Ruffus code

import os, sys

exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
sys.path.insert(0, os.path.abspath(os.path.join(exe_path,"..", "..","..")))

from ruffus import *


original_fasta = "original.fa"
database_file  = "human.protein.faa"

@split(original_fasta, "*.segment")
def splitFasta (seqFile, segments):
    """Split sequence file into
       as many fragments as appropriate
       depending on the size of original_fasta"""
    current_file_index = 0
    for line in open(original_fasta):
        #
        # start a new file for each accession line
        #
        if line[0] == '>':
            current_file_index += 1
            current_file = open("%d.segment" % current_file_index, "w")
        current_file.write(line)



@transform(splitFasta, suffix(".segment"), ".blastResult")
def runBlast(seqFile,  blastResultFile):
    """Run blast"""
    os.system("blastall -p blastp -d %s -i %s > %s" %
                (database_file, seqFile, blastResultFile))


@merge(runBlast, "final.blast_results")
def combineBlastResults (blastResultFiles, combinedBlastResultFile):
    """Combine blast results"""
    output_file = open(combinedBlastResultFile,  "w")
    for i in blastResultFiles:
        output_file.write(open(i).read())


pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)


#
#   Simulate interuption of the pipeline by
#        deleting the output of one of the BLAST jobs
#
os.unlink("4.blastResult")

pipeline_printout(sys.stdout, [combineBlastResults], verbose = 4)


#
#   Re-running the pipeline
#
pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)