comparison SAINT_preprocessing.py @ 14:c22c1209e65f draft

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13:febb6def95cb

        bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
        read_infile = open(infile, "r")
        for input_line in read_infile:
            input_line = input_line.strip()
            temp = input_line.split('\t')
            if "Accession Number" in str(temp):
                if baits[i] in temp:                    
                    number_bait = temp.index(str(baits[i]))
                    number_bait = number_bait - 9
                    bait_cache.append((number_bait, str(bait_line)))
                    # Locates the Bait names in the column names and then sets the Baits in the 
                    # correct order in the cache thus the - 9 because the baits start at the 9th
                    # column.
                else:
                    print "Error: bad bait " + str(baits[i])
                    sys.exit()
            else:
                pass
        i = i + 3

    bait_cache.sort()
    for cache_line in bait_cache:
        bait_file_tmp.write(cache_line[1])

                elif "_YEAST" in prot_id:
                    proteins.append(prot_id)
                elif "_MOUSE" in prot_id:
                    proteins.append(prot_id)
                else:
                    print "Accession must be uniprot ID or gene name"
    return ReturnValue2(data, proteins, header)


def make_inter(Scaffold_input):
    bait = readtab(baitfile)

14:c22c1209e65f

        bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
        read_infile = open(infile, "r")
        for input_line in read_infile:
            input_line = input_line.strip()
            temp = input_line.split('\t')
            bait_cache.append((number_bait, str(bait_line)))
        i = i + 3

    bait_cache.sort()
    for cache_line in bait_cache:
        bait_file_tmp.write(cache_line[1])

                elif "_YEAST" in prot_id:
                    proteins.append(prot_id)
                elif "_MOUSE" in prot_id:
                    proteins.append(prot_id)
                else:
                    print "Accession must be uniprot ID or gene"
    return ReturnValue2(data, proteins, header)


def make_inter(Scaffold_input):
    bait = readtab(baitfile)