Base complementer example in PaPy

basecompl_papy.py

__author__ = 'samuel'

from papy.core import Worker, Plumber, Piper
from papy.core import start_logger
from numap import NuMap

infile_name = "Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa.short"

def base_complement( inbox ):
    def basecompl_nucl(nucl):
        if nucl == 'A':
            return 'T'
        elif nucl == 'T':
            return 'A'
        elif nucl == 'C':
            return 'G'
        elif nucl == 'G':
            return 'C'
        else:
            return ''
    sequence = inbox[0]
    new_sequence = ""
    for nucl in sequence:
        new_sequence += basecompl_nucl(nucl)
    return new_sequence

def print_text( inbox ):
    text = inbox[0]
    print text

base_complementer = Worker(base_complement)
printer = Worker(print_text)

local_computer = NuMap()

base_complementer_node = Piper(base_complementer, parallel=local_computer)
printer_node = Piper(printer, parallel=local_computer, track=True)

network = Plumber()
network.add_pipe((base_complementer_node, printer_node))

end = network.get_outputs()[0]

network.start([(line for line in open(infile_name))])
network.run()
print "Finished!"