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gem
capsuledb
Commits
a8a89577
Commit
a8a89577
authored
Feb 16, 2012
by
Bertrand NÉRON
Browse files
bug fix T3SS_family typos
somewhere it was spelled with 2 l
parent
f97e6470
Changes
2
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Inline
Side-by-side
src/couchapp/secreton/templates/secretion_system.html
View file @
a8a89577
...
...
@@ -231,7 +231,7 @@
<h1>
Secretion system {{code}}
</h1>
<ul>
<li>
code: {{code}}
</li>
<li>
T3SS family:{{T3SS_famil
l
y}}
</li>
<li>
T3SS family:{{T3SS_family}}
</li>
</ul>
<h2>
Replicon
</h2>
<ul>
...
...
src/parser/parser.py
View file @
a8a89577
...
...
@@ -41,7 +41,7 @@ def system_parser( system_data ):
@rtype: dict
"""
system_db
=
{}
System_info
=
namedtuple
(
'System_info'
,
'code, T3SS_famil
l
y, replicon, genes'
)
System_info
=
namedtuple
(
'System_info'
,
'code, T3SS_family, replicon, genes'
)
Gene
=
namedtuple
(
'Gene'
,
'code, id, protein_length, strand, begin, end, match, full_score, e_value, best_domain_score, best_domain_evalue, c_value, coverage_profile, match_begin, match_end'
)
with
open
(
system_data
,
'r'
)
as
system_file
:
...
...
@@ -89,7 +89,7 @@ class SecretionSystem( Document ):
a representation of a secretion System to be use with couchdb
"""
code
=
StringProperty
(
required
=
True
)
T3SS_famil
l
y
=
StringProperty
()
T3SS_family
=
StringProperty
()
replicon
=
DictProperty
()
genes
=
ListProperty
()
...
...
@@ -131,7 +131,7 @@ def fill_db( server_uri, db_name, user, passwd, replicon_db , system_db , force_
secretion_system
=
SecretionSystem
()
secretion_system
.
_id
=
system
.
code
secretion_system
.
code
=
system
.
code
secretion_system
.
T3SS_famil
l
y
=
system
.
T3SS_famil
l
y
secretion_system
.
T3SS_family
=
system
.
T3SS_family
secretion_system
.
replicon
=
{
'name'
:
replicon
.
name
,
'taxid'
:
replicon
.
taxid
,
'strain'
:
replicon
.
strain
,
...
...
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