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cuff_bar.py
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cuff_bar.py
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#!/usr/bin/env python
from optparse import OptionParser
import numpy as np
import math, os, pdb, random, sys
import ggplot
################################################################################
# cuff_bar.py
#
################################################################################
################################################################################
# main
################################################################################
def main():
usage = 'usage: %prog [options] <fpkm_tracking> <gene1> <gene2> ...>'
parser = OptionParser(usage)
parser.add_option('-l', dest='log', default=False, help='log2 FPKM')
parser.add_option('-n', dest='names', default=None, help='Sample names, comma-separated')
parser.add_option('-p', dest='pseudocount', default=.125, type='float', help='Pseudocount for log FPKM [Default: %default]')
parser.add_option('-o', dest='out_dir', default='cuff_bars', help='Output directory [Default: %default]')
parser.add_option('-s', dest='samples', default=None, help='Samples to plot, comma-separated')
parser.add_option('-y', dest='yaxis_match', default=False, action='store_true', help='Match the y-axis of all plots [Default: %default]')
(options,args) = parser.parse_args()
if len(args) < 2:
parser.error('Must provide fpkm_tracking and genes.')
else:
fpkm_tracking = args[0]
genes = args[1:]
gene_sample_fpkm = read_fpkms(fpkm_tracking, genes, options.log, options.pseudocount)
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
if options.samples:
samples = options.samples.split(',')
else:
samples = sorted(gene_sample_fpkm[genes[0]].keys())
if options.names:
names = options.names.split(',')
else:
names = samples
ymin = 0
if options.log:
ymin = np.log2(options.pseudocount)
if options.yaxis_match:
ymax = max([gene_sample_fpkm[gene_name][sample][2] for sample in samples for gene_name in genes])
else:
ymax = None
for gene_name in genes:
df = {}
df['Sample'] = names
df['FPKM'] = [gene_sample_fpkm[gene_name][sample][0] for sample in samples]
df['conf_lo'] = [gene_sample_fpkm[gene_name][sample][1] for sample in samples]
df['conf_hi'] = [gene_sample_fpkm[gene_name][sample][2] for sample in samples]
out_pdf = '%s/%s.pdf' % (options.out_dir, gene_name)
ggplot.plot('%s/cuff_bar.r'%os.environ['RDIR'], df, [ymin, ymax, out_pdf])
################################################################################
# find_diff
#
# Return a set of only the differentially expressed genes.
################################################################################
def find_diff(diff_file):
diff_genes = set()
diff_in = open(diff_file)
diff_in.readline()
for line in diff_in:
a = line.split('\t')
a[-1] = a[-1].rstrip()
gene_id = a[0]
sig = a[-1]
if sig == 'yes':
diff_genes.add(gene_id)
diff_in.close()
return diff_genes
################################################################################
# read_fpkms
################################################################################
def read_fpkms(fpkm_file, genes, log_fpkm, pseudo):
gene_sample_fpkm = {}
fpkm_in = open(fpkm_file)
# parse headers into sample names
headers = fpkm_in.readline().split()
samples = [h[:-5] for h in headers if h == 'FPKM' or h[-5:] == '_FPKM']
for line in fpkm_in:
a = line.split('\t')
a[-1] = a[-1].rstrip()
gene_name = a[4]
if gene_name in genes:
gene_sample_fpkm[gene_name] = {}
for i in range(len(headers)):
if headers[i] == 'FPKM' or headers[i][-5:] == '_FPKM':
sample = headers[i][:-5]
status = a[i+3]
if status in ['FAIL','HIDATA']:
if log_fpkm:
gene_sample_fpkm[gene_name][sample] = tuple(3*[np.log2(pseudo)])
else:
gene_sample_fpkm[gene_name][sample] = (0, 0, 0)
else:
if log_fpkm:
gene_sample_fpkm[gene_name][sample] = (np.log2(pseudo+float(a[i])), np.log2(pseudo+float(a[i+1])), np.log2(pseudo+float(a[i+2])))
else:
gene_sample_fpkm[gene_name][sample] = (float(a[i]), float(a[i+1]), float(a[i+2]))
fpkm_in.close()
return gene_sample_fpkm
################################################################################
# __main__
################################################################################
if __name__ == '__main__':
main()
#pdb.runcall(main)