pb_assembly/FALCON/falcon_kit/mains/reduce_preads.py

"""
Creates a reduced version of preads4falcon.fasta file by writing only the preads
which are incident with 'G' edges in the final assembly graph.
"""



import argparse
import logging
import sys
from ..FastaReader import open_fasta_reader
from ..io import open_progress

default_sg_edges_list_fns = ['./sg_edges_list']

def run(fp_out, preads_fasta_fn, sg_edges_list_fns):
    # Workaround the Argparse issue. It does not override
    # the default argument value when the parameter is
    # used in the append mode, but instead adds to the default
    # list. https://bugs.python.org/issue16399
    # Instead, we will not specify the default value, and
    # check if the list is emptu here here, so that the user
    # can specify exactly the paths to the file(s).
    if not sg_edges_list_fns:
        sg_edges_list_fns = default_sg_edges_list_fns

    reads_in_layout = set()

    for fn in sg_edges_list_fns:
        with open_progress(fn) as fp_in:
            for l in fp_in:
                l = l.strip().split()
                """001039799:E 000333411:E 000333411 17524 20167 17524 99.62 G"""
                v, w, rid, s, t, aln_score, idt, type_ = l
                if type_ != "G":
                    continue
                r1 = v.split(":")[0]
                reads_in_layout.add(r1)
                r2 = w.split(":")[0]
                reads_in_layout.add(r2)

    with open_fasta_reader(preads_fasta_fn) as f:
        for r in f:
            if r.name not in reads_in_layout:
                continue
            fp_out.write('>{}\n{}\n'.format(r.name, r.sequence.upper()))

def main(argv=sys.argv):
    description = 'Create a reduced set of preads, with only those used in the final layout. Write to stdout.'
    parser = argparse.ArgumentParser(
            description=description,
            formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('--preads-fasta-fn', type=str,
            default='preads4falcon.fasta',
            help='Preads file, required to construct the contigs.')
    parser.add_argument('--sg-edges-list-fns', action='append',
            help='One or more files containing string graph edges, produced by ovlp_to_graph.py.')
    args = parser.parse_args(argv[1:])
    run(sys.stdout, **vars(args))

if __name__ == "__main__":
    logging.basicConfig(level=logging.INFO)
    main(sys.argv)