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SOaAS
dbman
Commits
fe053765
Commit
fe053765
authored
Jun 08, 2020
by
Lukas Jelonek
Browse files
Add pfam download
parent
5638d6f2
Changes
2
Hide whitespace changes
Inline
Side-by-side
dbman/main.py
View file @
fe053765
...
...
@@ -164,6 +164,7 @@ def run_in_tempdir(func=None, success=None, fail=None):
def
_recipes
(
args
):
recipes
=
{
'pfam'
:
{
'download'
:
{
'script'
:
_pkgres
(
'recipes/download_pfam.py'
)}},
'card'
:
{
'download'
:
{
'script'
:
_pkgres
(
'recipes/download_card.py'
)},
'blast'
:
{
'script'
:
_pkgres
(
'recipes/create_blast_dbs.py'
)},
'diamond'
:
{
'script'
:
_pkgres
(
'recipes/create_diamond_dbs.py'
)},
...
...
dbman/recipes/download_pfam.py
0 → 100755
View file @
fe053765
#!/usr/bin/env python3
import
dbman.helper
as
h
import
json
import
os
import
gzip
import
logging
logging
.
basicConfig
(
level
=
logging
.
INFO
)
dbname
=
"pfam"
dbdescription
=
"The Pfam database is a large collection of protein families"
url
=
"ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release"
def
read_version_info
(
version_fn
):
version_data
=
{}
with
gzip
.
open
(
version_fn
,
'rt'
)
as
f
:
for
line
in
f
:
(
key
,
value
)
=
line
.
split
(
':'
)
key
=
key
.
strip
()
value
=
value
.
strip
()
if
key
==
"Pfam release"
:
key
=
"version"
if
key
==
"Pfam-A families"
:
key
=
"families"
if
key
==
"Date"
:
key
=
"release_date"
if
key
==
"Based on UniProtKB"
:
key
=
"based_on_uniprotkb_version"
version_data
[
key
]
=
value
return
version_data
version_fn
=
h
.
download
(
url
+
'/Pfam.version.gz'
)
version_info
=
read_version_info
(
version_fn
)
# download archive
hmm_fn
=
h
.
download
(
url
+
"/Pfam-A.hmm.gz"
)
flatfile_fn
=
h
.
download
(
url
+
"/Pfam-A.hmm.dat.gz"
)
# lookup tags for fasta files
parts
=
[]
parts
.
append
({
'files'
:[
hmm_fn
],
'tags'
:
[
'profile'
,
'hmm'
,
'gzip'
,
'compressed'
]})
parts
.
append
({
'files'
:[
flatfile_fn
],
'tags'
:
[
'flatfile'
,
'annotation'
,
'gzip'
,
'compressed'
]})
parts
.
append
({
'files'
:[
version_fn
],
'tags'
:
[
'version_info'
,
'gzip'
,
'compressed'
]})
version_info
[
'parts'
]
=
parts
# write metadata file
h
.
create_metadata
(
dbname
,
"download"
,
dbdescription
,
other
=
version_info
)
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