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BBRIC
family-companion
Commits
f10a884d
Commit
f10a884d
authored
Feb 23, 2015
by
lcottret
Browse files
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Merge branch 'master' of
https://lcottret@bitbucket.org/carrere/orthomcl-companion.git
parents
cd8b81c7
15b5df4a
Changes
10
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10 changed files
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139 additions
and
79 deletions
+139
-79
README.md
README.md
+25
-7
lib/int/OrthomclCompanion/GroupAnalyses.pl
lib/int/OrthomclCompanion/GroupAnalyses.pl
+3
-33
lib/int/OrthomclCompanion/Parsers.pl
lib/int/OrthomclCompanion/Parsers.pl
+55
-4
lib/int/OrthomclCompanion/SpecificAndOrthologousProteins.pl
lib/int/OrthomclCompanion/SpecificAndOrthologousProteins.pl
+3
-22
lib/int/OrthomclCompanion/Utils.pl
lib/int/OrthomclCompanion/Utils.pl
+42
-2
web/js/int/src/controller/C_ViewResult.js
web/js/int/src/controller/C_ViewResult.js
+1
-1
web/js/int/src/view/grid/V_ListAnalyses.js
web/js/int/src/view/grid/V_ListAnalyses.js
+2
-2
web/js/int/src/view/panel/V_Home.js
web/js/int/src/view/panel/V_Home.js
+1
-1
web/templates/barplots/index.html
web/templates/barplots/index.html
+6
-6
web/templates/barplots/plot.js
web/templates/barplots/plot.js
+1
-1
No files found.
README.md
View file @
f10a884d
# README #
# README #
Outil d'aide à l'interprétation de résultats OrthoMCL
Outil d'aide à l'interprétation de résultats OrthoMCL
### What is this repository for? ###
*
Quick summary
### TODO ###
*
Version
*
[
Learn Markdown
](
https://bitbucket.org/tutorials/markdowndemo
)
### How do I get set up? ###
*
Import zip
La structure du zip doit etre:
zip/
|-- CODE1.fasta
|-- CODE1.iprscan
|-- CODE1.txt
|-- CODE2.fasta
|-- CODE2.iprscan
|-- CODE2.txt
|-- CODE3.fasta
|-- CODE3.iprscan
|-- CODE3.txt
|-- reference.txt
*
Diagrammes de Venn (JVENN)
*
Get description des termes GO (et pathways ?) pour iprscan v5
### INSTALL ###
*
Summary of set up
*
Configuration
*
Configuration
WEBAPP: Fichier site/cfg/site.cfg
WEBAPP: Fichier site/cfg/site.cfg
...
@@ -42,7 +60,7 @@ TESTER LE CLI-A
...
@@ -42,7 +60,7 @@ TESTER LE CLI-A
./bin/int/bbric_orthomcl-companion.pl --outdir test --analysis_cfg test/analysis.json --verbose
./bin/int/bbric_orthomcl-companion.pl --outdir test --analysis_cfg test/analysis.json --verbose
###
Who do I talk to?
###
###
AUTEURS
###
*
sebastien.carrere@toulouse.inra.fr
*
sebastien.carrere@toulouse.inra.fr
*
ludovic.cottret@toulouse.inra.fr
*
ludovic.cottret@toulouse.inra.fr
...
...
lib/int/OrthomclCompanion/GroupAnalyses.pl
View file @
f10a884d
...
@@ -16,6 +16,8 @@ sub ListGroupAndUniqueForAllProteomes
...
@@ -16,6 +16,8 @@ sub ListGroupAndUniqueForAllProteomes
my
(
$rh_orthomcl
,
$rh_species
,
$outdir
)
=
@_
;
my
(
$rh_orthomcl
,
$rh_species
,
$outdir
)
=
@_
;
my
%
ListGroupByCode
;
my
%
ListGroupByCode
;
my
$rh_specific
=
{};
my
$rh_specific
=
{};
&
Log
("
INFO - ListGroupAndUniqueForAllProteomes
");
foreach
my
$code
(
keys
%
{
$rh_species
})
foreach
my
$code
(
keys
%
{
$rh_species
})
{
{
...
@@ -55,38 +57,6 @@ sub ListGroupAndUniqueForAllProteomes
...
@@ -55,38 +57,6 @@ sub ListGroupAndUniqueForAllProteomes
return
;
return
;
}
}
=head3 function __DeleteSequencesFromGroupId
Title : __DeleteSequencesFromGroupId
Usage : &__DeleteSequencesFromGroupId($outdir,\%ListGroupByCode)
Prerequisite : none
Function : Keep only specific protein for each proteome
Returns : none
Args : hash ref of orthomcl groups,
Globals : none
=cut
sub
__DeleteSequencesFromGroupId
{
my
(
$rh_orthomcl
,
$rh_specific
,
$groupid
)
=
@_
;
foreach
my
$code
(
keys
%
{
$rh_orthomcl
->
{
$groupid
}})
{
foreach
my
$seqid
(
@
{
$rh_orthomcl
->
{
$groupid
}
->
{
$code
}})
{
if
(
!
defined
$rh_specific
->
{
$code
}
->
{
$seqid
})
{
&
Log
("
WARNING - __DeleteSequencesFromGroupId -
$seqid
not defined in
$code
sequence file
");
}
else
{
delete
$rh_specific
->
{
$code
}
->
{
$seqid
};
}
}
}
return
;
}
=head3 function PrintListGroupProteome
=head3 function PrintListGroupProteome
Title : PrintListGroupProteome
Title : PrintListGroupProteome
...
@@ -107,7 +77,7 @@ sub PrintListGroupProteome
...
@@ -107,7 +77,7 @@ sub PrintListGroupProteome
'
directory with for each proteome (one file / proteome), a list of all group with a protein of this proteome + unique protein
';
'
directory with for each proteome (one file / proteome), a list of all group with a protein of this proteome + unique protein
';
mkdir
"
$outdir
/
$subdirectory
";
mkdir
"
$outdir
/
$subdirectory
";
#
push (@A_OUTPUT_DATA, {'directory' => $subdirectory, 'description' => $subdirectory_description});
push
(
@A_OUTPUT_DATA
,
{'
directory
'
=>
$subdirectory
,
'
description
'
=>
$subdirectory_description
});
foreach
my
$code
(
keys
%
{
$rh_listgroupbycode
})
foreach
my
$code
(
keys
%
{
$rh_listgroupbycode
})
{
{
my
$fh_liste
=
&
GetStreamOut
("
$outdir
/
$subdirectory
/
$code
.list.txt
");
my
$fh_liste
=
&
GetStreamOut
("
$outdir
/
$subdirectory
/
$code
.list.txt
");
...
...
lib/int/OrthomclCompanion/Parsers.pl
View file @
f10a884d
...
@@ -14,6 +14,7 @@
...
@@ -14,6 +14,7 @@
sub
ParseIprscan
sub
ParseIprscan
{
{
my
$iprscan_file
=
shift
;
my
$iprscan_file
=
shift
;
&
Log
("
INFO - ParseIprscan
");
my
%
h_iprscan
=
();
my
%
h_iprscan
=
();
my
$firstline
=
`
grep --max-count=1 IPR
$iprscan_file
`;
my
$firstline
=
`
grep --max-count=1 IPR
$iprscan_file
`;
chomp
$firstline
;
chomp
$firstline
;
...
@@ -185,6 +186,7 @@ sub ParseProteomes
...
@@ -185,6 +186,7 @@ sub ParseProteomes
my
(
$rh_proteomes
)
=
@_
;
my
(
$rh_proteomes
)
=
@_
;
my
%
h_species
=
();
my
%
h_species
=
();
&
Log
("
INFO - ParseProteomes
");
foreach
my
$code
(
keys
%
{
$rh_proteomes
})
foreach
my
$code
(
keys
%
{
$rh_proteomes
})
{
{
...
@@ -238,6 +240,7 @@ sub ParseOrthomclResults
...
@@ -238,6 +240,7 @@ sub ParseOrthomclResults
{
{
my
(
$outfile
,
$version
)
=
@_
;
my
(
$outfile
,
$version
)
=
@_
;
&
Log
("
INFO - ParseOrthomclResults
");
my
%
h_orthomcl
=
();
my
%
h_orthomcl
=
();
my
$fh_in
=
&
GetStreamIn
(
$outfile
);
my
$fh_in
=
&
GetStreamIn
(
$outfile
);
...
@@ -336,9 +339,9 @@ sub BuildIprscanDBTables
...
@@ -336,9 +339,9 @@ sub BuildIprscanDBTables
foreach
my
$dbacc
(
keys
%
{
$rh_sequences
->
{
$seqid
}
->
{'
iprscan
'}
->
{
$dbname
}})
foreach
my
$dbacc
(
keys
%
{
$rh_sequences
->
{
$seqid
}
->
{'
iprscan
'}
->
{
$dbname
}})
{
{
$dbdesc
=
$rh_sequences
->
{
$seqid
}
->
{'
iprscan
'}
->
{
$dbname
}
->
{
$dbacc
};
$dbdesc
=
$rh_sequences
->
{
$seqid
}
->
{'
iprscan
'}
->
{
$dbname
}
->
{
$dbacc
};
print
$fh_out
"
$seqid
\t
$groupid
\t
"
.
$dbacc
.
"
\t
"
.
$dbdesc
.
"
\n
";
print
$fh_out
"
$seqid
\t
"
.
$dbacc
.
"
\t
"
.
$dbdesc
.
"
\n
";
$h_count
{
$dbname
}
->
{
$dbacc
}
=
0
unless
defined
$h_count
{
$dbname
}
->
{
$dbacc
};
$h_count
{
$dbname
}
->
{
$dbacc
}
=
{'
count
'
=>
0
,
'
desc
'
=>
$dbdesc
}
unless
defined
$h_count
{
$dbname
}
->
{
$dbacc
};
$h_count
{
$dbname
}
->
{
$dbacc
}
++
;
$h_count
{
$dbname
}
->
{
$dbacc
}
->
{'
count
'}
++
;
}
}
$fh_out
->
close
;
$fh_out
->
close
;
}
}
...
@@ -350,11 +353,59 @@ sub BuildIprscanDBTables
...
@@ -350,11 +353,59 @@ sub BuildIprscanDBTables
my
$fh_out
=
&
GetStreamOut
("
>
$outdir
/
$code
.iprscan.
$suffix
.
$dbname
.count.xls
");
my
$fh_out
=
&
GetStreamOut
("
>
$outdir
/
$code
.iprscan.
$suffix
.
$dbname
.count.xls
");
foreach
my
$dbacc
(
sort
{
$rh_local
->
{
$b
}
<=>
$rh_local
->
{
$a
}}
keys
%
{
$rh_local
})
foreach
my
$dbacc
(
sort
{
$rh_local
->
{
$b
}
<=>
$rh_local
->
{
$a
}}
keys
%
{
$rh_local
})
{
{
print
$fh_out
"
$dbacc
\t
"
.
$rh_local
->
{
$dbacc
}
.
"
\n
";
print
$fh_out
"
$dbacc
\t
"
.
$rh_local
->
{
$dbacc
}
->
{'
desc
'}
.
"
\t
"
.
$rh_local
->
{
$dbacc
}
->
{'
count
'}
.
"
\n
";
}
}
$fh_out
->
close
;
$fh_out
->
close
;
}
}
&
__BuildIprscanDBJSdata
(
\%
h_count
,
$code
,
$outdir
,
$suffix
);
return
;
return
;
}
}
sub
__BuildIprscanDBJSdata
{
my
(
$rh_count
,
$code
,
$outdir
,
$suffix
)
=
@_
;
if
(
scalar
(
keys
%
{
$rh_count
})
>
0
)
{
my
@a_json_data
=
();
foreach
my
$dbname
(
sort
keys
%
{
$rh_count
})
{
my
$rh_data
=
{'
title
'
=>
$dbname
,
'
data
'
=>
[]
,
'
path
'
=>
"
$code
.iprscan.
$suffix
.
$dbname
.xls
"}
;
my
$rh_local
=
$rh_count
->
{
$dbname
};
foreach
my
$dbacc
(
sort
{
$rh_local
->
{
$b
}
->
{'
count
'}
<=>
$rh_local
->
{
$a
}
->
{'
count
'}}
keys
%
{
$rh_local
})
{
push
(
@
{
$rh_data
->
{'
data
'}},
{
'
name
'
=>
$dbacc
,
'
count
'
=>
$rh_local
->
{
$dbacc
}
->
{'
count
'},
'
desc
'
=>
$rh_local
->
{
$dbacc
}
->
{'
desc
'}});
}
push
(
@a_json_data
,
$rh_data
);
}
my
$fh_out
=
&
GetStreamOut
("
>
$outdir
/
$code
.iprscan.
$suffix
.count.js
");
print
$fh_out
'
var data =
'
.
to_json
(
\
@a_json_data
)
.
'
;
';
$fh_out
->
close
;
my
$o_pp
=
New
ParamParser
("
$FindBin
::RealBin/../../site/cfg/site.cfg
");
my
$root_url
=
$o_pp
->
Get
('
portal_web_server
')
.
'
/
'
.
$o_pp
->
Get
('
portal_http_root
');
my
$fh_html_template
=
&
GetStreamIn
("
$FindBin
::RealBin/../../web/templates/barplots/index.html
");
my
$fh_html_out
=
&
GetStreamOut
("
$outdir
/
$code
.iprscan.
$suffix
.html
");
while
(
my
$line
=
<
$fh_html_template
>
)
{
$line
=~
s/data.js/$code.iprscan.$suffix.count.js/
;
$line
=~
s/%ROOT_URL%/$root_url/g
;
print
$fh_html_out
$line
;
}
$fh_html_out
->
close
;
$fh_html_template
->
close
;
copy
("
$FindBin
::RealBin/../../web/templates/barplots/plot.js
","
$outdir
/plot.js
");
}
return
;
}
1
;
1
;
lib/int/OrthomclCompanion/SpecificAndOrthologousProteins.pl
View file @
f10a884d
...
@@ -15,9 +15,10 @@ sub ExtractSpecificAndOrthologousProteins
...
@@ -15,9 +15,10 @@ sub ExtractSpecificAndOrthologousProteins
{
{
my
(
$rh_orthomcl
,
$rh_species
,
$outdir
)
=
@_
;
my
(
$rh_orthomcl
,
$rh_species
,
$outdir
)
=
@_
;
my
%
h_inparalogs
=
();
#my %h_specific = %{$rh_species};
&
Log
("
INFO - ExtractSpecificAndOrthologousProteins
");
my
%
h_inparalogs
=
();
my
$rh_specific
=
{};
my
$rh_specific
=
{};
...
@@ -57,26 +58,6 @@ sub ExtractSpecificAndOrthologousProteins
...
@@ -57,26 +58,6 @@ sub ExtractSpecificAndOrthologousProteins
return
;
return
;
}
}
sub
__DeleteSequencesFromGroupId
{
my
(
$rh_orthomcl
,
$rh_specific
,
$groupid
)
=
@_
;
foreach
my
$code
(
keys
%
{
$rh_orthomcl
->
{
$groupid
}})
{
foreach
my
$seqid
(
@
{
$rh_orthomcl
->
{
$groupid
}
->
{
$code
}})
{
if
(
!
defined
$rh_specific
->
{
$code
}
->
{
$seqid
})
{
&
Log
("
WARNING - __DeleteSequencesFromGroupId -
$seqid
not defined in
$code
sequence file
");
}
else
{
delete
$rh_specific
->
{
$code
}
->
{
$seqid
};
}
}
}
return
;
}
sub
IsOrthologousGroup
sub
IsOrthologousGroup
{
{
my
(
$rh_orthomcl
,
$groupid
)
=
@_
;
my
(
$rh_orthomcl
,
$groupid
)
=
@_
;
...
...
lib/int/OrthomclCompanion/Utils.pl
View file @
f10a884d
...
@@ -98,6 +98,7 @@ sub BuildSummaryFile
...
@@ -98,6 +98,7 @@ sub BuildSummaryFile
{
{
my
(
$rh_analysis_params
,
$outdir
)
=
@_
;
my
(
$rh_analysis_params
,
$outdir
)
=
@_
;
unshift
(
@A_OUTPUT_DATA
,
{'
directory
'
=>
'
input_data
',
'
description
'
=>
'
Input data
'});
foreach
my
$rh_output_data
(
@A_OUTPUT_DATA
)
foreach
my
$rh_output_data
(
@A_OUTPUT_DATA
)
{
{
my
$directory
=
$outdir
.
'
/
'
.
$rh_output_data
->
{'
directory
'};
my
$directory
=
$outdir
.
'
/
'
.
$rh_output_data
->
{'
directory
'};
...
@@ -116,7 +117,9 @@ sub BuildSummaryFile
...
@@ -116,7 +117,9 @@ sub BuildSummaryFile
$message
=
&
Cat
("
$directory
/README
");
$message
=
&
Cat
("
$directory
/README
");
}
}
my
@a_files
=
`
cd
$directory
; find -type f | grep -v 'error
\
|success
\
|README'
`;
my
$cmd
=
"
cd
$directory
; find -type f | grep -v -E 'error
\
|success
\
|README
\
|.js
\
|.count.xls
\
|.iprscan.*.xls'
";
&
Log
("
CMD -
$cmd
");
my
@a_files
=
`
$cmd
`;
chomp
@a_files
;
chomp
@a_files
;
$rh_output_data
->
{'
status
'}
=
$status
;
$rh_output_data
->
{'
status
'}
=
$status
;
...
@@ -124,6 +127,8 @@ sub BuildSummaryFile
...
@@ -124,6 +127,8 @@ sub BuildSummaryFile
$rh_output_data
->
{'
files
'}
=
\
@a_files
;
$rh_output_data
->
{'
files
'}
=
\
@a_files
;
}
}
my
%
h_data
=
('
analysis
'
=>
$rh_analysis_params
,
'
results
'
=>
\
@A_OUTPUT_DATA
);
my
%
h_data
=
('
analysis
'
=>
$rh_analysis_params
,
'
results
'
=>
\
@A_OUTPUT_DATA
);
my
$fh_out
=
&
GetStreamOut
("
$outdir
/results.json
");
my
$fh_out
=
&
GetStreamOut
("
$outdir
/results.json
");
...
@@ -144,7 +149,7 @@ sub CopyInputDataIntoOutdir
...
@@ -144,7 +149,7 @@ sub CopyInputDataIntoOutdir
{
{
my
(
$rh_analysis_params
,
$rh_species
,
$outdir
)
=
@_
;
my
(
$rh_analysis_params
,
$rh_species
,
$outdir
)
=
@_
;
mkdir
"
$outdir
/input_data
";
mkdir
"
$outdir
/input_data
";
mkdir
"
$outdir
/input_data/proteomes
";
mkdir
"
$outdir
/input_data/proteomes
";
my
$rh_proteomes
=
$rh_analysis_params
->
{'
proteomes
'};
my
$rh_proteomes
=
$rh_analysis_params
->
{'
proteomes
'};
...
@@ -167,6 +172,7 @@ sub CopyInputDataIntoOutdir
...
@@ -167,6 +172,7 @@ sub CopyInputDataIntoOutdir
}
}
}
}
mkdir
"
$outdir
/orthomcl_output/
";
mkdir
"
$outdir
/orthomcl_output/
";
copy
("
$WORKDIR
/orthomcl.out
",
"
$outdir
/orthomcl_output/
");
copy
("
$WORKDIR
/orthomcl.out
",
"
$outdir
/orthomcl_output/
");
$rh_analysis_params
->
{'
orthomcl
'}
->
{'
outfile
'}
=
"
./orthomcl_output/orthomcl.out
";
$rh_analysis_params
->
{'
orthomcl
'}
->
{'
outfile
'}
=
"
./orthomcl_output/orthomcl.out
";
...
@@ -174,4 +180,38 @@ sub CopyInputDataIntoOutdir
...
@@ -174,4 +180,38 @@ sub CopyInputDataIntoOutdir
}
}
=head3 function __DeleteSequencesFromGroupId
Title : __DeleteSequencesFromGroupId
Usage : &__DeleteSequencesFromGroupId($outdir,\%ListGroupByCode)
Prerequisite : none
Function : Keep only specific protein for each proteome
Returns : none
Args : hash ref of orthomcl groups,
Globals : none
=cut
sub
__DeleteSequencesFromGroupId
{
my
(
$rh_orthomcl
,
$rh_specific
,
$groupid
)
=
@_
;
foreach
my
$code
(
keys
%
{
$rh_orthomcl
->
{
$groupid
}})
{
foreach
my
$seqid
(
@
{
$rh_orthomcl
->
{
$groupid
}
->
{
$code
}})
{
if
(
!
defined
$rh_specific
->
{
$code
}
->
{
$seqid
})
{
&
Log
("
WARNING - __DeleteSequencesFromGroupId -
$seqid
not defined in
$code
sequence file
");
}
else
{
delete
$rh_specific
->
{
$code
}
->
{
$seqid
};
}
}
}
return
;
}
1
;
1
;
web/js/int/src/controller/C_ViewResult.js
View file @
f10a884d
...
@@ -116,7 +116,7 @@ Ext
...
@@ -116,7 +116,7 @@ Ext
'
value
'
:
this
'
value
'
:
this
.
createLink
(
.
createLink
(
json
.
analysis
.
orthomcl
.
outfile
,
json
.
analysis
.
orthomcl
.
outfile
,
url_base
+
"
/orthomcl_output
"
)
url_base
)
},
},
{
{
'
key
'
:
'
Version
'
,
'
key
'
:
'
Version
'
,
...
...
web/js/int/src/view/grid/V_ListAnalyses.js
View file @
f10a884d
...
@@ -19,7 +19,7 @@ Ext.define('BP.view.grid.V_ListAnalyses', {
...
@@ -19,7 +19,7 @@ Ext.define('BP.view.grid.V_ListAnalyses', {
dockedItems
:
[
{
dockedItems
:
[
{
xtype
:
'
toolbar
'
,
xtype
:
'
toolbar
'
,
items
:
[
'
<-
'
,
{
items
:
[
{
iconCls
:
'
icon-reload
'
,
iconCls
:
'
icon-reload
'
,
text
:
'
Reload
'
,
text
:
'
Reload
'
,
action
:
'
reload
'
action
:
'
reload
'
...
@@ -92,4 +92,4 @@ Ext.define('BP.view.grid.V_ListAnalyses', {
...
@@ -92,4 +92,4 @@ Ext.define('BP.view.grid.V_ListAnalyses', {
]
]
});
});
\ No newline at end of file
web/js/int/src/view/panel/V_Home.js
View file @
f10a884d
...
@@ -11,4 +11,4 @@ Ext.define('BP.view.panel.V_Home', {
...
@@ -11,4 +11,4 @@ Ext.define('BP.view.panel.V_Home', {
url
:
'
home.html
'
,
url
:
'
home.html
'
,
autoLoad
:
true
autoLoad
:
true
}
}
});
});
\ No newline at end of file
web/templates/barplots/index.html
View file @
f10a884d
...
@@ -4,14 +4,14 @@
...
@@ -4,14 +4,14 @@
<link
rel=
"stylesheet"
type=
"text/css"
<link
rel=
"stylesheet"
type=
"text/css"
href=
"
../..
/js/ext/extjs/resources/css/ext-all.css"
>
href=
"
%ROOT_URL%/web
/js/ext/extjs/resources/css/ext-all.css"
>
<link
rel=
"stylesheet"
type=
"text/css"
<link
rel=
"stylesheet"
type=
"text/css"
href=
"
../..
/resources/css/banner.css"
>
href=
"
%ROOT_URL%/web
/resources/css/banner.css"
>
<link
rel=
"stylesheet"
type=
"text/css"
<link
rel=
"stylesheet"
type=
"text/css"
href=
"
../..
/resources/css/custom.css"
>
href=
"
%ROOT_URL%/web
/resources/css/custom.css"
>
<link
rel=
"stylesheet"
type=
"text/css"
<link
rel=
"stylesheet"
type=
"text/css"
href=
"
../..
/resources/icons/icons.css"
>
href=
"
%ROOT_URL%/web
/resources/icons/icons.css"
>
<script
type=
"text/javascript"
src=
"
../..
/js/ext/extjs/ext-all.js"
></script>
<script
type=
"text/javascript"
src=
"
%ROOT_URL%/web
/js/ext/extjs/ext-all.js"
></script>
<script
type=
"text/javascript"
src=
"data.js"
></script>
<script
type=
"text/javascript"
src=
"data.js"
></script>
<script
type=
"text/javascript"
src=
"plot.js"
></script>
<script
type=
"text/javascript"
src=
"plot.js"
></script>
...
@@ -24,4 +24,4 @@
...
@@ -24,4 +24,4 @@
</body>
</body>
</html>
</html>
\ No newline at end of file
web/templates/barplots/plot.js
View file @
f10a884d
...
@@ -148,4 +148,4 @@ Ext
...
@@ -148,4 +148,4 @@ Ext
});
});
});
});
\ No newline at end of file
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