INNER CODE UNIT · Python

get_read_limit

Gabaldonlab/redundans · redundans.py:140

def get_read_limit(fasta, readLimit, verbose, log=sys.stderr):
    """Return read limit and libraries."""
    # limit no. of reads to align as fraction of genome size
    limit = 0
    if readLimit:
        faidx = FastaIndex(fasta)
        fastaSize = faidx.genomeSize
        limit = int(readLimit * fastaSize)
        if verbose:
            log.write(" Aligning %s mates per library...\n" % limit)
    return limit


def generate_gfa_file(file, threads="4"):
    """Return a gfa file generated using gfastats"""

    # First process the filename to add the new extension

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