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Louis BECQUEY
/
RNANetLegacy
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Authored by
Louis BECQUEY
2020-02-06 10:09:39 +0100
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5f7f3e629ef4b02e5007bc1d38e7c0dc777c44e0
5f7f3e62
1 parent
35318812
forgot some [] in subprocess.run for SINA
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RNAnet.py
RNAnet.py
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5f7f3e6
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@@ -774,10 +774,10 @@ def cm_realign(rfam_acc, chains, label):
# Run alignment
print
(
f
"
\t
> {label} (SINA)..."
,
flush
=
True
)
subprocess
.
run
(
"sina"
,
"-i"
,
path_to_seq_data
+
f
"realigned/{rfam_acc}++.fa"
,
subprocess
.
run
(
[
"sina"
,
"-i"
,
path_to_seq_data
+
f
"realigned/{rfam_acc}++.fa"
,
"-o"
,
path_to_seq_data
+
f
"realigned/{rfam_acc}++.afa"
,
"-r"
,
path_to_seq_data
+
"realigned/LSU.arb"
,
"--meta-fmt=csv"
)
"--meta-fmt=csv"
]
)
def
summarize_position
(
col
):
# this function counts the number of nucleotides at a given position, given a "column" from a MSA.
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