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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
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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
##gff-version
3
##gff-version 3
# Sequence Data: seqnum=1;seqlen=3480;seqhdr="H561_S27 L001_R1_001_(paired)_contig_1"
# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
H561_S27 Prodigal_v2.6.3 CDS 3 140 31.2 - 0 ID=1_1;partial=10;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.580;conf=99.92;score=31.21;cscore=19.39;sscore=11.82;rscore=11.19;uscore=-3.31;tscore=3.95;
...
...
test/data/annotate/exp_files/res_formatAll/prodigal/Replicons/test_runprokka_H299.fna
View file @
ea85c66d
>test_runprokka_H299.0001
3480
>test_runprokka_H299.0001
3480
AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT
...
...
test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test.0417.00002.gff
View file @
ea85c66d
##gff-version
3
##gff-version 3
##sequence-region test.0417.00002.0001 1 9603
##sequence-region test.0417.00002.0002 1 22446
##sequence-region test.0417.00002.0003 1 51012
...
...
test/data/annotate/exp_files/res_formatAll/prodigal/gff3/test_runprokka_H299.gff
View file @
ea85c66d
##gff-version
3
##gff-version 3
##sequence-region test_runprokka_H299.0001 1 3480
##sequence-region test_runprokka_H299.0002 1 7080
##sequence-region test_runprokka_H299.0003 1 2583
...
...
test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test.0417.00002.fna
View file @
ea85c66d
>test.0417.00002.0001
9603
>test.0417.00002.0001
9603
TCTCATACTACCCAATTTCTTAAAAGTGCAAATTTGTGAAGCTTATCCTGTTATTATTTT
AAGTTTCATGCCAAATTCTCTCACCAGATAATGCCGCCCTCTTCCGAAAAATAATCAAGA
GGCCAAACAATATCTAAAATGATACAACTGTATCTATTCCCCTGAAAAATACATTATTCA
...
...
test/data/annotate/exp_files/res_formatAll/prokka/Replicons/test_runprokka_H299.fna
View file @
ea85c66d
>test_runprokka_H299.0001
3480
>test_runprokka_H299.0001
3480
AGCAGCACGCTTTTTAATCCGTCCACCGGACCTTCAACCGGCCCTTCGCTGATGGCATCG
ATCACACTCAGCAGCTGCGTGGACTTCAGGTTGTCCTTCGCTTCGCGCGGGGTATGCCCC
TTACTGCTGCCTTTACCCATTCGTCATGCTCCATAAACGATAAAACCGCCCGGAGGCGGT
...
...
test/data/annotate/exp_files/res_formatAll/prokka/gff3/test.0417.00002.gff
View file @
ea85c66d
##gff-version
3
##gff-version 3
##sequence-region test.0417.00002.0001 1 9603
##sequence-region test.0417.00002.0002 1 22446
##sequence-region test.0417.00002.0003 1 51012
...
...
test/data/annotate/exp_files/res_formatAll/prokka/gff3/test_runprokka_H299.gff
View file @
ea85c66d
##gff-version
3
##gff-version 3
##sequence-region test_runprokka_H299.0001 1 3480
##sequence-region test_runprokka_H299.0002 1 7080
##sequence-region test_runprokka_H299.0003 1 2583
...
...
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