read_stats.py

#!/usr/bin/env python

# This script apparently looks at each sample replicate and computes the
# number of reads for that replicate, as well as the number of reads for
# all replicates. This is computed from the merged ELAND files, so it will
# include only uniquely mapped reads.

import sys
import os.path

from conf import ConfigSample

class Replicate:
    def __init__(self, name, mapped_reads_file, results_dir, read_files=None):
        self.name = name
        self.mapped_reads_file = mapped_reads_file
        self.results_dir = results_dir
        self.num_reads = -1
        if not read_files:
            self.read_files = []
        else:
            self.read_files = read_files

    def num_of_reads(self):
        if not os.path.exists(self.mapped_reads_file):
            print "Cannot find mapped reads file", self.mapped_reads_file
            return 0
        if self.num_reads < 0:
            self.num_reads = sum(1 for line in open(self.mapped_reads_file))
        return self.num_reads

def calc_stats(replicates, stats_file):
    for r in replicates:
        stats_file.write('num_reads=%s=%i\n' % (r.name, r.num_of_reads()))
        stats_file.write('read_files=%s=%s\n' % (r.name, str(r.read_files)))

def main(stats_file, sample_config_file):
    config = ConfigSample(sample_config_file)
    replicates = []
    for i, reads in enumerate(config.REPLICATES):
        rname = 'Rep'+str(i+1)
        replicates.append(Replicate(name=rname,
                                    mapped_reads_file=os.path.join(config.TEMP_DIR, config.RUN_NAME + '_' + rname, rname+'_merged_eland.txt'),
                                    results_dir=os.path.join(config.RESULTS_DIR, 'Rep'+str(i+1)),
                                    read_files=reads))
    allname = 'RepAll'
    all_replicates = Replicate(name=allname,
                               mapped_reads_file=os.path.join(config.TEMP_DIR, config.RUN_NAME + '_' + allname, allname + '_merged_eland.txt'),
                               results_dir=os.path.join(config.RESULTS_DIR, 'All'))
    replicates.append(all_replicates)

    sf = open(stats_file, 'a')
    calc_stats(replicates, sf)

if __name__ == '__main__':
    if len(sys.argv) != 3:
        print "Usage: read_stats.py <stats_file> <sample_config_file>"
        raise SystemExit(1)
    main(sys.argv[1], sys.argv[2])