Commit 9d1551e4 authored by Ivan Vanát's avatar Ivan Vanát
Browse files

-d should be working

parent 59cb1447

nested/cli/nester.py

+4 −3
Original line number Original line Diff line number Diff line
@@ -16,8 +16,9 @@ from nested.output.sketcher import Sketcher 
@click.option('--sketch', '-s', is_flag=True, default=False, help='Sketch output.')

@click.option('--sketch', '-s', is_flag=True, default=False, help='Sketch output.')

@click.option('--format', '-f', default='genome_browser', help='Format for GFF.')

@click.option('--format', '-f', default='genome_browser', help='Format for GFF.')

@click.option('--output_fasta_offset', '-o', default=0, help='Number of bases around the element included in output fasta files.')

@click.option('--output_fasta_offset', '-o', default=0, help='Number of bases around the element included in output fasta files.')

@click.option('--output_folder', '-d', default="", help='Output data folder.')

# TODO DATA_FOLDER

# TODO DATA_FOLDER

def main(input_fasta, sketch, format, output_fasta_offset):

def main(input_fasta, sketch, format, output_fasta_offset, output_folder):

    number_of_errors = 0

    number_of_errors = 0

    start_time = datetime.now()

    start_time = datetime.now()

    sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))

    sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))
@@ -31,8 +32,8 @@ def main(input_fasta, sketch, format, output_fasta_offset): 
        print('Processing {a}...'.format(a=sequence.id[:strlen]), end='\r')

        print('Processing {a}...'.format(a=sequence.id[:strlen]), end='\r')

        #try:

        #try:

        nester = Nester(sequence, i)

        nester = Nester(sequence, i)

        sketcher.create_gff(nester.nested_element, output_fasta_offset=output_fasta_offset, format=format)

        sketcher.create_gff(nester.nested_element, output_fasta_offset=output_fasta_offset, format=format, dirpath=output_folder)

        sketcher.create_solo_ltr_gff(nester.solo_ltrs)  

        sketcher.create_solo_ltr_gff(nester.solo_ltrs, dirpath=output_folder)  

        if sketch:

        if sketch:

            if format != 'default':

            if format != 'default':

                sketcher.create_gff(nester.nested_element, output_fasta_offset=output_fasta_offset)            

                sketcher.create_gff(nester.nested_element, output_fasta_offset=output_fasta_offset)

nested/output/sketcher.py

+11 −9
Original line number Original line Diff line number Diff line
@@ -15,16 +15,18 @@ class Sketcher(object): 
        self._solo_gff_maker = SoloGFFMaker()

        self._solo_gff_maker = SoloGFFMaker()

        self._gff_path = ''

        self._gff_path = ''





    def create_gff(self, nested_element, dirpath=None, output_fasta_offset=0, format='default'):

    def create_gff(self, nested_element, dirpath, output_fasta_offset=0, format='default'):

        if not dirpath:

        #if not dirpath:

            dirpath = DEFAULT_DIRPATH

        #    dirpath = DEFAULT_DIRPATH

        self._gff_maker.create_gff(nested_element, dirpath, output_fasta_offset, format)

        path = os.path.join(dirpath, DEFAULT_DIRPATH)        



        self._gff_maker.create_gff(nested_element, path, output_fasta_offset, format)

    def create_solo_ltr_gff(self, solo_ltrs, dirpath=None):



        if not dirpath:

    def create_solo_ltr_gff(self, solo_ltrs, dirpath):

            dirpath = DEFAULT_DIRPATH

        #if not dirpath:

        self._solo_gff_maker.create_solo_gff(solo_ltrs, dirpath)

         #   dirpath = DEFAULT_DIRPATH

        self._solo_gff_maker.move_ltrs_fasta(solo_ltrs.seqId, dirpath)

        path = os.path.join(dirpath, DEFAULT_DIRPATH)

        self._solo_gff_maker.create_solo_gff(solo_ltrs, path)

        self._solo_gff_maker.move_ltrs_fasta(solo_ltrs.seqId, path)

        

        





    def sketch(self, id, dirpath=None):

    def sketch(self, id, dirpath=None):