INNER CODE UNIT · Python

prepare_gapcloser

Gabaldonlab/redundans · redundans.py:329

def prepare_gapcloser(
    outdir,
    configFn,
    libFs,
    libRs,
    orientations,
    libIS,
    libISStDev,
    minlen,
    maxlen,
    limit,
    verbose,
    log,
):
    """Return SOAPdenovo2 config file needed by GapCloser."""
    lines = "[LIB]\navg_ins=%s\nreverse_seq=%s\nasm_flags=3\nrank=%s\npair_num_cutoff=5\nmap_len=35\nq1=%s\nq2=%s\n"
    config = ["max_rd_len=%s" % maxlen]
    for i, (fq1, fq2, orient, iSize, iFrac) in enumerate(

View source record →