def main(argv=None):
'''Command line options.'''
program_name = os.path.basename(sys.argv[0])
program_version = "v0.1"
program_build_date = "%s" % __updated__
program_version_string = '%%prog %s (%s)' % (program_version, program_build_date)
#program_usage = '''usage: spam two eggs''' # optional - will be autogenerated by optparse
program_longdesc = '''''' # optional - give further explanation about what the program does
program_license = "Copyright 2014 Jake Yeung (Laboratory for Advanced Genome Analysis) \
Licensed under the Apache License 2.0\nhttp://www.apache.org/licenses/LICENSE-2.0"
if argv is None:
argv = sys.argv[1:]
# setup option parser
parser = OptionParser(version=program_version_string, epilog=program_longdesc, description=program_license)
parser.add_option("-i", "--in", dest="infile", help="set input path containing list of filepaths [default: %default]", metavar="FILE")
parser.add_option("-o", "--out", dest="outfile", help="set output path for merged read counts table[default: %default]", metavar="FILE")
parser.add_option("-v", "--verbose", dest="verbose", action="count", help="set verbosity level [default: %default]")
parser.add_option("-n", "--nan", dest="nan", type="int", help="Output nan if sample does not have info on an miRNA.", metavar="INT")
# set defaults
parser.set_defaults(outfile="./out.txt", infile="./in.txt", nan=0)
# process options
(opts, args) = parser.parse_args(argv)
if opts.verbose > 0:
print("verbosity level = %d" % opts.verbose)
if opts.infile:
print("infile = %s" % opts.infile)
if opts.outfile:
print("outfile = %s" % opts.outfile)
# MAIN BODY #
# get list of files
filepaths = []
sampids = []
with open(opts.infile, 'rb') as infile:
infile_reader = csv.reader(infile, delimiter='\t')
for row in infile_reader:
# each row is a file path
filepaths.append(row[0])
sampids.append(row[1])
merged_dic = {}
for readsfile, sampid in zip(filepaths, sampids):
readsobj = AnnotatedReads.AnnotatedReads(readsfile, stats_file=None)
reads_dic = AnnotatedReads.index_annotatedreads_file(readsobj, count_id='reads', subdic=False)
for annot_count, annot in enumerate(reads_dic):
if annot not in merged_dic:
# init subdic
merged_dic[annot] = {}
merged_dic[annot].update({sampid: reads_dic[annot]})
if opts.verbose > 0:
print('Sample: %s added to merged_dic (%s mirna IDs)' %(sampid, annot_count))
#write to file
with open(opts.outfile, 'wb') as outfile:
outwriter = csv.writer(outfile, delimiter='\t')
#write header: mirna ID + samples
writeheader = ['id'] + sampids
outwriter.writerow(writeheader)
#write data: mirna ID + reads from samples
writerowcount = 0
for annot in merged_dic:
writerow = [annot] # append from mirnaID
for sampid in sampids:
#if sample has reads for miRNA: append that value
#otherwise, write nan
if sampid in merged_dic[annot]:
writerow.append(merged_dic[annot][sampid])
else:
writerow.append(opts.nan)
outwriter.writerow(writerow)
writerowcount += 1
if opts.verbose > 0:
print '%s rows written to file: %s' %(writerowcount, opts.outfile)
def main(argv=None):
'''Command line options.'''
program_name = os.path.basename(sys.argv[0])
program_version = "v0.1"
program_build_date = "%s" % __updated__
program_version_string = '%%prog %s (%s)' % (program_version, program_build_date)
#program_usage = '''usage: spam two eggs''' # optional - will be autogenerated by optparse
program_longdesc = '''''' # optional - give further explanation about what the program does
program_license = "Copyright 2014 Jake Yeung (Laboratory for Advanced Genome Analysis) \
Licensed under the Apache License 2.0\nhttp://www.apache.org/licenses/LICENSE-2.0"
if argv is None:
argv = sys.argv[1:]
# setup option parser
parser = OptionParser(version=program_version_string, epilog=program_longdesc, description=program_license)
parser.add_option("-t", "--tumour", dest="tumourfile", help="set input path for tumour [default: %default]", metavar="FILE")
parser.add_option("-b", "--benign", dest="benignfile", help="set input path for benign [default: %default]", metavar="FILE")
parser.add_option("-o", "--out", dest="outfile", help="set output path [default: %default]", metavar="FILE")
parser.add_option("-v", "--verbose", dest="verbose", action="count", help="set verbosity level [default: %default]")
parser.add_option("-r", "--reads_id", dest="reads_id", help="Extract raw reads or normalized reads (TPM)", metavar="TPM | reads")
# set defaults
parser.set_defaults(outfile="./out.txt", infile="./in.txt", reads_id="reads")
# process options
(opts, args) = parser.parse_args(argv)
if opts.verbose > 0:
print("verbosity level = %d" % opts.verbose)
if opts.infile:
print("tumourfile = %s" % opts.tumourfile)
if opts.outfile:
print("benignfile = %s" % opts.benignfile)
if opts.outfile:
print("outfile = %s" % opts.outfile)
if opts.reads_id:
print("reads_id = %s" % opts.reads_id)
# MAIN BODY #
tumour_annotatedreads = AnnotatedReads.AnnotatedReads(opts.tumourfile)
benign_annotatedreads = AnnotatedReads.AnnotatedReads(opts.benignfile)
benign_dic = AnnotatedReads.index_annotatedreads_file(benign_annotatedreads, count_id=opts.reads_id)
tumour_dic = AnnotatedReads.index_annotatedreads_file(tumour_annotatedreads, count_id=opts.reads_id)
'''
for annot in benign_dic:
print benign_dic[annot]
raw_input()
'''
#init outfile
outfile = open(opts.outfile, 'wb')
outwriter = csv.writer(outfile, delimiter='\t')
'''
# write header containing:
[mirna(annotations), annotatedreads_benign, annotatedreads_tumour, fold_change,
locations_benign,
locations_benign_annotatedreadss, locations_tumour, locations_tumour_annotatedreadss]
'''
writeheader = ['mirna',
'%s_benign_sum' %opts.reads_id,
'%s_tumour_sum' %opts.reads_id,
'%s_sum_fold_change' %opts.reads_id]
outwriter.writerow(writeheader)
for annot in benign_dic.keys():
try:
tumour_annotatedreads_sum = tumour_dic[annot]['%s' %opts.reads_id]
except KeyError:
continue
#calculate fold change, get locations and annotatedreadss lists
benign_annotatedreads_sum = benign_dic[annot]['%s' %opts.reads_id]
fold_change = float(tumour_annotatedreads_sum) / benign_annotatedreads_sum
# write row, matching to writeheader
writerow = [annot,
benign_annotatedreads_sum,
tumour_annotatedreads_sum,
fold_change]
outwriter.writerow(writerow)
outfile.close()
