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wzmetagene.py
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#!/usr/bin/env python
"""
Generate intervals for meta-gene plot.
Usage:
python ~/wzlib/pyutils/wzmetagene.py input_bed | les
"""
import argparse
import numpy as np
class Record(object):
def __init__(self, fields, args):
self.fields = fields
self.chrm = fields[0]
self.beg = int(fields[1])
self.end = int(fields[2])
if args.collapse:
self.mid = (self.beg + self.end + 1) / 2
self.beg = self.mid
self.end = self.mid
self.step1 = args.flankstep
self.step2 = args.flankstep
def sample_forward(self, args, index_func):
if self.step2 < 0:
return
step = self.step2
_window_beg = self.end
for i in range(args.flanknumber):
_window_end = _window_beg + step
if args.outer:
window_end = int(_window_end)
window_beg = window_end - 1
elif args.middle:
# trivial to awk, just for convenience
window_mid = int((_window_beg + _window_end)/2.0)
window_beg = window_mid-1
window_end = window_mid
elif args.step_and_swell:
window_beg = _window_beg - step/2.0
window_end = _window_beg + step/2.0
else:
window_beg = int(_window_beg)
window_end = int(_window_end)
index = index_func(i)
if index < 0:
if args.flankbygene:
reg = '(%d)-(%d)' % (-i-1, -i)
elif args.flanktoneighbor:
if args.fold:
reg = '(%d)-(%d)%%' % (
float(-i-1)/args.flanknumber/2*100, float(-i)/args.flanknumber/2*100)
else:
reg = '(%d)-(%d)%%' % (
float(-i-1)/args.flanknumber*100, float(-i)/args.flanknumber*100)
elif args.step_and_swell:
reg = '%d -/+%d' % (self.end - _window_beg, step/2.0)
else:
reg = '(%d)-(%d)' % (self.end - window_end, self.end - window_beg)
else:
if args.flankbygene:
reg = '%d-%d' % (i, i+1)
elif args.flanktoneighbor:
reg = '%d-%d%%' % (float(i)/args.flanknumber*100, float(i+1)/args.flanknumber*100)
elif args.step_and_swell:
reg = '%d -/+%d' % (_window_beg - self.end, step/2.0)
else:
reg = '%d-%d' % (window_beg - self.end, window_end - self.end)
# in collapsed case, you can have index 0
if index >= 0:
area = 1
else:
area = -1
if args.expansion > 0:
window_beg = max(window_beg - args.expansion,0)
window_end = window_end + args.expansion
if window_beg > 0 and window_end > window_beg:
print('%s\t%d\t%d\t%d\t%s\t%d\t%s' %
(self.chrm, window_beg, window_end,
index, reg, area, '\t'.join(self.fields)))
if args.flankstep_increase:
_window_beg = _window_beg + step*1.5
step *= 2
else:
_window_beg = _window_end
def sample_backward(self, args, index_func):
if self.step1 < 0:
return
step = self.step1
_window_end = self.beg
for i in range(args.flanknumber):
_window_beg = _window_end - step
if args.outer:
window_beg = int(_window_beg)
window_end = window_beg + 1
elif args.middle:
# trivial to awk, just for convenience
window_mid = int((_window_beg + _window_end)/2.0)
window_beg = window_mid-1
window_end = window_mid
elif args.step_and_swell:
window_beg = _window_end - step/2.0
window_end = _window_end + step/2.0
else:
window_beg = int(_window_beg)
window_end = int(_window_end)
index = index_func(i)
if index < 0:
if args.flankbygene:
reg = '(%d)-(%d)' % (-i-1, -i)
elif args.flanktoneighbor:
if args.fold:
reg = '(%d)-(%d)%%' % (
float(-i-1)/args.flanknumber/2*100, float(-i)/args.flanknumber/2*100)
else:
reg = '(%d)-(%d)%%' % (
float(-i-1)/args.flanknumber*100, float(-i)/args.flanknumber*100)
elif args.step_and_swell:
reg = '%d -/+%d' % (_window_end - self.beg, step/2.0)
else:
reg = '(%d)-(%d)' % (window_beg - self.beg, window_end - self.beg)
else:
if args.flankbygene:
reg = '%d-%d' % (i, i+1)
elif args.flanktoneighbor:
if args.fold:
reg = '%d-%d%%' % (
float(i)/args.flanknumber/2*100, float(i+1)/args.flanknumber/2*100)
else:
reg = '%d-%d%%' % (
float(i)/args.flanknumber*100, float(i+1)/args.flanknumber*100)
elif args.step_and_swell:
reg = '%d -/+%d' % (self.beg - _window_end, step/2.0)
else:
reg = '%d-%d' % (self.beg - window_end, self.beg - window_beg)
# in collapsed case, you can have index 0
if index >= 0:
area = 1
else:
area = -1
if args.expansion > 0:
window_beg = max(window_beg - args.expansion,0)
window_end = window_end + args.expansion
if window_beg > 0 and window_end > window_beg:
print('%s\t%d\t%d\t%d\t%s\t%d\t%s' %
(self.chrm, window_beg, window_end,
index, reg, area, '\t'.join(self.fields)))
if args.flankstep_increase:
_window_end = _window_end - step*1.5
step *= 2
else:
_window_end = _window_beg
def sample_internal(self, args, index_func):
if args.outer:
sentinels = list(np.linspace(self.beg+1, self.end, args.numinternal))
for i in range(len(sentinels)):
window_end = int(sentinels[i])
window_beg = window_end - 1
if args.expansion > 0:
window_beg = max(window_beg - args.expansion,0)
window_end = window_end + args.expansion
index = index_func(i)
if window_beg > 0 and window_end > window_beg:
print('%s\t%d\t%d\t%d\t%d%%\t0\t%s' %
(self.chrm, window_beg, window_end, index,
float(index)/(args.numinternal-1)*100, '\t'.join(self.fields)))
return
sentinels = list(np.linspace(self.beg, self.end, args.numinternal+1))
for i in range(len(sentinels)-1):
window_beg = int(sentinels[i])
window_end = int(sentinels[i+1])
if args.middle:
window_mid = int((sentinels[i] + sentinels[i+1])/2)
window_beg = window_mid-1
window_end = window_mid
if args.expansion > 0:
window_beg = max(window_beg - args.expansion,0)
window_end = window_end + args.expansion
index = index_func(i)
# 0 for internal
if window_beg > 0 and window_end > window_beg:
print('%s\t%d\t%d\t%d\t%d-%d%%\t0\t%s' %
(self.chrm, window_beg, window_end, index,
float(index)/args.numinternal*100,
float(index+1)/args.numinternal*100, '\t'.join(self.fields)))
def process_record(r, r0, r2):
if args.flankbygene:
r.step1 = float(r.end - r.beg + 1) / (args.numinternal)
r.step2 = r.step1
elif args.flanktoneighbor:
if r0 is None or r.beg < r0.end:
r.step1 = -1
else:
r.step1 = float(r.beg - r0.end + 1) / (args.flanknumber)
if args.fold:
r.step1 /= 2
if r2 is None or r.end > r2.beg:
r.step2 = -1
else:
r.step2 = float(r2.beg - r.end + 1) / (args.flanknumber)
if args.fold:
r.step2 /= 2
if args.strand is None:
strand = '+'
else:
strand = r.fields[args.strand-1]
if args.ignoreend:
args.numinternal = 1
if strand == '+':
r.end = r.beg + 1
else:
r.beg = r.end - 1
if args.fold:
r.sample_backward(args, lambda i: -i-1)
r.sample_internal(args, lambda i: min(i, args.numinternal-1-i))
r.sample_forward(args, lambda i: -i-1)
if strand == '+':
r.sample_backward(args, lambda i: -i-1)
r.sample_internal(args, lambda i: i)
r.sample_forward(args, lambda i: args.numinternal+i)
else:
r.sample_forward(args, lambda i: -i-1)
r.sample_internal(args, lambda i: args.numinternal-1-i)
r.sample_backward(args, lambda i: args.numinternal+i)
return
def main(args):
if args.collapse:
if args.outer: # inference: if only outer point is printed, then keep the collapsed middle
args.numinternal = 1
else:
args.numinternal = 0
r0 = None # the previous record
r = None # the current record
r2 = None # the next record
for line in args.table:
r2 = Record(line.strip('\n').split('\t'), args)
if r is not None: # skip the first line
if r.chrm == r2.chrm:
process_record(r, r0, r2)
else: # chromosome switch
process_record(r, r0, None)
r0 = r
r = r2
# the last record
r2 = None
process_record(r, r0, r2)
return
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Generate meta gene')
parser.add_argument('table', help="Input bed file", type = argparse.FileType('r'), default='-')
# report middle point for each sampled interval
parser.add_argument('--middle', action = 'store_true',
help = 'use middle point of each interval as the sentinel')
parser.add_argument('--outer', action = 'store_true',
help = 'use outer point of each interval as the sentinel')
parser.add_argument('--collapse', action = 'store_true',
help = 'collapse initial interval to middle')
# the collapsecenter is obsolete, instead use --collapse --outer
# parser.add_argument('--collapsecenter', action = 'store_true',
# help = 'collapse initial interval to middle but center one interval "on" the middle point')
parser.add_argument('--step_and_swell', action = 'store_true',
help = 'swell to step size, use inner points')
# controls flanking length
# parser.add_argument('-f', '--flank', default=10000, type=int,
# help = 'length of flanking to plot, default 10kb')
# --flank is also obsolete, it is replaced by --flankstep X --flanknumber Y
parser.add_argument('--flanktoneighbor', action = 'store_true',
help = 'length of flanking is dependent on the nearest record')
parser.add_argument('--flankbygene', action = 'store_true', # previously called varyflank
help = 'allow the size of flanking steps to vary according to the gene length')
parser.add_argument('-f', '--flankstep', type = int, default=100,
help = 'plot each X bases for flanking sequences, by default false (-1), this overrides -f (default 100)')
parser.add_argument('--flankstep_increase', action = 'store_true',
help = 'flanking step size doubles every step')
parser.add_argument('-m', '--flanknumber', type = int, default=30,
help = 'number of points to sample in the flanking region (default 30)')
parser.add_argument('--expansion', type=int, default=0,
help = 'number of bases to expand in the two directions')
# I don't think you need to specify window size, just do it by --middle and awk-expand
# parser.add_argument('-w', '--windowsize', type = int, default=None,
# help='Window Size, default to step size (non-overlapping windows)')
# controls internal sampling
parser.add_argument('-n', '--numinternal', type = int, default=30,
help = 'number of points to sample in the genic/internal region, --middle ignores this (default 30)')
# others
parser.add_argument('--fold', action = 'store_true',
help = 'use the same index for intervals from two sides the target, usually used when strand is irrelevant')
parser.add_argument('-s', '--strand', type=int, default=None,
help = 'the field which contains strand information, if None then ignore strand')
parser.add_argument('--ignoreend', action='store_true',
help = 'ignore the end of the input interval')
parser.set_defaults(func=main)
args = parser.parse_args()
try:
args.func(args)
except IOError:
exit