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Louis BECQUEY
/
RNANet
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Authored by
Khodor HANNOUSH
2021-04-05 16:41:44 +0200
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Commit
0281da313156cd7221aec5cb5f3e6aa4317c2613
0281da31
1 parent
8b6b41c8
Removed all dependencies with pydca for the moment
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1 changed file
with
4 additions
and
4 deletions
RNAnet.py
RNAnet.py
View file @
0281da3
...
...
@@ -2681,13 +2681,13 @@ def work_pssm_remap(f):
data
=
[(
f
,
j
,
cm_coords
[
j
-
1
])
+
tuple
(
pssm_info
[:,
j
-
1
])
+
(
consensus
[
j
-
1
],
cm_2d
[
j
-
1
])
for
j
in
sorted
(
columns_to_save
)]
sql_execute
(
conn
,
"""INSERT INTO align_column (rfam_acc, index_ali, cm_coord, freq_A, freq_C, freq_G, freq_U, freq_other, gap_percent, consensus, cons_sec_struct)
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?
, ?, ?, ?, ?
) ON CONFLICT(rfam_acc, index_ali) DO
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) ON CONFLICT(rfam_acc, index_ali) DO
UPDATE SET cm_coord=excluded.cm_coord, freq_A=excluded.freq_A, freq_C=excluded.freq_C, freq_G=excluded.freq_G, freq_U=excluded.freq_U,
freq_other=excluded.freq_other,
gap_percent=excluded.gap_percent, consensus=excluded.consensus, cons_sec_struct=excluded.cons_sec_struct;"""
,
many
=
True
,
data
=
data
)
# Add an unknown values column, with index_ali 0 (for nucleotides unsolved in 3D giving a gap '-' but found facing letter in the alignment)
sql_execute
(
conn
,
f
"""INSERT OR IGNORE INTO align_column (rfam_acc, index_ali, cm_coord, freq_A, freq_C, freq_G, freq_U, freq_other,
fields_A, fields_C, fields_G, fields_U,
gap_percent, consensus, cons_sec_struct)
gap_percent, consensus, cons_sec_struct)
VALUES (?, 0, NULL, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, '-', NULL);"""
,
data
=
(
f
,))
...
...
@@ -2734,8 +2734,8 @@ def work_save(c, homology=True):
if
homology
:
df
=
pd
.
read_sql_query
(
f
"""
SELECT index_chain, old_nt_resnum, nt_position, nt_name, nt_code, nt_align_code, cm_coord,
is_A, is_C, is_G, is_U, is_other, freq_A, freq_C, freq_G, freq_U, freq_other,
fields_A, fields_C, fields_G,
fields_U,
gap_percent, consensus, cons_sec_struct, dbn, paired, nb_interact, pair_type_LW, pair_type_DSSR,
is_A, is_C, is_G, is_U, is_other, freq_A, freq_C, freq_G, freq_U, freq_other,
gap_percent, consensus, cons_sec_struct, dbn, paired, nb_interact, pair_type_LW, pair_type_DSSR,
alpha, beta, gamma, delta, epsilon, zeta, epsilon_zeta, chi, bb_type, glyco_bond, form, ssZp, Dp,
eta, theta, eta_prime, theta_prime, eta_base, theta_base,
v0, v1, v2, v3, v4, amplitude, phase_angle, puckering FROM
...
...
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