sumcov.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""usage: blobtools sumcov          -i FASTA -c COV... 
                                    [-h|--help] 

    Options:
        -h --help                   show this

        -i, --infile FASTA          FASTA file of assembly. Headers are split at whitespaces.  
        -c, --cov COV               COV file(s) to sum up
"""

from __future__ import division
from docopt import docopt
import lib.BtCore as bt
import lib.BtLog as BtLog
import lib.BtIO as BtIO
import lib.BtPlot as BtPlot
from os.path import dirname, isfile

def readFasta(infile):
    header = ''
    with open(infile) as fh: 
        for l in fh: 
            if l[0] == '>':
                yield l[1:-1].split()[0]
            else:
                pass

def parseFasta(infile):
    fasta_order = []
    fasta_dict = {}
    for name in readFasta(infile):
        fasta_order.append(name)
        fasta_dict[name] = 0.0
    return fasta_dict, fasta_order

if __name__ == '__main__':
    main_dir = dirname(__file__)
    #print data_dir
    args = docopt(__doc__)
    assembly_f = args['--infile']
    cov_fs = args['--cov']
    
    fasta_dict = {}
    fasta_order = []
    if not isfile(assembly_f):
        BtLog.error('0', assembly_f)
    else:
        fasta_dict, fasta_order = parseFasta(assembly_f)
    
    for cov_f in cov_fs:
        if not isfile(cov_f):
            BtLog.error('0', cov_f)
        else:
            lib_cov_dict = BtPlot.parseCovFile(cov_f)
            for name in fasta_order:
                fasta_dict[name] = fasta_dict.get(name, 0.0) + lib_cov_dict[name]
                    
    
    for name in fasta_order:
        print "%s\t%s" % (name, fasta_dict[name])