Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bakta update to 1.5.0 #4787

Merged
merged 19 commits into from
Sep 16, 2022
Merged

Bakta update to 1.5.0 #4787

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
fe1cdf8
add a new tool BAKTA for genome annotation
pimarin Aug 17, 2022
76e2e36
update bad indentation in shed.yml
pimarin Aug 17, 2022
57d22d2
change file for size test
pimarin Aug 17, 2022
41ae8a9
remove a F letter added by mistake
pimarin Aug 17, 2022
94b9778
Add a checkbox for skip options
pimarin Aug 22, 2022
f03acf3
change the help text format and change the regex
pimarin Aug 23, 2022
d6bfb37
add validator for organism level
pimarin Aug 23, 2022
b378166
add regex and help
pimarin Aug 23, 2022
ea03a6f
fix in the help part
pimarin Sep 1, 2022
6558937
update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool v…
pimarin Sep 15, 2022
ee013f7
rebase
pimarin Sep 16, 2022
bcdd39d
change file for size test
pimarin Aug 17, 2022
56fa36a
Add a checkbox for skip options
pimarin Aug 22, 2022
bacec9d
add regex and help
pimarin Aug 23, 2022
b763bf8
fix in the help part
pimarin Sep 1, 2022
bfdbe49
update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool v…
pimarin Sep 15, 2022
46b71a4
rebase and update to 1.5.0
pimarin Sep 16, 2022
21518de
Merge branch 'bakta' of github.com:pimarin/tools-iuc into bakta
pimarin Sep 16, 2022
5252262
restore 0 version
pimarin Sep 16, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions tools/bakta/bakta.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -233,10 +233,10 @@
<param name="db_select" value="test-db-bakta"/>
<param name="input_file" value="NC_002127.1.fna"/>
</section>
<output name="logfile" value="TEST_1/TEST_1.log" lines_diff="4">
<output name="logfile" value="TEST_1/TEST_1.log" lines_diff="10">
<assert_contents>
<has_text_matching n="1" expression="Genome size: 1,330 bp"/>
<has_n_lines n="90" delta="1"/>
<has_n_lines n="94" delta="1"/>
</assert_contents>
</output>
<output name="annotation_tsv" value="TEST_1/TEST_1.tsv" lines_diff="1"/>
Expand Down
2 changes: 1 addition & 1 deletion tools/bakta/macro.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">1.4.2</token>
<token name="@TOOL_VERSION@">1.5.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.05</token>
<xml name="version_command">
Expand Down
15 changes: 8 additions & 7 deletions tools/bakta/test-data/TEST_1/TEST_1.embl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,16 @@ OS .
OC .
XX
CC Annotated with Bakta
CC Software: v1.4.2
CC Database: v3.0
CC Software: v1.5.0
CC Database: v4.0
CC DOI: 10.1099/mgen.0.000685
CC URL: github.com/oschwengers/bakta
CC
CC ##Genome Annotation Summary:##
CC Annotation Date :: 08/22/2022, 13:06:54
CC Annotation Date :: 09/16/2022, 07:31:59
CC Annotation Pipeline :: Bakta
CC Annotation Software version :: v1.4.2
CC Annotation Database version :: v3.0
CC Annotation Software version :: v1.5.0
CC Annotation Database version :: v4.0
CC CDSs :: 2
CC tRNAs :: 0
CC tmRNAs :: 0
Expand All @@ -28,6 +28,7 @@ CC CRISPR Arrays :: 0
CC oriCs/oriVs :: 0
CC oriTs :: 0
CC gaps :: 0
CC pseudogenes :: 0
XX
FH Key Location/Qualifiers
FH
Expand All @@ -39,25 +40,25 @@ FT /locus_tag="IHHALP_00005"
FT CDS 413..736
FT /product="hypothetical protein"
FT /locus_tag="IHHALP_00005"
FT /protein_id="gnl|Bakta|IHHALP_00005"
FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
FT MAD"
FT /codon_start=1
FT /transl_table=11
FT /protein_id="gnl|Bakta|IHHALP_00005"
FT /inference="ab initio prediction:Prodigal:2.6"
FT gene complement(join(971..1330,1..141))
FT /locus_tag="IHHALP_00010"
FT CDS complement(join(971..1330,1..141))
FT /product="hypothetical protein"
FT /locus_tag="IHHALP_00010"
FT /protein_id="gnl|Bakta|IHHALP_00010"
FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
FT IPI"
FT /codon_start=1
FT /transl_table=11
FT /protein_id="gnl|Bakta|IHHALP_00010"
FT /inference="ab initio prediction:Prodigal:2.6"
XX
SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other;
Expand Down
17 changes: 9 additions & 8 deletions tools/bakta/test-data/TEST_1/TEST_1.gbff
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LOCUS contig_1 1330 bp DNA circular BCT 22-AUG-2022
LOCUS contig_1 1330 bp DNA circular BCT 16-SEP-2022
DEFINITION plasmid unnamed1, complete sequence.
ACCESSION contig_1
VERSION contig_1
Expand All @@ -7,16 +7,16 @@ SOURCE None
ORGANISM .
.
COMMENT Annotated with Bakta
Software: v1.4.2
Database: v3.0
Software: v1.5.0
Database: v4.0
DOI: 10.1099/mgen.0.000685
URL: github.com/oschwengers/bakta

##Genome Annotation Summary:##
Annotation Date :: 08/22/2022, 13:06:54
Annotation Date :: 09/16/2022, 07:31:59
Annotation Pipeline :: Bakta
Annotation Software version :: v1.4.2
Annotation Database version :: v3.0
Annotation Software version :: v1.5.0
Annotation Database version :: v4.0
CDSs :: 2
tRNAs :: 0
tmRNAs :: 0
Expand All @@ -27,6 +27,7 @@ COMMENT Annotated with Bakta
oriCs/oriVs :: 0
oriTs :: 0
gaps :: 0
pseudogenes :: 0
FEATURES Location/Qualifiers
source 1..1330
/mol_type="genomic DNA"
Expand All @@ -36,25 +37,25 @@ FEATURES Location/Qualifiers
CDS 413..736
/product="hypothetical protein"
/locus_tag="IHHALP_00005"
/protein_id="gnl|Bakta|IHHALP_00005"
/translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
MAD"
/codon_start=1
/transl_table=11
/protein_id="gnl|Bakta|IHHALP_00005"
/inference="ab initio prediction:Prodigal:2.6"
gene complement(join(971..1330,1..141))
/locus_tag="IHHALP_00010"
CDS complement(join(971..1330,1..141))
/product="hypothetical protein"
/locus_tag="IHHALP_00010"
/protein_id="gnl|Bakta|IHHALP_00010"
/translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
IPI"
/codon_start=1
/transl_table=11
/protein_id="gnl|Bakta|IHHALP_00010"
/inference="ab initio prediction:Prodigal:2.6"
ORIGIN
1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc
Expand Down
4 changes: 2 additions & 2 deletions tools/bakta/test-data/TEST_1/TEST_1.gff3
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
##gff-version 3
##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
# Annotated with Bakta
# Software: v1.4.2
# Database: v3.0
# Software: v1.5.0
# Database: v4.0
# DOI: 10.1099/mgen.0.000685
# URL: github.com/oschwengers/bakta
##sequence-region contig_1 1 1330
Expand Down
4 changes: 2 additions & 2 deletions tools/bakta/test-data/TEST_1/TEST_1.hypotheticals.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta
#Database v3.0, https://doi.org/10.5281/zenodo.4247252
#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta
#Database v4.0, https://doi.org/10.5281/zenodo.4247252
#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs
contig_1 413 736 + IHHALP_00005 12.1 10.4
contig_1 971 141 - IHHALP_00010 18.9 7.7
8 changes: 4 additions & 4 deletions tools/bakta/test-data/TEST_1/TEST_1.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,11 +80,11 @@
}
],
"run": {
"start": "2022-08-22 13:06:53",
"end": "2022-08-22 13:06:54"
"start": "2022-09-16 07:31:58",
"end": "2022-09-16 07:31:59"
},
"version": {
"bakta": "1.4.2",
"db": "3.0"
"bakta": "1.5.0",
"db": "4.0"
}
}
8 changes: 6 additions & 2 deletions tools/bakta/test-data/TEST_1/TEST_1.log
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,10 @@ predict & annotate CDSs...
amrfinder: 0
protein sequences: 0
combine annotations and mark hypotheticals...
analyze hypothetical proteins: 2
detect pseudogenes...
pseudogene candidates: 0
found pseudogenes: 0
analyze hypothetical proteins: 2
detected Pfam hits: 0
calculated proteins statistics
revise special cases...
Expand Down Expand Up @@ -68,13 +71,14 @@ annotation summary:
CRISPR arrays: 0
CDSs: 2
hypotheticals: 2
pseudogenes: 0
signal peptides: 0
sORFs: 0
gaps: 0
oriCs/oriVs: 0
oriTs: 0

export annotation results to: /tmp/tmpb092rhfs/job_working_directory/000/2/working
export annotation results to: /tmp/tmpmnqj1xog/job_working_directory/000/2/working
human readable TSV...
GFF3...
INSDC GenBank & EMBL...
Expand Down
4 changes: 2 additions & 2 deletions tools/bakta/test-data/TEST_1/TEST_1.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#Annotated with Bakta (v1.4.2): https://github.com/oschwengers/bakta
#Database (v3.0): https://doi.org/10.5281/zenodo.4247252
#Annotated with Bakta (v1.5.0): https://github.com/oschwengers/bakta
#Database (v4.0): https://doi.org/10.5281/zenodo.4247252
#Sequence Id Type Start Stop Strand Locus Tag Gene Product DbXrefs
contig_1 cds 413 736 + IHHALP_00005 hypothetical protein
contig_1 cds 971 141 - IHHALP_00010 hypothetical protein
5 changes: 3 additions & 2 deletions tools/bakta/test-data/TEST_1/TEST_1.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ ncRNAs: 0
ncRNA regions: 0
CRISPR arrays: 0
CDSs: 2
pseudogenes: 0
hypotheticals: 2
signal peptides: 0
sORFs: 0
Expand All @@ -23,7 +24,7 @@ oriVs: 0
oriTs: 0

Bakta:
Software: v1.4.2
Database: v3.0
Software: v1.5.0
Database: v4.0
DOI: 10.1099/mgen.0.000685
URL: github.com/oschwengers/bakta
15 changes: 8 additions & 7 deletions tools/bakta/test-data/TEST_2/TEST_2.embl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,16 @@ OS Escherichia coli o157:h7 Sakai
OC .
XX
CC Annotated with Bakta
CC Software: v1.4.2
CC Database: v3.0
CC Software: v1.5.0
CC Database: v4.0
CC DOI: 10.1099/mgen.0.000685
CC URL: github.com/oschwengers/bakta
CC
CC ##Genome Annotation Summary:##
CC Annotation Date :: 08/22/2022, 13:07:08
CC Annotation Date :: 09/16/2022, 07:32:10
CC Annotation Pipeline :: Bakta
CC Annotation Software version :: v1.4.2
CC Annotation Database version :: v3.0
CC Annotation Software version :: v1.5.0
CC Annotation Database version :: v4.0
CC CDSs :: 2
CC tRNAs :: 0
CC tmRNAs :: 0
Expand All @@ -28,6 +28,7 @@ CC CRISPR Arrays :: 0
CC oriCs/oriVs :: 0
CC oriTs :: 0
CC gaps :: 0
CC pseudogenes :: 0
XX
FH Key Location/Qualifiers
FH
Expand All @@ -41,25 +42,25 @@ FT /locus_tag="IHHALP_00005"
FT CDS 413..736
FT /product="hypothetical protein"
FT /locus_tag="IHHALP_00005"
FT /protein_id="gnl|Bakta|IHHALP_00005"
FT /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
FT AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
FT MAD"
FT /codon_start=1
FT /transl_table=11
FT /protein_id="gnl|Bakta|IHHALP_00005"
FT /inference="ab initio prediction:Prodigal:2.6"
FT gene complement(join(971..1330,1..141))
FT /locus_tag="IHHALP_00010"
FT CDS complement(join(971..1330,1..141))
FT /product="hypothetical protein"
FT /locus_tag="IHHALP_00010"
FT /protein_id="gnl|Bakta|IHHALP_00010"
FT /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
FT EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
FT YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
FT IPI"
FT /codon_start=1
FT /transl_table=11
FT /protein_id="gnl|Bakta|IHHALP_00010"
FT /inference="ab initio prediction:Prodigal:2.6"
XX
SQ Sequence 1330 BP; 330 A; 291 C; 310 G; 399 T; 0 other;
Expand Down
17 changes: 9 additions & 8 deletions tools/bakta/test-data/TEST_2/TEST_2.gbff
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LOCUS NC_002127.1 1330 bp DNA circular BCT 22-AUG-2022
LOCUS NC_002127.1 1330 bp DNA circular BCT 16-SEP-2022
DEFINITION Escherichia coli o157:h7 Sakai plasmid pOSAK1, complete sequence.
ACCESSION NC_002127
VERSION NC_002127.1
Expand All @@ -7,16 +7,16 @@ SOURCE Escherichia coli o157:h7 Sakai
ORGANISM Escherichia coli o157:h7 Sakai
.
COMMENT Annotated with Bakta
Software: v1.4.2
Database: v3.0
Software: v1.5.0
Database: v4.0
DOI: 10.1099/mgen.0.000685
URL: github.com/oschwengers/bakta

##Genome Annotation Summary:##
Annotation Date :: 08/22/2022, 13:07:08
Annotation Date :: 09/16/2022, 07:32:10
Annotation Pipeline :: Bakta
Annotation Software version :: v1.4.2
Annotation Database version :: v3.0
Annotation Software version :: v1.5.0
Annotation Database version :: v4.0
CDSs :: 2
tRNAs :: 0
tmRNAs :: 0
Expand All @@ -27,6 +27,7 @@ COMMENT Annotated with Bakta
oriCs/oriVs :: 0
oriTs :: 0
gaps :: 0
pseudogenes :: 0
FEATURES Location/Qualifiers
source 1..1330
/mol_type="genomic DNA"
Expand All @@ -38,25 +39,25 @@ FEATURES Location/Qualifiers
CDS 413..736
/product="hypothetical protein"
/locus_tag="IHHALP_00005"
/protein_id="gnl|Bakta|IHHALP_00005"
/translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
MAD"
/codon_start=1
/transl_table=11
/protein_id="gnl|Bakta|IHHALP_00005"
/inference="ab initio prediction:Prodigal:2.6"
gene complement(join(971..1330,1..141))
/locus_tag="IHHALP_00010"
CDS complement(join(971..1330,1..141))
/product="hypothetical protein"
/locus_tag="IHHALP_00010"
/protein_id="gnl|Bakta|IHHALP_00010"
/translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
EEQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDR
YVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFALKKG
IPI"
/codon_start=1
/transl_table=11
/protein_id="gnl|Bakta|IHHALP_00010"
/inference="ab initio prediction:Prodigal:2.6"
ORIGIN
1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc
Expand Down
4 changes: 2 additions & 2 deletions tools/bakta/test-data/TEST_2/TEST_2.gff3
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@
##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
# organism Escherichia coli o157:h7 Sakai
# Annotated with Bakta
# Software: v1.4.2
# Database: v3.0
# Software: v1.5.0
# Database: v4.0
# DOI: 10.1099/mgen.0.000685
# URL: github.com/oschwengers/bakta
##sequence-region NC_002127.1 1 1330
Expand Down
4 changes: 2 additions & 2 deletions tools/bakta/test-data/TEST_2/TEST_2.hypotheticals.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#Annotated with Bakta v1.4.2, https://github.com/oschwengers/bakta
#Database v3.0, https://doi.org/10.5281/zenodo.4247252
#Annotated with Bakta v1.5.0, https://github.com/oschwengers/bakta
#Database v4.0, https://doi.org/10.5281/zenodo.4247252
#Sequence Id Start Stop Strand Locus Tag Mol Weight [kDa] Iso El. Point Pfam hits Dbxrefs
NC_002127.1 413 736 + IHHALP_00005 12.1 10.4
NC_002127.1 971 141 - IHHALP_00010 18.9 7.7
8 changes: 4 additions & 4 deletions tools/bakta/test-data/TEST_2/TEST_2.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,11 +79,11 @@
}
],
"run": {
"start": "2022-08-22 13:07:07",
"end": "2022-08-22 13:07:08"
"start": "2022-09-16 07:32:09",
"end": "2022-09-16 07:32:10"
},
"version": {
"bakta": "1.4.2",
"db": "3.0"
"bakta": "1.5.0",
"db": "4.0"
}
}
Loading