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

petite correction des descriptions

parent eb8c3b9d
...@@ -67,17 +67,17 @@ while (<IN>) { ...@@ -67,17 +67,17 @@ while (<IN>) {
=over =over
=item B<input> =item INPUT
name of the input fastq file. name of the input fastq file.
=item B<--help> =item HELP
Print this usage message. Print this usage message.
=back =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. 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, ...@@ -104,4 +104,4 @@ colorspace, csfasta,
csfastq_to_csfasta.pl my_reads.cut.csfastq > my_reads.cut.csfasta csfastq_to_csfasta.pl my_reads.cut.csfastq > my_reads.cut.csfasta
=cut =cut
\ No newline at end of file
...@@ -2,15 +2,15 @@ ...@@ -2,15 +2,15 @@
=pod =pod
=head1 NAME =head1 NAME
extract_netcglyc_results.pl extract_netcglyc_results.pl
=head1 SYNOPSIS =head1 SYNOPSIS
extract_netcglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <> 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!!! --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") --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 <> ...@@ -19,9 +19,7 @@ extract_netcglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION =head1 DESCRIPTION
extract_netcglyc_results.pl - This program is part of a pipeline of programs for SNP annotation. 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
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 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 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. if allele2 has a prediction and allele1 doesn't, then there is gain of signal.
......
...@@ -2,15 +2,15 @@ ...@@ -2,15 +2,15 @@
=pod =pod
=head1 NAME =head1 NAME
extract_netcglyn_results.pl extract_netcglyn_results.pl
=head1 SYNOPSIS =head1 SYNOPSIS
extract_netcglyn_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <> 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!!! --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") --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 <> ...@@ -20,10 +20,7 @@ extract_netcglyn_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION =head1 DESCRIPTION
extract_netcglyn_results.pl - This program is part of a pipeline of programs for SNP annotation. 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
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 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 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. if allele2 has a prediction and allele1 doesn't, then there is gain of signal.
......
...@@ -2,15 +2,15 @@ ...@@ -2,15 +2,15 @@
=pod =pod
=head1 NAME =head1 NAME
extract_netoglyc_results.pl extract_netoglyc_results.pl
=head1 SYNOPSIS =head1 SYNOPSIS
extract_netoglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <> 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!!! --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") --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 <> ...@@ -20,9 +20,7 @@ extract_netoglyc_results.pl -arg1 <> -arg2 <> -arg3 <> -arg4 <>
=head1 DESCRIPTION =head1 DESCRIPTION
extract_netoglyc_results.pl - This program is part of a pipeline of programs for SNP annotation. 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/
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 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 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. 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" ...@@ -30,13 +30,7 @@ __synopsis__ = "getNbAllAllelesFromVcf.py INPUT --output OUTPUT"
__date__ = "02/2015" __date__ = "02/2015"
__authors__ = "Claire Hoede" __authors__ = "Claire Hoede"
__keywords__ = "genotype, vcf, reads for each alleles" __keywords__ = "genotype, vcf, reads for each alleles"
__description__ = """Write a tabulated file with count __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"
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(): def get_args():
""" """
......
Command line : Command line :
./scripts_to_json.pl ../ ./scripts_to_json.pl -d ../bin
1) SI ERREURS DANS LES PODS 1) SI ERREURS DANS LES PODS
génère un fichier wrong_scripts.txt avec la liste des fichiers à corriger 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 : \ ...@@ -142,6 +142,17 @@ my $doc_bash = "\n\nEXAMPLE OF DOCUMENTATION FOR BASH SCRIPTS : \
##DESCRIPTION = \"mon_script.sh prints Coucou\" ##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"){ if (-s "wrong_scripts.txt"){
`rm -f out.json`; `rm -f out.json`;
open (WRONG,">>wrong_scripts.txt"); open (WRONG,">>wrong_scripts.txt");
...@@ -150,6 +161,7 @@ if (-s "wrong_scripts.txt"){ ...@@ -150,6 +161,7 @@ if (-s "wrong_scripts.txt"){
print WRONG $doc_perl; print WRONG $doc_perl;
print WRONG $doc_python; print WRONG $doc_python;
print WRONG $doc_bash; print WRONG $doc_bash;
print WRONG $doc_R;
close WRONG; close WRONG;
} }
...@@ -161,9 +173,9 @@ sub scan_file(){ ...@@ -161,9 +173,9 @@ sub scan_file(){
my $fic=shift; my $fic=shift;
my $nbfile=shift; my $nbfile=shift;
#my $f="${cur_dir}/$fic"; #my $f="${cur_dir}/$fic";
my ($name, $synopsis, $date, $authors, $keywords, $description)=("","","","","",""); my ($name, $synopsis, $date, $authors, $keywords, $description)=("","","","","","");
my $error_msg=""; my $error_msg="";
$nb_scripts++; $nb_scripts++;
#### PERL FILES######################################################################################## #### PERL FILES########################################################################################
if($fic=~/.*\.pl/){ if($fic=~/.*\.pl/){
...@@ -233,13 +245,13 @@ sub scan_file(){ ...@@ -233,13 +245,13 @@ sub scan_file(){
} }
if ($_ =~ m/^__description__/g){ if ($_ =~ m/^__description__/g){
($description) = $_ =~ m/__description__ = "([^"]+)"/; ($description) = $_ =~ m/__description__ = "([^"]+)"/;
$nb_field++; $nb_field++;
} }
} }
if ($nb_field < 6) if ($nb_field < 6)
{ {
$error_msg="$fic is wrong\n"; $error_msg="$fic is wrong\n";
} }
close FIC; close FIC;
} }
...@@ -353,7 +365,6 @@ sub scan_file(){ ...@@ -353,7 +365,6 @@ sub scan_file(){
sub write_sections($$){ sub write_sections($$){
my $name = shift; my $name = shift;
my $synopsis = shift; my $synopsis = shift;
my $date = shift; my $date = shift;
my $authors = shift; my $authors = shift;
...@@ -396,7 +407,7 @@ scrips_to_json.pl ...@@ -396,7 +407,7 @@ scrips_to_json.pl
=head1 DESCRIPTION =head1 DESCRIPTION
Writes a JSON file from a file or a directory passed in parameter. 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 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. If not, a JSON file containing documentation elements is created.
......
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