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Omnicrobe
text-mining-workflow
Merge requests
!59
Resolve "erreur avec le script d'accés au données de genbank"
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Resolve "erreur avec le script d'accés au données de genbank"
75-erreur-avec-le-script-d-acces-au-donnees-de-genbank
into
dev
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0
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2
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0
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2
Merged
Mouhamadou Ba
requested to merge
75-erreur-avec-le-script-d-acces-au-donnees-de-genbank
into
dev
2 years ago
Overview
0
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2
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0
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2
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Closes
#75 (closed)
Edited
2 years ago
by
Mouhamadou Ba
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dev
version 1
eebb8b16
2 years ago
dev (base)
and
latest version
latest version
95d151ba
2 commits,
2 years ago
version 1
eebb8b16
1 commit,
2 years ago
2 files
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softwares/scripts/extractGB.py
+
5
−
2
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@@ -45,7 +45,10 @@ def get_values(record):
if
feature
.
type
==
'
source
'
:
# TaxID
taxID
=
feature
.
qualifiers
[
'
db_xref
'
][
0
].
replace
(
'
taxon:
'
,
''
)
if
'
db_xref
'
in
feature
.
qualifiers
:
taxID
=
feature
.
qualifiers
[
'
db_xref
'
][
0
].
replace
(
'
taxon:
'
,
''
)
else
:
taxID
=
0
# Strain
if
'
strain
'
in
feature
.
qualifiers
:
@@ -127,7 +130,7 @@ if __name__ == '__main__':
# --- Ecriture --- #
#if (source != "" or host != "" or country != "") and taxID in dict_ncbi :
if
(
source
!=
""
or
host
!=
""
)
and
taxID
in
dict_ncbi
:
if
(
source
!=
""
or
host
!=
""
)
and
taxID
!=
0
and
taxID
in
dict_ncbi
:
#outfile.write(accession + "\t" + str(length) + "\t" + species + "\t" + strain + "\t" + taxID + "\t" + journal + "\t" + source + "\t" + host + "\t" + country + " \n")
outfile
.
write
(
accession
+
"
\t
"
+
str
(
length
)
+
"
\t
"
+
species
+
"
\t
"
+
strain
+
"
\t
"
+
taxID
+
"
\t
"
+
journal
+
"
\t
"
+
source
+
"
\t
"
+
host
+
"
\n
"
)
ok
+=
1
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