petite correction des descriptions

bin/csfastq_to_csfasta.pl

@@ -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

bin/extract_netcglyc_results.pl

@@ -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.

bin/extract_netnglyc_results.pl

@@ -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.

bin/extract_netoglyc_results.pl

@@ -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.

bin/getNbAllAllelesFromVcf.py

@@ -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():
 	"""

doc/README

 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

doc/scripts_to_json.pl

@@ -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.