def trim(reads, left_trim=0, right_trim=0, min_length=10, append_label=False):
"""Trim reads from left and/pr right side.
min_length is set to 10 by default and is the minimum
length of the resulting read. If read length < min_length,
the read is not trimmed and returned as is
"""
return gt.trim(reads.__iter__(), left_trim, right_trim, min_length, append_label)
def test_chain_filter_indirect():
infile = gt.InputFile(testfiles["bedconvert.map"])
filtered = gt.trim(gt.unique(infile, 2), left=10, right=10)
count = 0
for t in filtered:
count += 1
assert len(t.read) == 81
assert count == 1
def test_chain_filter_indirect():
infile = gt.InputFile(testfiles["bedconvert.map"])
filtered = gt.trim(gt.unique(infile, 2), left=10, right=10)
count = 0
for t in filtered:
count += 1
assert len(t.read) == 81
assert count == 1
def trim(reads, left_trim=0, right_trim=0, min_length=10, append_label=False):
"""Trim reads from left and/pr right side.
min_length is set to 10 by default and is the minimum
length of the resulting read. If read length < min_length,
the read is not trimmed and returned as is
"""
return gt.trim(reads.__iter__(), left_trim, right_trim, min_length,
append_label)
