def fixpartials(args):
    p = OptionParser(fixpartials.__doc__)
    p.set_outfile()
    opts, args = p.parse_args(args)

    if len(args) != 3:
        sys.exit(not p.print_help())

    gffile, gfasta, partials, = args

    gff = make_index(gffile)
    genome = Fasta(gfasta, index=True)
    partials = LineFile(partials, load=True).lines

    # all_transcripts = [f.id for f in gff.features_of_type("mRNA", \
    #     order_by=("seqid", "start"))]
    seen = set()
    fw = must_open(opts.outfile, "w")
    for gene in gff.features_of_type('gene',  order_by=('seqid', 'start')):
        children = AutoVivification()
        cflag = False
        transcripts = list(gff.children(gene, level=1, order_by=('start')))
        for transcript in transcripts:
            trid, seqid, strand = transcript.id, transcript.seqid, transcript.strand

            for child in gff.children(transcript, order_by=('start')):
                ftype = child.featuretype
                if ftype not in children[trid]: children[trid][ftype] = []
                children[trid][ftype].append(child)

            five_prime, three_prime = True, True
            nstart, nstop = (None, None), (None, None)
            cds_span = [children[trid]['CDS'][0].start, \
                children[trid]['CDS'][-1].stop]
            new_cds_span = [x for x in cds_span]

            start_codon = (cds_span[0], cds_span[0] + 2)
            stop_codon = (cds_span[1] - 2, cds_span[1])
            if strand == '-': start_codon, stop_codon = stop_codon, start_codon

            if trid in partials:
                seen.add(trid)
                start_codon_fasta = _fasta_slice(genome, seqid, \
                    start_codon[0], start_codon[1], strand)
                stop_codon_fasta = _fasta_slice(genome, seqid, \
                    stop_codon[0], stop_codon[1], strand)

                if not is_valid_codon(start_codon_fasta, type='start'):
                    five_prime = False
                    nstart = scan_for_valid_codon(start_codon, strand, \
                        seqid, genome, type='start')

                if not is_valid_codon(stop_codon_fasta, type='stop'):
                    three_prime = False
                    nstop = scan_for_valid_codon(stop_codon, strand, \
                        seqid, genome, type='stop')

                logging.debug("feature={0} ({1})".format(trid, strand) + \
                ", 5'={0}, 3'={1}".format(five_prime, three_prime) + \
                ", {0} <== {1} ==> {2}".format(nstart if strand == '+' else nstop, \
                    cds_span, nstop if strand == '+' else nstart))

            if not five_prime or not three_prime:
                if nstart != (None, None) and (start_codon != nstart):
                    i = 0 if strand == '+' else 1
                    new_cds_span[i] = nstart[i]
                if nstop != (None, None) and (stop_codon != nstop):
                    i = 1 if strand == '+' else 0
                    new_cds_span[i] = nstop[i]
                new_cds_span.sort()

            if set(cds_span) != set(new_cds_span):
                cflag = True
                # if CDS has been extended, appropriately adjust all relevent
                # child feature (CDS, exon, UTR) coordinates
                for ftype in children[trid]:
                    for idx in range(len(children[trid][ftype])):
                        child_span = (children[trid][ftype][idx].start, \
                            children[trid][ftype][idx].stop)
                        if ftype in ('exon', 'CDS'):
                            # if exons/CDSs, adjust start and stop according to
                            # new CDS start and stop, respectively
                            if child_span[0] == cds_span[0]:
                                children[trid][ftype][idx].start = new_cds_span[0]
                            if child_span[1] == cds_span[1]:
                                children[trid][ftype][idx].stop = new_cds_span[1]
                        elif ftype.endswith('UTR'):
                            # if *_prime_UTR, adjust stop according to new CDS start and
                            #                 adjust start according to new CDS stop
                            if child_span[1] == cds_span[0]:
                                children[trid][ftype][idx].stop = new_cds_span[0]
                            if child_span[0] == cds_span[1]:
                                children[trid][ftype][idx].start = new_cds_span[1]

                transcript.start, transcript.stop = \
                    children[trid]['exon'][0].start, children[trid]['exon'][-1].stop

        if cflag:
            _gene_span = range_minmax([(tr.start, tr.stop) for tr in transcripts])
            gene.start, gene.stop = _gene_span[0], _gene_span[1]

        # print gff file
        print >> fw, gene
        for transcript in transcripts:
            trid = transcript.id
            print >> fw, transcript
            for cftype in children[trid]:
                for child in children[trid][cftype]:
                    print >> fw, child

    fw.close()
The working directory is the same before and after a call to
dataset/ETHPy150Open tanghaibao/jcvi/formats/gff.py/fixpartials--crossover with--dataset/ETHPy150Open kuri65536/python-for-android/python-modules/twisted/twisted/python/test/test_release.py/BookBuilderTests.test_noSideEffects