Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
Laura Denies
PathoFact
Commits
bed04135
Commit
bed04135
authored
Sep 21, 2020
by
Laura Denies
Browse files
Upload New File
parent
f1c0c5a3
Changes
1
Hide whitespace changes
Inline
Side-by-side
analytical_code/hmmfetch_toxic.sh
0 → 100644
View file @
bed04135
#! /bin/bash -l
hmmfetch
=
"/work/projects/ecosystem_biology/local_tools/hmmer-3.1b1-linux-intel-x86_64/binaries/hmmfetch"
#KEGG
db
=
KEGG
hmm_file
=
/work/projects/ecosystem_biology/data/hmm/KEGG/KO.hmm
IDs
=
ID_mini_KEGG_newest_2.txt
keggout_file
=
$db
.hmm
$hmmfetch
-f
$hmm_file
$IDs
>>
$keggout_file
#META-cyc
#db=metacyc
#hmm_file=/work/projects/ecosystem_biology/data/hmm/$db/$db.hmm
#metacycout_file=$db.hmm
#IDs=ID_mini_MetaCyc.txt
#$hmmfetch -f $hmm_file $IDs >>$metacycout_file
#Pfam
db
=
Pfam-A
hmm_file
=
/work/projects/ecosystem_biology/data/hmm/
$db
/
$db
.hmm
pfamout_file
=
$db
.hmm
IDs
=
ID_mini_Pfam_newest_2.txt
$hmmfetch
-f
$hmm_file
$IDs
>>
$pfamout_file
#TIGR
db
=
tigrpfam
hmm_file
=
/work/projects/ecosystem_biology/data/hmm/TIGRPFAM/
$db
.hmm
tigrpfamout_file
=
$db
.hmm
IDs
=
ID_mini_TIGR_newest_2.txt
$hmmfetch
-f
$hmm_file
$IDs
>>
$tigrpfamout_file
#swissprot
db
=
swissprot
hmm_file
=
/work/projects/ecosystem_biology/data/hmm/SwissProt/
$db
.hmm
swissprotout_file
=
$db
.hmm
IDs
=
ID_mini_Swiss_newest_2.txt
$hmmfetch
-f
$hmm_file
$IDs
>>
$swissprotout_file
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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