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applied-bioinformatics
Docker Tripal
Commits
51b295f7
Commit
51b295f7
authored
Sep 23, 2021
by
Sven Warris
Browse files
Started with example data and upload script
parent
c9bd2054
Changes
3
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python-tripal/data/ITAG4.0_gene_models.gff
0 → 100644
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51b295f7
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python-tripal/data/S_lycopersicum_chromosomes.4.00.fa
0 → 100644
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51b295f7
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inary files /dev/null and b/python-tripal/data/S_lycopersicum_chromosomes.4.00.fa differ
python-tripal/example.py
0 → 100644
View file @
51b295f7
from
tripal
import
TripalInstance
ti
=
TripalInstance
(
tripal_url
=
'http://localhost:3000/'
,
username
=
'admin'
,
password
=
'changeme'
)
# Create human species
#org = ti.organism.add_organism(genus="Solanum", species="lycopersicum", common="Tomato", abbr="SOLYC4.0")
# Then display the list of organisms
orgs
=
ti
.
organism
.
get_organisms
()
for
org
in
orgs
:
print
(
'{} {}'
.
format
(
org
[
'genus'
],
org
[
'species'
]))
# Create an analysis
an
=
ti
.
analysis
.
add_analysis
(
name
=
"Main assembly"
,
program
=
"SolGenomicsNetwork assembler"
,
programversion
=
"1.0"
,
algorithm
=
"Unknown"
,
sourcename
=
"src"
,
sourceversion
=
"2.1beta"
,
date_executed
=
"2020-09-20"
)
ans
=
ti
.
analysis
.
get_analyses
()
# And load some data
ti
.
analysis
.
load_fasta
(
fasta
=
"./data/S_lycopersicum_chromosomes.4.00.fa"
,
analysis_id
=
ans
[
0
][
'analysis_id'
],
organism_id
=
orgs
[
0
][
'organism_id'
])
ti
.
analysis
.
load_gff3
(
gff
=
"./data/ITAG4.0_gene_models.gff"
,
analysis_id
=
ans
[
0
][
'analysis_id'
],
organism_id
=
orgs
[
0
][
'organism_id'
])
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