Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Menu
Open sidebar
bird_pipeline_registry
SRP-pipeline
Commits
cfca8577
Commit
cfca8577
authored
Oct 22, 2020
by
Philippe BORDRON
Browse files
Update according to StringDB changes
parent
0d89f00c
Changes
2
Hide whitespace changes
Inline
Side-by-side
SCRIPTS/make_html.py
View file @
cfca8577
...
...
@@ -305,11 +305,12 @@ for c in conditionVS:
g
=
dict
()
g
[
"category"
]
=
ls
[
0
]
term
=
ls
[
1
]
id
=
ls
[
1
].
split
(
'
.
'
)
id
=
ls
[
1
].
split
(
'
:
'
)
category
=
id
[
0
]
uid
=
'.'
.
join
(
id
[
1
:])
taxa
=
ls
[
4
]
if
g
[
"category"
]
in
[
"Component"
,
"Process"
,
"Function"
]:
term
=
'<a href="http://amigo.geneontology.org/amigo/term/
GO:
{}" target="_blank">{}</a>'
.
format
(
uid
,
term
)
term
=
'<a href="http://amigo.geneontology.org/amigo/term/{}" target="_blank">{}</a>'
.
format
(
term
,
term
)
if
g
[
"category"
]
==
"InterPro"
:
term
=
'<a href="https://www.ebi.ac.uk/interpro/entry/{}" target="_blank">{}</a>'
.
format
(
term
,
term
)
if
g
[
"category"
]
==
'KEGG'
:
...
...
@@ -324,11 +325,13 @@ for c in conditionVS:
term
=
'<a href="https://reactome.org/content/detail/R-{}" target="_blank">{}</a>'
.
format
(
term
,
term
)
if
g
[
"category"
]
==
'SMART'
:
term
=
'<a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN={}" target="_blank">{}</a>'
.
format
(
term
,
term
)
if
g
[
"category"
]
==
'NetworkNeighborAL'
:
term
=
'<a href="https://string-db.org/cgi/network?network_cluster_id={}&input_query_species={}" target="_blank">{}</a>'
.
format
(
term
,
taxa
,
term
)
g
[
"term"
]
=
term
g
[
"number_of_genes"
]
=
ls
[
2
]
g
[
"number_of_genes_in_background"
]
=
ls
[
3
]
g
[
"gene_ratio"
]
=
str
(
"%.2f"
%
(
int
(
ls
[
2
])
/
int
(
ls
[
3
])))
g
[
"ncbiTaxonId"
]
=
ls
[
4
]
g
[
"ncbiTaxonId"
]
=
taxa
gc
=
[]
for
g1
,
g2
in
zip
(
ls
[
5
].
split
(
','
),
ls
[
6
].
split
(
','
)):
fc
=
templateVars
[
"deseqres"
][
c
[
"condition1"
]
+
"__vs__"
+
c
[
"condition2"
]][
"fc"
][
g1
]
...
...
TEMPLATE/index_SA.html
View file @
cfca8577
...
...
@@ -419,7 +419,8 @@
UniProt Keywords (Keyword),
PFAM Protein Domains (Pfam),
INTERPRO Protein Domains and Features (InterPro),
SMART Protein Domains (SMART).
SMART Protein Domains (SMART),
String Local Network Cluster (NetworkNeighborAL).
</p>
{% if stringParams[i.condition1+"__vs__"+i.condition2].counts == 0 %}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment