def split_fastafile(fastafile, maxreadlen=32000):
pf = fastafile.split(".")[0]
smallfastafile = pf + "-small.fasta"
bigfastafile = pf + "-big.fasta"
shredfastafile = pf + "-big.depth1.fasta"
if need_update(fastafile, (smallfastafile, shredfastafile)):
filter([fastafile, str(maxreadlen), "--less", "-o", smallfastafile])
filter([fastafile, str(maxreadlen), "-o", bigfastafile])
shred(["--depth=1", "--shift={0}".format(maxreadlen / 100), \
"--readlen={0}".format(maxreadlen), \
"--fasta", bigfastafile])
return smallfastafile, shredfastafile
def split_fastafile(fastafile, maxreadlen=32000):
pf = fastafile.split(".")[0]
smallfastafile = pf + "-small.fasta"
bigfastafile = pf + "-big.fasta"
shredfastafile = pf + "-big.depth1.fasta"
if need_update(fastafile, (smallfastafile, shredfastafile)):
filter([fastafile, str(maxreadlen), "--less", "-o", smallfastafile])
filter([fastafile, str(maxreadlen), "-o", bigfastafile])
shred(["--depth=1", "--shift={0}".format(maxreadlen / 100), \
"--readlen={0}".format(maxreadlen), \
"--fasta", bigfastafile])
return smallfastafile, shredfastafile
def split_fastafile(fastafile, maxreadlen=32000):
from jcvi.formats.fasta import filter
pf = fastafile.split(".")[0]
smallfastafile = pf + "-small.fasta"
bigfastafile = pf + "-big.fasta"
shredfastafile = pf + "-big.depth1.fasta"
maxreadlen = str(maxreadlen)
if need_update(fastafile, (smallfastafile, shredfastafile)):
filter([fastafile, maxreadlen, "--less", "-o", smallfastafile])
filter([fastafile, maxreadlen, "-o", bigfastafile])
shred(["--depth=1", "--readlen={0}".format(maxreadlen), \
"--fasta", bigfastafile])
return smallfastafile, shredfastafile
def split_fastafile(fastafile, maxreadlen=32000):
from jcvi.formats.fasta import filter
pf = fastafile.split(".")[0]
smallfastafile = pf + "-small.fasta"
bigfastafile = pf + "-big.fasta"
shredfastafile = pf + "-big.depth1.fasta"
maxreadlen = str(maxreadlen)
if need_update(fastafile, (smallfastafile, shredfastafile)):
filter([fastafile, maxreadlen, "--less", "-o", smallfastafile])
filter([fastafile, maxreadlen, "-o", bigfastafile])
shred(["--depth=1", "--readlen={0}".format(maxreadlen), \
"--fasta", bigfastafile])
return smallfastafile, shredfastafile