_histogram_path, output_statistics_histogram)
b26d50dd3226 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 commit 0e04a4c237677c1f5be1950babcf8591097996a9 bgruening parents: diff changeset	462 return {'distribution': freq}

Mercurial > repos > bgruening > repmatch_gff3

annotate repmatch_gff3_util.py @ 0:b26d50dd3226 draft default tip