Add new script and some update

bin/blat_parser.pl

@@ -4,8 +4,9 @@ use strict;
 use Pod::Usage;
 use Getopt::Long;
 
-my ($man, $help, $nb_best);
+my ($man, $help, $focus, $nb_best);
 GetOptions(
+	'f=s'  => \$focus,
 	'b=i'  => \$nb_best,
 	'help' => \$help,
 	'man'  => \$man,
@@ -14,18 +15,16 @@ GetOptions(
 pod2usage(1) if ($help);
 pod2usage(-exitstatus => 0, -verbose => 2) if ($man);
 pod2usage(-exitstatus => 0, -verbose => 1) if (-t);
+$focus ||= 'q';
 $nb_best ||= 1;
 
 my (%option, $line);
-do {
-	$line = <STDIN>;
-} until $line =~ /^\d+/;
-
 $option{'m'} = 1;
 $option{'p'} = pslIsProtein($line) || 0;
 
 my %h;
-while ($line) {
+my $f = $focus eq 'q' ? 9 : 13;
+while ($line = <STDIN>) {
 	next unless ($line =~ /^\d+/);
 	my @t = split(/\t/,$line);
 	my $pid = sprintf("%.1f",get_pid(@t));
@@ -33,29 +32,28 @@ while ($line) {
 	$t[15] += 1;
 	my $Qcov = sprintf("%.1f%",(abs($t[12]-$t[11])-$t[5]+1)/$t[10]*100);
 	my $Tcov = sprintf("%.1f%",(abs($t[16]-$t[15])-$t[7]+1)/$t[14]*100);
-	my @list = (get_score(@t),$t[11],$t[12],$t[10],$Qcov,$pid.'%',$t[8],$t[13],$t[15],$t[16],$t[14],$Tcov,$t[4],$t[5],$t[6],$t[7]);
-	if (exists($h{$t[9]})) {
-		scalar(@{$h{$t[9]}}) == $nb_best ? push_if_better(\@{$h{$t[9]}}, \@list) : push_and_sort(\@{$h{$t[9]}},\@list);
+	my @list = ($t[9],get_score(@t),$t[11],$t[12],$t[10],$Qcov,$pid.'%',$t[8],$t[13],$t[15],$t[16],$t[14],$Tcov,$t[4],$t[5],$t[6],$t[7]);
+	if (exists($h{$t[$f]})) {
+		scalar(@{$h{$t[$f]}}) == $nb_best ? push_if_better(\@{$h{$t[$f]}}, \@list) : push_and_sort(\@{$h{$t[$f]}},\@list);
 	}
 	else {
-		push(@{$h{$t[9]}},\@list);
+		push(@{$h{$t[$f]}},\@list);
 	}
-	$line = <STDIN>;
 }
 
 print join("\t",qw(qName score qStart qEnd qSize qCoverage identity strand tName tStart tEnd tSize tCoverage qNumInsert qBaseInsert tNumInsert tBaseInsert))."\n";
 
 foreach my $seq (sort keys %h) {
 	foreach my $match (@{$h{$seq}}) {
-		print join("\t",$seq,@$match)."\n";
+		print join("\t",@$match)."\n";
 	}
 }
 
 sub push_if_better {
 	my ($first, $second) = @_;
-	return unless (${$$first[-1]}[0] < $$second[0]);
+	return unless (${$$first[-1]}[1] < $$second[1]);
 	$$first[-1] = $second;
-	my @t = sort { $$b[0] <=> $$a[0] } @$first;
+	my @t = sort { $$b[1] <=> $$a[1] } @$first;
 	@$first = @t;
 	return;
 }
@@ -63,7 +61,7 @@ sub push_if_better {
 sub push_and_sort {
 	my ($first, $second) = @_;
 	push(@$first, $second);
-	my @t = sort { $$b[0] <=> $$a[0] } @$first;
+	my @t = sort { $$b[1] <=> $$a[1] } @$first;
 	@$first = @t;
 	return;
 }
@@ -183,9 +181,13 @@ sub pslIsProtein {
     
  Prints the manual page and exits.
     
+=item B<-f>
+    
+ Focus best matches extraction on query (q) or target (t) [q]
+
 =item B<-b>
     
- Max number of best matches to print for each query [1]
+ Max number of best matches to extract [1]
 
 =back
 
@@ -203,7 +205,7 @@ sub pslIsProtein {
 
 =head1 VERSION
 
- 1
+ 2
 
 =head1 DATE
 

bin/build_matrix_from_CXreport.py

@@ -58,10 +58,10 @@ for line in f :
         if previous_strand != strand and int(previous_pos)+1 == int(pos) and int(previous_c_met)>0:
             C_previous_m=float(float(previous_c_met)/(float(previous_c_met)+float(previous_c_unmet))*100)
             C_m=float(float(c_met)/(float(c_met)+float(c_unmet))*100)
-            if previous_strand == "+" :
+            if previous_strand != strand :
                 N_values_forward.append(C_previous_m)
-            else :
-                N_values_reverse.append(C_previous_m)
+                N_values_reverse.append(C_m)
+
             fout.write( "\t".join([previous_pos,str(C_previous_m),str(C_m),previous_strand])+"\n" )
             
     (previous_chr,previous_pos,previous_strand,previous_c_met,previous_c_unmet,previous_c_context)=(chr,pos,strand,c_met,c_unmet,c_context)
@@ -72,4 +72,4 @@ else :
     N_values_reverse.append(C_previous_m)    
 
 print "Correlation on forward VS reverse values : " + str(pearsonr(N_values_forward,N_values_reverse))
-fout.close()
\ No newline at end of file
+fout.close()

bin/colstat.sh

+#!/bin/sh
+
+##NAME = "colstat.sh" 
+##SYNOPSIS = "colstat.sh [-h] [INT(default 1)]" 
+##DATE = "2012"
+##AUTHORS = "Jean Marc Aury, Genoscope CEA. Maria Bernard"
+##KEYWORDS = "compute statistcs on integer column"
+##DESCRIPTION = "colstat index_col"
+
+
+pg=`basename $0`
+
+usage() {
+    echo USAGE :
+    echo "       $pg <field number : int>"
+    echo "       Return statistics from a set of value (stdin). Optionnal argument is the field where to find the dataset, 1 by default."
+    exit 1
+}
+
+field=1
+
+while [ $1 ]
+do
+    case $1 in
+      "-h") usage ;;
+      *) field=$1 ;;
+    esac 
+    shift
+done
+
+gawk -v field=$field '
+
+BEGIN {
+  if(field=="") { field=1; }
+}
+
+NF<field {
+  printerr("Not enough field : NF="NF" and field="field"\n");
+  exit;
+}
+
+NF>0 {
+  n++;
+  s+=$field;
+  a[n]=$field;
+
+}
+
+n==1 { 
+  min=$field;
+  max=$field; 
+}
+
+
+NF>0 {
+  if ($field<min) min=$field;
+  if ($field>max) max=$field;
+}
+
+
+END {
+  # Calcul de la moyenne
+  mean=0;
+  if(n > 0) { mean=s/n ; }
+
+  # calcul de l ecart type
+  for (i=1; i<=n; i++ ) {
+    x=a[i];
+    sum_ecart += ( (x-mean) * (x-mean ) )
+  }   
+  SD=0;
+  if(n>0) { SD=sqrt(sum_ecart / n) ; }
+
+  # calcul de la mediane
+  nbelem = asort(a);
+  med = a[int((nbelem+1)/2)];
+
+  printf("%s %d   %s %d   %s %.2f   %s %.2f   %s %.2f   %s %.2f   %s %.2f\n",   "Nombre=",n,"Somme=",s,"Moyenne=",mean,"SD=",SD,"max=",max, "min=", min, "Mediane=", med);
+}
+
+
+function printerr(message) {
+  printf("%s\n", message) > "/dev/fd/2";
+}'

bin/count_unique_seq.pl

+#!/usr/bin/perl
+use strict;
+use warnings;
+use Getopt::Long;
+use Pod::Usage;
+
+my %options;
+
+Getopt::Long::Configure("no_ignorecase");
+Getopt::Long::Configure("bundling");
+GetOptions(	\%options,
+	'fasta=s',     # fasta file
+	'fastq=s',     # fastq file
+	'output',      # write sequences ?
+	'help|h',      # help
+        ) or pod2usage(-verbose => 1);
+
+pod2usage(-verbose => 1,-noperldoc => 1) if (exists $options{'help'});
+pod2usage(-message => "A fasta or fastq file must be provided !",-verbose => 1) if (! exists $options{'fasta'} && ! exists $options{'fastq'});
+
+# Main
+my %h;
+
+if (exists $options{'fasta'}){
+    open FASTA,$options{'fasta'};
+    while(<FASTA>){
+        next if (/^>/);
+        chomp;
+        if (exists $h{$_}){
+            $h{$_}++;
+        }
+        else{
+            $h{$_}=1;
+        }
+    }
+    close FASTA;
+}
+
+if (exists $options{'fastq'}){
+    open FASTQ,$options{'fastq'};
+    while(<FASTQ>){
+        chomp;
+        next if not ($_ =~ /^[actgnACTGN]+$/);
+        if (exists $h{$_}){
+            $h{$_}++;
+        }
+        else{
+            $h{$_}=1;
+        }
+    }
+    close FASTQ;
+}
+
+
+
+if (exists $options{'output'}){
+    foreach my $k (keys %h){
+        print $k,"\t",$h{$k},"\n";
+    }
+}
+else{
+    my $nbr = keys (%h);
+    print $nbr;
+}
+
+=pod
+
+=head1 NAME
+
+count_unique_seq.pl
+
+=head1 SYNOPSIS
+
+count_unique_seq.pl [--fasta FILE] [--fastq FILE] [--output] [--help]
+
+=head1 DESCRIPTION
+
+count_unique_seq.pl counts the number of unique sequences (remove redundancy)
+outputs sequences and their occurences if --output
+
+=head1 AUTHORS
+
+Olivier Rue
+
+=head1 VERSION
+
+1
+
+=head1 DATE
+
+05/2013
+
+=head1 KEYWORDS
+
+count sequences unique fasta fastq
+
+=head1 EXAMPLE
+
+perl count_unique_seq.pl --fasta myfile.fa
+
+=cut
+

bin/distrib_class.sh

+#!/bin/sh
+
+##NAME = "distrib_class.sh" 
+##SYNOPSIS = "distrib_class.sh [-h] [<SIZE_OF_BIN>INT(default 10)] [<COLUMN_INDEX>INT(default 1)]" 
+##DATE = "2012"
+##AUTHORS = "Jean Marc Aury, Genoscope CEA. Maria Bernard"
+##KEYWORDS = "compute histogram distribution on integer column"
+##DESCRIPTION = "distrib_class.sh <window : int> <field number : int>"
+
+pg=`basename $0`
+
+usage() {
+    echo USAGE :
+    echo "       $pg <window : int> <field number : int> <field value : int>"
+    echo "       Return a bin distribution (y axes = number of cases) from a set of values (stdin)"
+    echo "         First argument is the size of the bin, 10 by default"
+    echo "         Second argument is the field where to find the dataset, 1 by default"
+    echo "         Third argument is the field of the value for each element, none by default"
+    exit 1
+}
+
+
+WIN=
+FIELD=
+FVALUE=
+
+while [ $1 ]
+do
+    case $1 in
+      "-h") usage ;;
+      *) if [ "$WIN" = "" ]; then WIN=$1; elif [ "$FIELD" = "" ]; then FIELD=$1; else FVALUE=$1; fi ;;
+    esac 
+    shift
+done
+
+gawk -v win=$WIN -v field=$FIELD -v fvalue=$FVALUE 'BEGIN { if(win=="") { win=10; } if(field == "") { field=1; } mul=1; while(win < 1) { win=win*10; mul=mul*10; }} { value = 1; if(fvalue != "") { value = $(fvalue); } offset=1; if(val < 0) { offset = -1; } val = int($field*mul); if(val%win ==0 ) { idp[val]+=value; idp2[val]++; } else { idp[int((val/win)+offset)*win]+=value; idp2[int((val/win)+offset)*win]++; } tot++; } END{ for(i in idp) { if(fvalue == "") { idp2[i]=1; } print i/mul, idp[i]/idp2[i]; } }' | sort -k1,1n

bin/distrib_class_percent.sh

+#!/bin/sh
+
+##NAME = "distrib_class_percent.sh" 
+##SYNOPSIS = "distrib_class_percent.sh [-h] [<SIZE_OF_BIN>INT(default 10)] [<COLUMN_INDEX>INT(default 1)]" 
+##DATE = "2012"
+##AUTHORS = "Jean Marc Aury, Genoscope CEA. Maria Bernard"
+##KEYWORDS = "compute histogram distribution on integer column transform in proportion (percent)"
+##DESCRIPTION = "distrib_class_percent <window : int> <field number : int>"
+
+
+pg=`basename $0`
+
+usage() {
+    echo USAGE :
+    echo "       $pg <window : int> <field number : int>"
+    echo "       Return a bin distribution (y axes = % of cases) from a set of values (stdin)"
+    echo "         First argument is the size of the bin, 10 by default"
+    echo "         Second argument is the field where to find the dataset, 1 by default"
+    exit 1
+}
+
+WIN=
+FIELD=
+
+while [ $1 ]
+do
+    case $1 in
+      "-h") usage ;;
+      *) if [ "$WIN" = "" ]; then WIN=$1; else FIELD=$1; fi ;;
+    esac 
+    shift
+done
+
+gawk -v win=$WIN -v field=$FIELD 'BEGIN { if(win=="") { win=10; } if(field == "") { field=1; } mul=1; while(win < 1) { win=win*10; mul=mul*10; }} { offset=1; if(val < 0) { offset = -1; } val = int($field*mul); if(val%win == 0 ) { idp[val]++; } else { idp[int((val/win)+offset)*win]++; } tot++; } END{ for(i in idp) { print i/mul, (idp[i]/tot)*100; } }' | sort -k1,1n

bin/extract_variants_from_VCF.pl

+#!/usr/bin/perl
+#use strict;
+use warnings;
+use Getopt::Long;
+use Pod::Usage;
+my %options;
+my %h_type = (
+    'SNP'       => 1,
+    'INDEL'     => 1,
+);
+
+Getopt::Long::Configure("no_ignorecase");
+Getopt::Long::Configure("bundling");
+GetOptions(\%options,
+	'man',
+	'h|help',
+	'f|file=s',
+	't|type=s',
+	'o|output=s'
+)
+or pod2usage(-verbose => 1);
+
+pod2usage(-verbose => 2) if (exists $options{'man'});
+pod2usage(-verbose => 1) if (exists $options{'h'});
+pod2usage(-message => "Please provide A VCF file ! (-f)",-verbose => 1) if (! exists $options{'f'});
+pod2usage(-message => "Please specify if you want to extract SNP or INDEL ! (-t)",-verbose => 1) if (! exists($options{'t'}) || ! exists $h_type{$options{'t'}});
+#pod2usage(-message => "Please specify the output file ! (-o)",-verbose => 1) if (! exists $options{'o'});
+
+
+
+my $output = *STDOUT;
+my $file=$options{'f'};
+my $type=$options{'t'};
+
+if (exists ($options{'o'})){
+	$output = $options{'o'};
+	open($output, ">$output") or die "can't open $output: $!\n";
+}
+
+
+my @line;
+
+open FILE,$file or die "Cannot open file $file\n";
+while(<FILE>){
+	chomp();
+	if(/^#/){
+		print $output $_,"\n";
+		next;
+	}
+	# SNP case
+	if ($type eq 'SNP'){
+		@line = split(/\s/,$_);
+		if ( (length($line[3]) == 1 && length($line[4]) == 1) || (length($line[3]) == 1 && $line[4] =~ m/[ACGT],[ACGT]/ && length($line[4]) == 3) ){
+			for (my $i=0;$i<=2;$i++){
+				print $output $line[$i],"\t";
+			}
+			for (my $i=3;$i<scalar(@line)-1;$i++){
+				print $output $line[$i],"\t";
+			}
+			print $output $line[scalar(@line)-1],"\n";
+		}
+		else{
+			next;
+		}
+	}
+	# INDEL case
+	else {
+		@line = split(/\s/,$_);
+		next if ( (length($line[3]) == 1 && length($line[4]) == 1) || (length($line[3]) == 1 && $line[4] =~ m/[ACGT],[ACGT]/ && length($line[4]) == 3) );
+		for (my $i=0;$i<=2;$i++){
+			print $output $line[$i],"\t";
+		}
+		for (my $i=3;$i<scalar(@line)-1;$i++){
+			print $output $line[$i],"\t";
+		}
+		print $output $line[scalar(@line)-1],"\n";
+	}
+}
+
+close FILE;
+
+
+=pod
+
+=head1 NAME
+
+extract_variants_from_VCF.pl
+
+=head1 SYNOPSIS
+
+extract_variants_from_VCF.pl -f FILE -t [SNP|INDEL] [options]
+
+=head1 OPTIONS
+
+-o <FILE>	: output FILE
+
+=head1 DESCRIPTION
+
+Extracts SNP or INDEL from a VCF file.
+
+=head1 AUTHORS
+
+Olivier Rue
+
+=head1 VERSION
+
+1
+
+=head1 DATE
+
+06/2012
+
+=head1 KEYWORDS
+
+VCF, extract, SNP, INDEL, variants
+
+=head1 EXAMPLE
+
+./extract_variants_from_VCF.pl -f snp_and_indel.vcf -t SNP -o only_snp.vcf
+
+=cut

bin/fasta_split.pl

@@ -2,6 +2,8 @@
 
 use Pod::Usage;
 use Getopt::Long;
+use FindBin;
+use lib $FindBin::RealBin;
 use bioutils;
 
 BEGIN

bin/final_count_file.pl

@@ -10,8 +10,8 @@ final_count.pl
 
 final_count.pl [options] 
 -arg1 <Path to genome bowtie2bd fasta file (/bank2/bowtie2db/genome.fa)> 
--arg2<Path to your merged.gtf file> 
--arg3<Path to your project> 
+-arg2 <Path to your merged.gtf file> 
+-arg3 <Path to your project> 
 
 =head1  OPTIONS
 

bin/length_histogram.py

@@ -3,6 +3,7 @@
 from Bio import SeqIO
 import sys
 import string
+import math
 import matplotlib.mlab as mlab
 import matplotlib.pyplot as plt
 from optparse import *
@@ -15,9 +16,11 @@ __keywords__ = "fasta histogram length"
 __description__ = "This script generate a histogram of the length of the sequences."
 __version__ = '1.0'
 
-parser = OptionParser(usage="Usage: length_histogram.py -i FILE ")
+parser = OptionParser(usage="Usage: length_histogram.py -i FILE -l")
 parser.add_option("-i", "--in", dest="fasta_file",
                   help="The fasta file", metavar="FILE")
+parser.add_option("-l", "--log", action="store_true", dest="log",
+                  help="Log10 x axis")
 (options, args) = parser.parse_args()
 
 if options.fasta_file == None :
@@ -25,12 +28,16 @@ if options.fasta_file == None :
     sys.exit(1)
 else :
 
-	x = []
-	for seq_record in SeqIO.parse(open(options.fasta_file, "rU"), "fasta") :
-		x.append(len(seq_record.seq.tostring()))
+    x = []
+    if options.log == None :
+        for seq_record in SeqIO.parse(open(options.fasta_file, "rU"), "fasta") :
+            x.append(len(seq_record.seq.tostring()))
+    else :
+        for seq_record in SeqIO.parse(open(options.fasta_file, "rU"), "fasta") :
+            x.append(math.log(len(seq_record.seq.tostring()),10))
 
-	plt.hist(x, 50, facecolor='green', alpha=0.75)
-	plt.grid(True)
-	plt.savefig(options.fasta_file+".lengthhist.png")
-	
-	sys.exit(0)
\ No newline at end of file
+    plt.hist(x, 50, facecolor='green', alpha=0.75)
+    plt.grid(True)
+    plt.savefig(options.fasta_file+".lengthhist.png")
+
+    sys.exit(0)

bin/not_documented/bioutils.pm

+package bioutils;
+
+use strict;
+
+=head1 Description
+
+  Contains some usefull functions such as
+
+=head2 reverse(seq)
+
+  seq is a string, this function returns another string with all characters in reverse order
+
+=head2 complement(seq)
+
+  seq is a flat nucleic acid sequence stored in a string, 
+  this function returns the complement of the sequence (in uppercase)
+
+=head2 translate(seq)
+
+  seq is a flat nucleic acid sequence stored in a string, 
+  this function returns the proteic translation of this sequence (in uppercase)
+
+=head2 fasta2flat(file) fasta2flat(file, AC)
+
+  file is the path of a FASTA formated file.
+  This function returns the first flat sequence of this file or the one with the given 
+  accession number AC (an accession number is a valid identifier WITHOUT internal blanks)
+
+=head2 flat2fasta(file, AC, seq, line_length)
+
+  This function APPENDS a sequence to a FASTA formatted file (file), 
+  creates a header line with AC and formats the sequence (seq) with line_length375
+  characters per lines
+
+=head2 fasta_cut(file, begin, end)
+
+  This function reads a ONE ENTRY FASTA file and return the sub sequence from begin to end
+  
+=head2 fasta_length(file)
+
+  This function reads a ONE ENTRY FASTA file and return the length of the sequence
+
+=head2 flat2gb(file, LOCUS, seq)
+
+  This function CREATE a GenBank formated file containing the sequence