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from io import StringIO
from numpy import allclose
from bx.motif.io import transfac
sample = """
VV TRANSFAC MATRIX TABLE, Rel.3.2 26-06-1997
XX
//
AC a
XX
ID V$MYOD_01
XX
DT 19.10.92 (created); ewi.
DT 16.10.95 (updated); ewi.
XX
NA MyoD
XX
DE myoblast determination gene product
XX
BF T00526; MyoD; Species: mouse, Mus musculus.
XX
P0 A C G T
01 100 200 200 0 S
02 200 100 200 0 R
03 300 0 100 100 A
04 0 500 0 0 C
05 500 0 0 0 A
06 0 0 400 100 G
07 0 100 400 0 G
08 0 0 0 500 T
09 0 0 500 0 G
10 0 100 200 200 K
11 0 200 0 300 Y
12 100 0 300 100 G
XX
BA 5 functional elements in 3 genes
XX
//
AC M00002
XX
ID V$E47_01
XX
DT 19.10.92 (created); ewi.
DT 16.10.95 (updated); ewi.
XX
NA E47
XX
DE E47
XX
BF T00207; E47; Species: human, Homo sapiens.
XX
P0 A C G T
00 400 400 300 0 N
02 200 500 400 0 S
03 300 200 400 200 N
04 200 0 900 0 G
05 0 1100 0 0 C
06 1100 0 0 0 A
07 0 0 1100 0 G
08 100 200 800 0 G
09 0 0 0 1100 T
10 0 0 1100 0 G
11 0 0 400 700 K
12 100 400 300 300 N
13 100 600 200 200 C
14 100 400 400 200 N
15 100 400 200 300 N
XX
BA 11 selected strong binding sites for E47, E47-MyoD, E12+MyoD
BA and (weak) for E12
XX
CC Group I in [903]; 5 sites selected in vitro for binding to E12N
CC (=N-terminally truncated E12); matrix corrected according to
CC the published sequences
XX
RN [1]
RA Sun X.-H., Baltimore D.
RT An inhibitory domain of E12 transcription factor prevents
RT DNA binding in E12 homodimers but not in E12 heterodimers
RL Cell 64:459-470 (1991).
XX
""" # noqa: W291
def test_reader():
input = StringIO(sample)
motifs = list(transfac.TransfacReader(input))
assert len(motifs) == 2
# Single value parse
assert motifs[1].accession == "M00002"
# Value list parse
assert motifs[1].dates == ["19.10.92 (created); ewi.", "16.10.95 (updated); ewi."]
# Matrix parse
assert motifs[1].matrix.sorted_alphabet == ["A", "C", "G", "T"]
assert allclose(motifs[1].matrix.values[0], [400, 400, 300, 0])
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