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Amandine PERRIN
pipeline_annotation
Commits
ea85c66d
Commit
ea85c66d
authored
Oct 05, 2021
by
Amandine PERRIN
Browse files
change tab to space between rep name and info in Replicons directory
parent
647a117b
Pipeline
#66654
passed with stages
in 5 minutes and 38 seconds
Changes
9
Pipelines
1
Show whitespace changes
Inline
Side-by-side
PanACoTA/utils.py
View file @
ea85c66d
...
...
@@ -1148,7 +1148,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile, logger):
# - add its name with its original name to
# - write header ("<contig name> <size>") to replicon file
if
prev_cont
:
cont
=
"
\t
"
.
join
([
prev_cont
,
str
(
cont_size
)])
+
"
\n
"
cont
=
"
"
.
join
([
prev_cont
,
str
(
cont_size
)])
+
"
\n
"
prevcont_nohead
=
prev_cont
.
split
(
">"
)[
1
]
prev_orig_name_nohead
=
prev_orig_name
.
split
(
">"
)[
1
]
if
prev_orig_name_nohead
:
...
...
@@ -1172,7 +1172,7 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile, logger):
cont_size
+=
len
(
line
.
strip
())
# Write last contig, if there is one (if gpath not empty)
if
prev_cont
:
cont
=
"
\t
"
.
join
([
prev_cont
,
str
(
cont_size
)])
+
"
\n
"
cont
=
"
"
.
join
([
prev_cont
,
str
(
cont_size
)])
+
"
\n
"
prevcont_nohead
=
""
.
join
(
prev_cont
.
split
(
">"
)[
1
:])
prev_orig_name_nohead
=
prev_orig_name
.
split
(
">"
)[
1
]
if
prev_orig_name_nohead
:
...
...
test/data/annotate/exp_files/H299_H561.fasta_small-prodigalRes/test_runprodigal_small_H299.gff
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff
View file @
ea85c66d
test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff
View file @
ea85c66d
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