Commit a4456f74 authored by Claire Hoede's avatar Claire Hoede
Browse files

petite correction des descriptions

parent eb8c3b9d
......@@ -67,17 +67,17 @@ while (<IN>) {
=over
=item B<input>
=item INPUT
name of the input fastq file.
=item B<--help>
=item HELP
Print this usage message.
=back
=head1 B<DESCRIPTION>
=head1 DESCRIPTION
This script will read the FASTQ file passed as input and return only the rows corresponding to the colorspace.
......@@ -104,4 +104,4 @@ colorspace, csfasta,
csfastq_to_csfasta.pl my_reads.cut.csfastq > my_reads.cut.csfasta
=cut
\ No newline at end of file
=cut
......@@ -2,15 +2,15 @@
=pod
=head1 NAME
=head1 NAME
extract_netcglyc_results.pl
=head1 SYNOPSIS
=head1 SYNOPSIS
extract_netcglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 OPTIONS
=head1 OPTIONS
--infile string, the path to the protein sequence query file - !!!the sequence name should be the short name!!!
--encodingfile string, the path of the file containing the encoded protein names (long name "..._allele1" <-> short name "_seq")
......@@ -19,9 +19,7 @@ extract_netcglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION
extract_netcglyc_results.pl - This program is part of a pipeline of programs for SNP annotation.
It uses a program called netcglyc and predicts C-mannosylation sites in mammalian protein on amino acid:
http://www.cbs.dtu.dk/services/NetCGlyc/output.php
extract_netcglyc_results.pl - This program is part of a pipeline of programs for SNP annotation. It uses a program called netcglyc and predicts C-mannosylation sites in mammalian protein on amino acid: http://www.cbs.dtu.dk/services/NetCGlyc/output.php
if the 2 alleles of a protein show a different signal then there is loss or gain of signal.
if allele1 has a prediction and allele2 doesn't, then there is loss of signal.
if allele2 has a prediction and allele1 doesn't, then there is gain of signal.
......
......@@ -2,15 +2,15 @@
=pod
=head1 NAME
=head1 NAME
extract_netcglyn_results.pl
=head1 SYNOPSIS
=head1 SYNOPSIS
extract_netcglyn_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 OPTIONS
=head1 OPTIONS
--infile string, the path to the protein sequence query file - !!!the sequence name should be the short name!!!
--encodingfile string, the path of the file containing the encoded protein names (long name "..._allele1" <-> short name "_seq")
......@@ -20,10 +20,7 @@ extract_netcglyn_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION
extract_netcglyn_results.pl - This program is part of a pipeline of programs for SNP annotation.
It uses a program called netnglyc and predicts N-Glycosylation sites in human proteins on amino acid
using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons:
http://www.cbs.dtu.dk/services/NetNGlyc/output.php
extract_netcglyn_results.pl - This program is part of a pipeline of programs for SNP annotation. It uses a program called netnglyc and predicts N-Glycosylation sites in human proteins on amino acid using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons: http://www.cbs.dtu.dk/services/NetNGlyc/output.php
if the 2 alleles of a protein show a different signal then there is loss or gain of signal.
if allele1 has a prediction and allele2 doesn't, then there is loss of signal.
if allele2 has a prediction and allele1 doesn't, then there is gain of signal.
......
......@@ -2,15 +2,15 @@
=pod
=head1 NAME
=head1 NAME
extract_netoglyc_results.pl
=head1 SYNOPSIS
=head1 SYNOPSIS
extract_netoglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 OPTIONS
=head1 OPTIONS
--infile string, the path to the protein sequence query file - !!!the sequence name should be the short name!!!
--encodingfile string, the path of the file containing the encoded protein names (long name "..._allele1" <-> short name "_seq")
......@@ -20,9 +20,7 @@ extract_netoglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION
extract_netoglyc_results.pl - This program is part of a pipeline of programs for SNP annotation.
It uses a program called netoglyc and predicts O-glycosylation sites in mammalian protein on amino acid
http://www.cbs.dtu.dk/services/NetOGlyc/
extract_netoglyc_results.pl - This program is part of a pipeline of programs for SNP annotation. It uses a program called netoglyc and predicts O-glycosylation sites in mammalian protein on amino acid http://www.cbs.dtu.dk/services/NetOGlyc/
if the 2 alleles of a protein show a different signal then there is loss or gain of signal.
if allele1 has a prediction and allele2 doesn't, then there is loss of signal.
if allele2 has a prediction and allele1 doesn't, then there is gain of signal.
......
......@@ -30,13 +30,7 @@ __synopsis__ = "getNbAllAllelesFromVcf.py INPUT --output OUTPUT"
__date__ = "02/2015"
__authors__ = "Claire Hoede"
__keywords__ = "genotype, vcf, reads for each alleles"
__description__ = """Write a tabulated file with count
of each read for each alternative allele whatever the alleles number.
The objective is to import the file in R to compute real alleles frequencies.
Columns in the output file will be
#chrom #pos #nbAlt #DPTotal #nbRef #nbAlt1 ... #nbAltn
WARNING : for this first version your vcf file has to have only one sample
In the output file column not used for a variant is filled by NA"""
__description__ = "Write a tabulated file with count of each read for each alternative allele whatever the alleles number. The objective is to import the file in R to compute real alleles frequencies. Columns in the output file will be #chrom #pos #nbAlt #DPTotal #nbRef #nbAlt1 ... #nbAltn WARNING : for this first version your vcf file has to have only one sample. In the output file column not used for a variant is filled by NA"
def get_args():
"""
......
Command line :
./scripts_to_json.pl ../
./scripts_to_json.pl -d ../bin
1) SI ERREURS DANS LES PODS
génère un fichier wrong_scripts.txt avec la liste des fichiers à corriger
......
......@@ -142,6 +142,17 @@ my $doc_bash = "\n\nEXAMPLE OF DOCUMENTATION FOR BASH SCRIPTS : \
##DESCRIPTION = \"mon_script.sh prints Coucou\"
";
my $doc_R = "\n\nEXAMPLE OF DOCUMENTATION FOR R SCRIPTS : \
##NAME = \"mon_script.R\"
##SYNOPSIS = \"mon_script.R |OPTIONS]\"
##EXAMPLE = \"Rscript mon_script.R > STDOUT\"
##DATE = \"05/2012\"
##AUTHORS = \"Author\"
##KEYWORDS = \"bidule bidou\"
##DESCRIPTION = \"mon_script.R prints Coucou\"
#";
#
if (-s "wrong_scripts.txt"){
`rm -f out.json`;
open (WRONG,">>wrong_scripts.txt");
......@@ -150,6 +161,7 @@ if (-s "wrong_scripts.txt"){
print WRONG $doc_perl;
print WRONG $doc_python;
print WRONG $doc_bash;
print WRONG $doc_R;
close WRONG;
}
......@@ -161,9 +173,9 @@ sub scan_file(){
my $fic=shift;
my $nbfile=shift;
#my $f="${cur_dir}/$fic";
my ($name, $synopsis, $date, $authors, $keywords, $description)=("","","","","","");
my $error_msg="";
$nb_scripts++;
my ($name, $synopsis, $date, $authors, $keywords, $description)=("","","","","","");
my $error_msg="";
$nb_scripts++;
#### PERL FILES########################################################################################
if($fic=~/.*\.pl/){
......@@ -233,13 +245,13 @@ sub scan_file(){
}
if ($_ =~ m/^__description__/g){
($description) = $_ =~ m/__description__ = "([^"]+)"/;
$nb_field++;
$nb_field++;
}
}
if ($nb_field < 6)
{
$error_msg="$fic is wrong\n";
$error_msg="$fic is wrong\n";
}
close FIC;
}
......@@ -353,7 +365,6 @@ sub scan_file(){
sub write_sections($$){
my $name = shift;
my $synopsis = shift;
my $date = shift;
my $authors = shift;
......@@ -396,7 +407,7 @@ scrips_to_json.pl
=head1 DESCRIPTION
Writes a JSON file from a file or a directory passed in parameter.
Works with PERL, PYTHON and BASH scripts.
Works with PERL, PYTHON, BASH and R scripts.
If your script(s) is/are not well documented, the file wrong_scripts.txt is created and contains bad scripts.
If not, a JSON file containing documentation elements is created.
......
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