/usr/lib/python2.7/dist-packages/biotools/complement.py is in python-biotools 1.2.12-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | #!/usr/bin/env python
from biotools.sequence import isprot
_ref = {
'DNA': {
'A': 'T', 'T': 'A', 'a': 't', 't': 'a',
'C': 'G', 'G': 'C', 'c': 'g', 'g': 'c',
'R': 'Y', 'Y': 'R', 'r': 'y', 'y': 'r',
' ': ' ', '-': '-'
},
'RNA': {
'A': 'U', 'U': 'A', 'a': 'u', 'u': 'a',
'C': 'G', 'G': 'C', 'c': 'g', 'g': 'c',
'R': 'Y', 'Y': 'R', 'r': 'y', 'y': 'r',
' ': ' ', '-': '-'
}
}
def complement(s):
'''
Creates the complement of a sequence, which can then be reversed by using
`seq[::-1]`, if it needs to be reversed. This function accepts either
`Sequence`s or strings.
'''
if isprot(s):
return s
has_u = ('U' in s or 'u' in s)
has_t = ('T' in s or 't' in s)
if has_u and not has_t:
repl = _ref['RNA']
elif has_t and not has_u:
repl = _ref['DNA']
else:
repl = _ref['DNA']
value = ''.join(repl.get(c, 'N') for c in s)
try:
return s.__class__("complement(%s)" % s.name, value,
original=s.original, start=s.start,
end=s.end, step=s.step, qual=s.qual)
except (AttributeError, TypeError):
return s.__class__(value)
if __name__ == '__main__':
assert complement('ATCGTAGCTGATCGAT') == 'TAGCATCGACTAGCTA'
assert complement('AUCGUAGCUGAUCGAU') == 'UAGCAUCGACUAGCUA'
print(complement('AUCgu--cuGAUCGAU'))
|