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"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit fb4c29f720748f46ff501140f2cd306bab6614f9"
author nml
date Fri, 29 May 2020 13:51:50 -0400
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ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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1 #!/usr/bin/env perl
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3 #==============================================================================================
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5 # Script to output statistsics and histograms for reads and contigs/isotigs
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8 # Outputs include:
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9 # Mean, N50, StdDev or reads or contig lengths,
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10 # Mean and Modal read or contig lengths.
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11 # Number of reads or contigs > 1 kb in length
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12 # Summed contig length (by number of contigs, in sorted order)
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13 # Histogram of read or contig lengths,
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14 # Graph of sums of read-lengths
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15 # File of reads or contigs sorted by read or contig length
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16 # Test for mono/di-nucelotide repeats
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17 # Randomly selected reads or contigs
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20 # Needs gnuplot installed to create the histograms:
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21 # On Fedora/Redhat linux: sudo yum install gnuplot
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22 # On Ubuntu/Debian: sudo apt-get install gnuplot
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24 # Uses a linux pipe to call gnu-plot directly, rather than as a separate shell script.
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26 # Original written by Sujai Kumar, 2008-09-05 University of Edinburgh
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27 # Modified by Stephen: 29-Apr-2009:
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28 # Last changed by Stephen: 9-Aug-2010
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31 # Usage: fasta_summary.pl -i infile.fasta -o process_reads -t read OR contig OR isotig (to use 'read' or 'contig' or 'isotig' in the output table & graphs. Isotig is for 'runAssembly -cdna ...' output file '454Isotigs.fna') [-r 1 to indicate count simple nucleotide repeats] [-n number of random reads to output] [-c cutoff_length] [-l 1 to indicate output the longest read] [-f (s or t or w) for spacer, tab or wiki format table output.]
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33 # Note: The parameters above in the [] are optional.
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35 # eg: fasta_summary.pl -i myfile.fasta -o process_reads -t read
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36 # Where:
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37 # -i reads or contigs as input, in fasta format.
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38 # -o output_dir (created if it doesn't exist)
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39 # -t read, contig or isotig
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41 # Gives back
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42 # - N50
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43 # - num of contigs > 1 kb
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44 # - num of contigs
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45 # - Read or Contig Histogram and graphs.
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46 # - Summed contig length (by number of contigs, in sorted order)
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48 #==============================================================================================
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51 use strict;
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52 use warnings;
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53 use Getopt::Long;
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55 my $infile;
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56 my $output_dir;
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57 my $type='read'; # Defaults to 'read' at present
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58 my $repeats=1;
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59 my $num_random_reads_to_output=0;
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60 my $cutoff_length=-1; # -1 means won't check this cutoff
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61 my $longest_read=-1; # -1 mean's don't output the sequence for the longest read.
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62 my $doCommify=1; # Outputs statistics numbers in format: 9,999,999
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63 my $format="t"; # "s"=spaces between columns, "t"=tabs between columns, "w"=wiki '||' and '|'.
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64 my $bucket1=0; # For optional exact length histogram distribution as asked for by JH.
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66 if ($#ARGV==-1) {die "
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67 Usage:
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69 fasta_summary.pl -i infile.fasta -o output_dir -t ( read | contig | isotig ) [ -r 0 ] [ -n num_reads ] [ -c cutoff_length ] [ -l 1 ] [ -d 0 ] [ -f (w | t ) ] [ -bucket1 ]
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71 where:
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73 -i or -infile infile.fasta : input fatsa file of raeds, contigs or isotigs,
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75 -o or -output_dir output_directory : directory to put output stats and graphs into.
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77 -t or -type (read or contig or isotig) : for displaying the graph title, where type is 'read' or 'contig' or 'isotig'.
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79 -r or -repeats 0 or 1 : 1=count number of reads that contain over 70% simple mono-nucleotide and di-nucleotide repeat bases; 0=don't count.
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81 -n or -number num_reads : For outputting specified number of randomly selected reads or contigs.
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83 -c or -cutoff cutoff_length : Give a number of reads to do extra analysis (calculating again the number of reads and number of bases in reads above this length)
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85 -l or -longest 0 or 1 : 1=Output the longest read; 0= don't output the longest read
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87 -d or -doCommify 0 or 1 : Output numbers formatted with commas to make easier to read: 0=no commas, default=1
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89 -f or -format w or t : w=wiki_format (ie. table with || and | for column dividers), t=tabs between column symbols for the wiki pages, default is spaces between columns.
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91 -b or -bucket1 : To also output histogram file of exact read lengths (ie. bucket size of 1)
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94 eg: For 454 reads: fasta_summary.pl -i RawReads.fna -o read_stats -t read
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95 For 454 isotigs: fasta_summary.pl -i 454Isotigs.fna -o isotig_stats -t isotig
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96
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97 ";}
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98
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99 GetOptions (
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100 "infile=s" => \$infile,
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101 "output_dir=s" => \$output_dir,
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102 "type=s" => \$type, ## type is 'read' or 'contig' or 'isotig' - for displaying the graph title
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103 "repeats=i" => \$repeats, # To count simple repeats
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104 "number=i" => \$num_random_reads_to_output, # For outputting specified number of random reads
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105 "cutoff=i" => \$cutoff_length, # Give a number of reads to do extra analysis (calculating again the number of reads and number of bases in reads above this length)
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106 "longest=i" => \$longest_read, # Output the longest read.
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107 "doCommify=i" => \$doCommify, # Output numbers formatted with commas to make easier to read: 0=no commas, default=1
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108 "format=s" => \$format, # "w"=wiki_format (ie. table with || and | for column dividers), "t"=tabs between column symbols for the wiki pages, default is spaces between columns.
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109 "bucket1" => \$bucket1, # To also output histogram file of exact read lengths (ie. bucket size of 1)
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110 );
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111 if ($#ARGV>-1) {die "Unused options specified: @ARGV\n";}
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112 if ( (! defined $infile) || ($infile eq '') ) {die "\nPlease give input fasta file, preceeded by the '-i' option\n\n";}
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113 if ( (! defined $output_dir) || ($output_dir eq '') ) {die "Please give output_directory, preceeded by the '-o' option\n\n";}
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114 if ( (! defined $type) || (($type ne 'contig') && ($type ne 'read') && ($type ne 'isotig')) ) {die "ERROR: On commandline: -t type must be 'contig' or 'read' or 'isotig'\n\n";}
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115
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116
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117 my ($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab);
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118 if ($format eq 's') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=('',' ','', '',' ','', "\n",'');}
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119 elsif ($format eq 't') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=("\t","\t",'', "","\t",'', "\n",'');} # There is correctly a tab for the $L, but not the $Lh.
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120 elsif ($format eq 'w') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=('| ',' | ',' |', '|| ',' || ',' ||', '|| ',' || ');}
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121 else {die "\nInvalid output format code: '$format'. Should be 's', 't' or 'w'.\n\n";}
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122
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123 ### create output_dir if it doesn't exist
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124 if (-d $output_dir) {
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125 print STDERR " Directory '$output_dir' exists, so the existing fasta_summary.pl output files will be overwritten\n";
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126 } else {
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127 mkdir $output_dir;
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128 print STDERR " Directory '$output_dir' created\n";
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129 }
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130
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131 my $gc_count = 0;
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132
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133 #--------------- Read in contigs from fasta file -------------------
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134
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135 open INFILE, "<$infile" or die "Failed to open file: '$infile' : $!";
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136 open STATS, ">$output_dir/stats.txt" or die "Failed to open $output_dir/stats.txt: '' : $!";
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137
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138 my $header = <INFILE>;
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139 if (! defined($header) ) {print "\n** ERROR: First line of input fasta file is undefined - so file must be empty **\n\n"; print STATS "No sequences found\n"; exit 1;}
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140 if ($header!~/^>/) {print "\nERROR: First line of input fasta file should start with '>' BUT first line is: '$header'\n"; print STATS "No sequences found\n"; exit 1;}
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141
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142 my $seq = "";
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143 my @sequences;
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144
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145 while (<INFILE>) {
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146 if (/^>/) {
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147 push @sequences, [length($seq), $header, $seq];
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148 $header = $_;
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149 $seq = "";
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150 } else {
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151 chomp;
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152 $gc_count += tr/gcGC/gcGC/;
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153 $seq .= $_;
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154 }
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155 }
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156 push @sequences, [length($seq), $header, $seq];
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157 close INFILE;
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158 if ($#sequences==-1) {print "\nERROR: There are zero sequences in the input file: $infile\n\n"; print STATS "No sequences found\n"; exit 1;}
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159
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160
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161 my $all_contigs_length=0;
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162 foreach (@sequences) {$all_contigs_length += $_->[0];}
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163 if ($all_contigs_length==0) {print "\nERROR: Length of all contigs is zero\n\n"; exit 2;}
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164
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165 # Find number and number of bases in reads greater than the optional cut-off length given at command-line.
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166 my $num_reads_above_cutoff=0;
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167 my $num_of_bases_in_reads_above_cutoff=0;
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168 if ($cutoff_length>0)
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169 {
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170 foreach (@sequences)
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171 {
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172 if ($_->[0]>=$cutoff_length) {$num_of_bases_in_reads_above_cutoff+= $_->[0]; $num_reads_above_cutoff++;}
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173 }
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174 }
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175
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176
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177 #--------------- Gather Plots Data, Find N50, Print sorted contig file -------------------
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178
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179 my $summed_contig_length = 0;
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180 my @summed_contig_data; # <-- For graph of summed length (in number of bases) versus number of contigs.
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181 my @summed_contig_data_contigLens; # <-- Added by SJBridgett to get graph of summed contig length versus min. contig length included (ie. X-axis is sort of inverse of above)
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182
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183 my $contig1k_count = 0;
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184 my $contig1k_length = 0;
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185
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186 open SORTED, ">$output_dir/sorted_contigs.fa" or die $!;
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187
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188 # top row in stats file
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189 #print STATS "N50\nMax contig size\nNumber of bases in contigs\nNumber of contigs\nNumber of contigs >=1kb\nNumber of contigs in N50\nNumber of bases in contigs >=1kb\nGC Content of contigs\n";
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190
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191 my $N50size=-1;
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192 my $N50_contigs = 0;
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193
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194 my @sorted_by_contig_length = sort {$b->[0] <=> $a->[0]} @sequences;
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195
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196 ### variables and initialization for histogram (stored in @bins)
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197 my $max = $sorted_by_contig_length[0][0];
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198 my $mean= $all_contigs_length/($#sequences+1); # <-- Added by Stephen Bridgett. Note: as $# gives the highest index number, so add 1 as arrays are zero-based.
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199
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200 # Calculate standard deviation
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201 my $sumsquares = 0;
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202 foreach (@sequences) {$sumsquares += ($_->[0] - $mean) ** 2;} # <-- Taken from John's "mean_fasta_length.pl" script.
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203 my $stddev = ( $sumsquares/($#sequences+1) ) ** 0.5;
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204
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205 my $min = 0;
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206 # Aim for approximately 100 bins, so
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207
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208 my $bin_size=1;
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209 my $min_max_range=$max - $min;
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210 # $bin_size = ($min_max_range)/(99); # (99 is 100-1) so 1000/100
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211 if ($min_max_range>=100000000) {$bin_size=1000000;}
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212 elsif ($min_max_range>=10000000) {$bin_size=100000;}
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213 elsif ($min_max_range>=1000000) {$bin_size=10000;}
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214 elsif ($min_max_range>=100000) {$bin_size=1000;}
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215 elsif ($min_max_range>=10000) {$bin_size=100;}
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216 else {$bin_size=10;} # elsif ($min_max_range>=1000) {$bin_size=10;}
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217 #elsif ($min_max_range>=100) {$bin_size=1;}
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218 #elsif ($min_max_range>=10) {}
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219 #elsif ($min_max_range>=1) {}
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220 # WAS: my $bin_size = ($type eq 'contig') ? 1000 : 10;
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221
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222 my @bins;
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223 $#bins = int(($min_max_range)/$bin_size) + 1; # <-- Set the bins array size.
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224 foreach (@bins) {$_ = 0};
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225
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226 foreach (@sorted_by_contig_length) {
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227
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228 my $curr_contig_length = $_->[0];
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229 push @summed_contig_data_contigLens, $curr_contig_length; # <-- added by Stephen.
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230
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231 $bins[int(($curr_contig_length + 1 - $min)/$bin_size)]++;
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232
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233 $summed_contig_length += $curr_contig_length;
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234 push @summed_contig_data, $summed_contig_length;
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235
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236 ### sorted contigs file
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237 print SORTED $_->[1] . $_->[2] . "\n";
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238
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239 if ($curr_contig_length >= 1000) {
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240 $contig1k_count++;
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241 $contig1k_length += $curr_contig_length;
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242 }
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243
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244 $N50_contigs++ unless ($N50size>-1); # Was unless $N50_found
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245
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246 if ($summed_contig_length > ($all_contigs_length / 2) and $N50size == -1) {
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247 $N50size = $curr_contig_length;
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248 }
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249 }
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250
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251
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252 if ($bucket1!=0)
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253 {
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254 =pod
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255 # This firsdt method works and agress with the second, but the lengths are in reverse order, at the @sorted_by_contig_length array was sorted with longest contig first.
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256 open BUCKET1, ">$output_dir/lengths_hist1.txt" or die "Failed to open file '$output_dir/lengths_hist1.txt' : $!\n";
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257 print BUCKET1 "Length\tFrequency\n";
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258 my $len=-1;
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259 my $count=0;
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260 foreach (@sorted_by_contig_length)
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261 {
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262 if ( $len != $_->[0] ) {if ($len>-1) {print BUCKET1 "$len\t$count\n";} $len=$_->[0]; $count=0;}
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263 $count++;
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264 }
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265 if ($len>-1) {print BUCKET1 "$len\t$count\n";} # Print length of final length grouping.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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266 close BUCKET1;
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267 =cut
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268 open BUCKET1, ">$output_dir/lengths_hist1_with_zeros.txt" or die "Failed to open file '$output_dir/lengths_hist1_with_zeros.txt' : $!\n";
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269 print BUCKET1 "Length\tFrequency\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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270 my @bucket=(); # To check the result by using array.
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271 foreach (@sequences)
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272 {
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273 my $len=$_->[0];
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274 if (defined $bucket[$len]) {$bucket[$len]++;}
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275 else {$bucket[$len]=1;}
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276 }
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277 for (my $i=0; $i<=$#bucket; $i++)
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278 # for (my $i=$#bucket; $i>=0; $i--) # <-- for reverse order
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279 {
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280 if (defined $bucket[$i]) {print BUCKET1 "$i\t$bucket[$i]\n";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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281 else {print BUCKET1 "$i\t0\n";} # Can uncomment this later if don't want zeros in the output.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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282 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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283 close BUCKET1;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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284 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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285
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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286
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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287 my $type_plural=$type.'s';
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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288 print STATS $Lh."Statistics for $type lengths:".$Mhnotab.$Rh."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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289 print STATS $L."Min $type length:".$M.&commify_if($sorted_by_contig_length[$#sequences][0],$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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290 print STATS $L."Max $type length:".$M.&commify_if($max,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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291 printf STATS $L."Mean %s length:".$M."%.2f".$R."\n", $type,$mean; # <-- Added by Stephen Bridgett, April 2009.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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292 printf STATS $L."Standard deviation of %s length:".$M."%.2f".$R."\n", $type,$stddev; ## <-- Added by Stephen Bridgett, May 2009.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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293 print STATS $L."Median $type length:".$M.&commify_if($sorted_by_contig_length[int($#sequences/2)][0],$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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294 print STATS $L."N50 $type length:".$M.&commify_if($N50size,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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295
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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296 print STATS $Lhnewline."Statistics for numbers of $type_plural:".$Mhnotab.$Rh."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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297 print STATS $L."Number of $type_plural:".$M.&commify_if($#sequences+1,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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298 print STATS $L."Number of $type_plural >=1kb:".$M.&commify_if($contig1k_count,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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299 print STATS $L."Number of $type_plural in N50:".$M.&commify_if($N50_contigs,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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300
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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301 print STATS $Lhnewline."Statistics for bases in the $type_plural:".$Mhnotab.$Rh."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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302 print STATS $L."Number of bases in all $type_plural:".$M.&commify_if($all_contigs_length,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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303 print STATS $L."Number of bases in $type_plural >=1kb:".$M.&commify_if($contig1k_length,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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304 printf STATS $L."GC Content of %s:".$M."%.2f %%".$R."\n", $type_plural,(100*$gc_count/$all_contigs_length);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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305
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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306 if ($cutoff_length>0)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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307 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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308 print STATS $Lhnewline."Statistics for $type_plural >= $cutoff_length bp in length:".$Mhnotab.$Rh."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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309 print STATS $L."Number of $type_plural >= $cutoff_length bp:".$M.&commify($num_reads_above_cutoff,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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310 print STATS $L."\tNumber of bases in $type_plural >= $cutoff_length bp:".$M.&commify($num_of_bases_in_reads_above_cutoff,$doCommify).$R."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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311 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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312
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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313 if ($repeats==1) {&countRepeats();}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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314
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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315 print STATS "\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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316
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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317
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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318 # Output random selection of reads if requested on commandline:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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319 my $fastaLineLen=60; # <-- The line length used for 454 sffinfo output, but could use a value read from input file (but be careful not to read a short line)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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320 if ($num_random_reads_to_output>0)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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321 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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322 my @randlist;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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323 if ($num_random_reads_to_output<($#sequences+1))
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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324 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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325 print STATS "\nSome randomly selected reads:\n\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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326 @randlist= &getListOfRandomNumbers($#sequences, $num_random_reads_to_output); # Don't use ($#sequences + 1), just ($#sequences) otherwise would be outside the array.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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327 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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328 else # Just print all the sequences:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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329 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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330 print STATS "\nAll ".($#sequences+1)." reads:\n\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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331 for (my $i=0;$i<=$#sequences;$i++) {push @randlist,$i;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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332 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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333 &print_sequences(\@randlist)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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334 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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335
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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336
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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337 # Print the longest read:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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338 if ($longest_read>0)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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339 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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340 my $length_of_longest_read=-1;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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341 my @longest_read=();
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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342 my $i=0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
343 foreach (@sequences)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
344 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
345 if ($_->[0]>$length_of_longest_read) {$length_of_longest_read=$_->[0]; $longest_read[0]=$i;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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346 $i++;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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347 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
348 if ($length_of_longest_read>0) {print STATS "\nLongest read:\n"}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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349 &print_sequences(\@longest_read);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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350 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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351
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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352
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
353 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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354 print STATS "\n$type\tSummed\nlength\tlength\n"; # <-- Added by Stephen Bridgett, but better to produce a graph instead.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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355
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
356 my $i=0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
357 foreach (@summed_contig_data) {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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358 # print STATS $sorted_by_contig_length[$i]->[0]."\t".$summed_contig_data_contigLens[$i]."\t".$_."\t".$summed_contig_data[$i]."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
359 print STATS $sorted_by_contig_length[$i]->[0]."\t".$_."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
360 $i++;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
361 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
362 =cut
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
363
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
364 open SUMMED, ">$output_dir/summed_contig_lengths.dat" or die $!;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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365 print SUMMED join "\n",@summed_contig_data;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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366 close SUMMED;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
367
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
368 open HISTOGRAMBINS, ">$output_dir/histogram_bins.dat" or die $!;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
369 my $bin_size_counter = 0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
370 foreach (@bins) {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
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371 print HISTOGRAMBINS eval($bin_size_counter++ * $bin_size + $bin_size/2) . "\t$_\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
372 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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373 close HISTOGRAMBINS;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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374
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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375
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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376 # Graph of cumulative (summed) number of reads on y-axis, versus length of read (decending order) on x-axis
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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377 open SUMREAD_READLEN, ">$output_dir/sum_reads_vs_read_len.dat" or die $!;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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378 #my $read_counter= 0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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379 my $read_counter= $#sorted_by_contig_length+1;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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380
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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381 foreach (@sorted_by_contig_length) {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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382 # $read_counter++;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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383 $read_counter--;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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384 print SUMREAD_READLEN "$_->[0]\n"; # $read_counter
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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385 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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386 close SUMREAD_READLEN;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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387
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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388
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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389
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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390
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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391 my $properType=ucfirst($type); # Makes the first letter an upper case letter, ie. 'Config' or 'Read'
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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392 #if ($type eq 'contig')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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393 # {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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394 # print the outcome of the gnu_plot as may have a write permissions error sometimes.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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395 my $YHistogramScaleType = ($type eq 'read') ? '' : 'log y'; # Not using log scale for reads, just for contig/isotigs.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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396 &plot_graph('histogram', "$output_dir/histogram_bins.dat", "Histogram of $type lengths", "$properType length", "Number of $type_plural", '0.9', $YHistogramScaleType);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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397 &plot_graph('line', "$output_dir/summed_contig_lengths.dat", "Summed $type lengths", "Number of $type_plural", "Summed $type length in bases", '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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398 &plot_graph('line', "$output_dir/sum_reads_vs_read_len.dat", "X-axis gives the Number of $type_plural that are greater than the $properType-length given on the Y-axis", "$properType length", "Cummulative number of $type_plural", '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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399
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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400 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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401 # print `gnuplot_histogram.sh $output_dir/histogram_bins.dat`;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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402
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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403 &plot_graph("$output_dir/summed_contig_lengths.dat", 'Summed contig lengths', 'Number of contigs', 'Summed contig length in bases', '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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404 # print `gnuplot_summedcontigs.sh $output_dir/summed_contig_lengths.dat`;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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405
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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406 &plot_graph('line', "$output_dir/sum_reads_vs_read_len.dat", 'X-axis gives the Number of contigs that are greater than the Contig-length given on the Y-axis', 'Contig length', 'Cummulative number of contigs', '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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407 # print `gnuplot_sum_contig_vs_contig_len.sh $output_dir/sum_reads_vs_read_len.dat`;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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408 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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409 elsif ($type eq 'read')
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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410 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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411
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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412 # print `gnuplot_readshistogram_logY.sh $output_dir/histogram_bins.dat`; # There's also optionally a "...._linearY.sh"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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413
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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414 &plot_graph('line', "$output_dir/summed_contig_lengths.dat",'Summed read lengths', 'Number of reads', 'Summed read length in bases', '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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415 # print `gnuplot_summedreads.sh $output_dir/summed_contig_lengths.dat`;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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416
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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417 &plot_graph('line', "$output_dir/sum_reads_vs_read_len.dat", 'X-axis gives the Number of reads that are greater than the Read-length given on the Y-axis', 'Read length', 'Cummulative number of reads', '0.9', '');
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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418 # print `gnuplot_sum_reads_vs_read_len.sh $output_dir/sum_reads_vs_read_len.dat`;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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419 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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420 else {die "\n** ERROR: Invalid type='$type' **\n\n";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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421 =cut
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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422
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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423 close SORTED;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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424 close STATS;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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425
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426
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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427 # Use pipe to plot directly with gnuplot, rather than calling a separate shell script:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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428 # http://www.vioan.ro/wp/2008/09/30/calling-gnuplot-from-perl/
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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429 # http://forums.devshed.com/perl-programming-6/plotting-with-gnuplot-within-perl-script-549682.html
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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430 # Another option is the perl module: GnuplotIF: http://lug.fh-swf.de/perl/GnuplotIF.html OR: http://lug.fh-swf.de/perl/
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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431
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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432 # PlPlot: Perl: http://search.cpan.org/~dhunt/PDL-Graphics-PLplot-0.47/plplot.pd
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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433 # http://plplot.sourceforge.net/
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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434 # dislin: http://www.mps.mpg.de/dislin/overview.html
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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435 # MathGL: http://mathgl.sourceforge.net/index.html
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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436
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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437
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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438 sub plot_graph
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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439 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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440 # Plots a histogram or xy-line graph
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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441 # Parameters: GraphType (histogram/line) DataFile, Title, X-label, Y-label, Y-range
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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442 # Graphfile should end with '.png'
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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443 # The $yloglinear is 'log y' for log, or '' for linear
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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444 my ($graphtype, $datafile, $title,$xlabel,$ylabel,$yrange,$yloglinear)=@_; # yrange for reads: 0.1, and for contigs: 0.9
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
445
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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446 my $graphstyle='';
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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447 if ($graphtype eq 'histogram') {$graphstyle="plot \"$datafile\" using 1:2 with boxes";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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448 elsif ($graphtype eq 'line') {$graphstyle="plot \"$datafile\" using 1 with lines";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
449 else {die "\n** ERROR: Invalid graphtype='$graphtype'\n\n";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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450 my $yloglinearscale= ($yloglinear eq '') ? '' : "set $yloglinear";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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451
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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452 # To capture any errors that are normally sent from gnuplot to stderr, could use: open3 pipe interface:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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453 # http://www.clintoneast.com/articles/perl-open3-example.php
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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454 # http://hell.org.ua/Docs/oreilly/perl2/prog/ch16_03.htm
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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455 # But the following should be fine, as the stderr will display when running the script anyway.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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456 # If needed a simpler way would be to sent the output to a file using eg: open (GNUPLOT, "|gnuplot > gnu_out.txt 2>&1") or die .... The read the resulting file.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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457 open (GNUPLOT, "|gnuplot") or die "\n**ERROR: Failed to open gnuplot : $!\n\n **";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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458 print GNUPLOT <<ENDPLOT;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
459 set terminal png
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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460 set output "$datafile.png"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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461 set nokey
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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462 $yloglinearscale
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
463 set xlabel "$xlabel"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
464 set ylabel "$ylabel"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
465 set yrange [$yrange:]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
466 set title "$title"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
467 $graphstyle
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
468 ENDPLOT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
469 close(GNUPLOT);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
470 if ($? != 0) {print "\n** WARNING: GNUplot pipe returned non-zero status: '$?'\n\n";} # $? is the status returned by the last pipe close (or backtick or system operator)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
471 if (! -e "$datafile.png") {die "\n** ERROR: Failed to create '$datafile.png'**\n\n";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
472
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
473 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
474 #PNG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
475 set term png small xFFFFFF
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
476 set output "$file.png"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
477 set size 1 ,1
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
478 set nokey
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
479 set data style line
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
480 set xlabel "frequency" font "VeraMono,10"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
481 set title "Fast Fourier Transform" font "VeraMono,10"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
482 set grid xtics ytics
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
483 set xtics 100
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
484 plot "$file" using 1:2 w lines 1
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
485 =cut
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
486
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
487 #WAS PREVIOUSLY AS .sh script
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
488 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
489 # The 'gnuplot_readshistogram_logY.sh' is:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
490 set terminal png
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
491 set output "$1.png"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
492 set log y
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
493 set xlabel "Read length"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
494 set ylabel "Frequency"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
495 set yrange [0.9:]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
496 set title "Histogram of read lengths"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
497 plot "$1" using 1:2 with boxes
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
498 =cut
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
499 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
500
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
501
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
502 # Was previously a separate .sh file:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
503 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
504 #!/bin/sh
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
505 gnuplot << EOF
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
506 set terminal png
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
507 set output "$1.png"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
508 set xlabel "Number of contigs"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
509 set ylabel "Summed contig length in bases"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
510 set yrange [0.9:]
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
511 set title "Summed contig lengths"
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
512 plot "$1" using 1 with lines
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
513 EOF
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
514 =cut
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
515
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
516
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
517
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
518
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
519 # Added function to count number of simple dinucleotide repeats:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
520 sub countRepeats
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
521 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
522 # To count the number of sequences that contain mostly repeats.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
523 # This would be faster if called a C program on the file.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
524
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
525 # Common simple repeats are listed here: http://www.bioinfo.de/isb/2005/05/0041/
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
526 # Dinucleotide
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
527 # AT/TA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
528 # AC/TG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
529 # AG/TC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
530 # CG/GC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
531 # Trinucleotide
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
532 # AAT/TTA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
533 # CTA/GAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
534 # ATG/TAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
535 # ACT/TGA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
536 # CTC/GAG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
537 # AGG/TCC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
538 # CAG/GTC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
539 # AAG/TTC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
540 # ATA/TAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
541 # CAA/GTT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
542 # AGC/TCG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
543 # ACA/TGT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
544 # ACG/TGC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
545 # AGA/TCT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
546 # ACC/TGG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
547 # Other
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
548 # Tetranucleotide
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
549 # AAAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
550 # AAAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
551 # CACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
552 # AACA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
553 # AATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
554 # AAGA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
555 # TGAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
556 # AAAG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
557 # ACAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
558 # AATG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
559 # AGCC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
560 # Other
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
561 # Pentanucleotide
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
562 # AAAAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
563 # AATTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
564 # GCTAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
565 # ATAAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
566 # AAAAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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567 # AAACA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
568 # ATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
569 # TTGCC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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570 # Other
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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571
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
572 # I also add mono-nucleotide repeats: - ie. just all T's, or A's, etc
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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573 # Just consider the dinucleotide repeats for now:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
574 my ($ATseq,$CGseq,$ACseq,$TGseq,$AGseq,$TCseq)=(0,0,0,0,0,0);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
575 my ($AAseq,$TTseq,$CCseq,$GGseq)=(0,0,0,0);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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576 foreach (@sequences)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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577 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
578 my $seq_len=$_->[0];
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
579 my $seq=$_->[2]; # This copy might be slow, maybe should just stick with using the reference.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
580 my $mnt=0.35*$seq_len; # Mononucleotide threshold: HERE 0.35 also means 70%; 0.4 means 80% dinucleotide repeats, as really one base so 0.5 = 100%
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
581 my $dnt=0.35*$seq_len; # Dinucleotide threshold: 0.35 means 70%; 0.4 means 80% dinucleotide repeats, as two bases so 0.5 = 100%
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
582 my ($AT,$CG,$AC,$TG,$AG,$TC)=(0,0,0,0,0,0);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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583 my ($AA,$TT,$CC,$GG)=(0,0,0,0);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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584 # See: http://www.allinterview.com/showanswers/76719.html
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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585
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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586 # AT/TA seems most common repeat so process it first to save time:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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587 while ($seq=~/AT/g) {$AT++;} if ($AT>$dnt) {$ATseq++; next;} # AT is same as TA. If has 80% AT's then won't have 80% AC etc.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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588 while ($seq=~/CG/g) {$CG++;} if ($CG>$dnt) {$CGseq++; next;} # CG is same as GC.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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589 # AC,TG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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590 while ($seq=~/AC/g) {$AC++;} if ($AC>$dnt) {$ACseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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591 while ($seq=~/TG/g) {$TG++;} if ($TG>$dnt) {$TGseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
592 # AG/TC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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593 while ($seq=~/AG/g) {$AG++;} if ($AG>$dnt) {$AGseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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594 while ($seq=~/TC/g) {$TC++;} if ($TC>$dnt) {$TCseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
595
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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596 # Added my simple mononucleotde repeat count:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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597 while ($seq=~/AA/g) {$AA++;} if ($AA>$mnt) {$AAseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
598 while ($seq=~/TT/g) {$TT++;} if ($TT>$mnt) {$TTseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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599 while ($seq=~/CC/g) {$CC++;} if ($CC>$mnt) {$CCseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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600 while ($seq=~/GG/g) {$GG++;} if ($GG>$mnt) {$GGseq++; next;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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601 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
602
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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603 my $num_seq=($#sequences+1);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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604 my $total_din_repeats_seq= $ACseq+$TGseq+$ATseq+$AGseq+$TCseq+$CGseq;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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605 my $percent_din_repeats=100*$total_din_repeats_seq/$num_seq;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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606 print STATS "\nSimple Dinucleotide repeats:\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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607 printf STATS "\tNumber of %s with over 70%% dinucleotode repeats:\t%.2f %% (%d %s)\n", $type_plural, $percent_din_repeats, $total_din_repeats_seq, $type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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608 printf STATS "\tAT:\t%.2f %% (%d %s)\n", (100*$ATseq/$num_seq),$ATseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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609 printf STATS "\tCG:\t%.2f %% (%d %s)\n", (100*$CGseq/$num_seq),$CGseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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610 printf STATS "\tAC:\t%.2f %% (%d %s)\n", (100*$ACseq/$num_seq),$ACseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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611 printf STATS "\tTG:\t%.2f %% (%d %s)\n", (100*$TGseq/$num_seq),$TGseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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612 printf STATS "\tAG:\t%.2f %% (%d %s)\n", (100*$AGseq/$num_seq),$AGseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
613 printf STATS "\tTC:\t%.2f %% (%d %s)\n", (100*$TCseq/$num_seq),$TCseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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614
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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615 my $total_mono_repeats_seq= $AAseq+$TTseq+$CCseq+$GGseq;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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616 my $percent_mono_repeats=100*$total_mono_repeats_seq/$num_seq;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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617 print STATS "\nSimple mononucleotide repeats:\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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618 printf STATS "\tNumber of %s with over 50%% mononucleotode repeats:\t%.2f %% (%d %s)\n", $type_plural, $percent_mono_repeats, $total_mono_repeats_seq, $type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
619 printf STATS "\tAA:\t%.2f %% (%d %s)\n", (100*$AAseq/$num_seq),$AAseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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620 printf STATS "\tTT:\t%.2f %% (%d %s)\n", (100*$TTseq/$num_seq),$TTseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
621 printf STATS "\tCC:\t%.2f %% (%d %s)\n", (100*$CCseq/$num_seq),$CCseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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622 printf STATS "\tGG:\t%.2f %% (%d %s)\n", (100*$GGseq/$num_seq),$GGseq,$type_plural;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
623
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
624 return $percent_din_repeats+$percent_mono_repeats;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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625 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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626
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
627
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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628 sub commify_if
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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629 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
630 # If doCommify is >0 then converts output to commas.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
631 # Formats '1234567890.01' with commas as "1,234,567,890.01
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
632 # Based on: http://www.perlmonks.org/?node_id=110137
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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633 my ($number,$doCommify)=@_;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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634 if ($doCommify > 0) {$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
635 return $number;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
636 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
637
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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638
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
639 #--------------- Produce ordered list of random numbers -------------------
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
640 # This is copied from: my_random_contigs.pl
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
641
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
642 sub getListOfRandomNumbers
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
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diff changeset
643 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
644 # Use: @list=getListOfRandomNumbers(200,20); to return sorted list of 20 numbers in range from 0 to 200 inclusive.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
645 my %list2=();
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
646 my $i=0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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647 my $MaxNumber=$_[0];
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
648 my $NumToPick=$_[1];
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
649 while ($i<$NumToPick)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
650 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
651 my $intRand = int(rand($MaxNumber+1)); # For Zero-based perl-arrays. The +1 means this generates random integers between 0 and $MaxNumber. (See: http://perldoc.perl.org/functions/rand.html )
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
652 if ($intRand>$MaxNumber) {$intRand=$MaxNumber} # Just to be extra sure that don't exceed $MaxNumber.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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parents:
diff changeset
653 if ( !exists($list2{$intRand}) ) {$list2{$intRand}=1; $i++;}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
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diff changeset
654 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
655 #foreach my $key(keys %list2) {print "$key ";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
656 # Sort the list of numbers:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
657 #my @SortedList2 = sort { $a <=> $b } keys(%list2);
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
658 #return @SortedList2;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
659 return (sort { $a <=> $b } keys(%list2));
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
660 #print "Sorted list of ".$NumToPick." random numbers:\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
661 #foreach my $num(@SortedList2) {print "$num\n";}
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
662 #print "\n\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
663 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
664
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
665
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
666 sub print_sequences
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
667 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
668 # Print the sequences wrapping sequences using index array, at line length of '$fastaLineLen' characters:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
669 # Uses the global '@sequences' array.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
670 my $sequence_indexes_list=$_[0]; # This is an array reference, not the array itself.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
671 foreach my $num(@{$sequence_indexes_list})
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
672 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
673 #print "$num (max=$#sequences)\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
674 print STATS $sequences[$num]->[1]; # Prints the header, no "\n" needed after it.
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
675 my $pos=0;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
676 my $seqlen=$sequences[$num]->[0];
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
677 while ($pos<$seqlen)
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
678 {
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
679 print STATS substr($sequences[$num]->[2],$pos,$fastaLineLen)."\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
680 $pos+=$fastaLineLen;
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
681 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
682 print STATS "\n";
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
683 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
684 }
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
685
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
686
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
687 =pod
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
688 # Some test runs for mono-nucleotides and dinucelotides:
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
689 >FUOMOGO01AQV42DUMMYA length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
690 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
691 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
692 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
693 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
694 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
695 >FUOMOGO01AQV42DUMMYB length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
696 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
697 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
698 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
699 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
700 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
701 >FUOMOGO01AQV42DUMMYC length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
702 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
703 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
704 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
705 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
706 >FUOMOGO01AQV42DUMMYD length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
707 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
708 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
709
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
710 >FUOMOGO01AQV42 length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
711 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
712 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
713 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
714 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
715 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
716 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
717 >FUOMOGO01AUK0D length=214 xy=0231_0843 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
718 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
719 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
720 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
721 ACACACACACACACACACACACGACGACGACGAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
722 >FUOMOGO01AUB7C length=64 xy=0228_1718 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
723 ATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
724 TACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
725 >FUOMOGO01AU00B length=213 xy=0236_1097 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
726 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
727 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
728 ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
729 ACACACACACACACACACACGACGACGACGACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
730 >FUOMOGO01ATYRT length=169 xy=0224_0695 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
731 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
732 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
733 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
734 >FUOMOGO01ARMLN length=400 xy=0197_2201 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
735 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
736 TATAGTAGTAGTAGTATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
737 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
738 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
739 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
740 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
741 TATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
742 >FUOMOGO01AVGRX length=44 xy=0241_1051 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
743 TATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
744 >FUOMOGO01ASZ6K length=315 xy=0213_0922 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
745 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
746 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
747 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
748 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
749 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
750 TGTGTGTGTGTGTGT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
751 >FUOMOGO01ARSZF length=65 xy=0199_2281 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
752 TATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTAC
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
753 GTACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
754 >FUOMOGO01AYV8U length=49 xy=0280_1324 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
755 ATATATATATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
756 >FUOMOGO01AYV9X length=40 xy=0280_1363 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
757 TATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
758 >FUOMOGO01AUX4M length=40 xy=0235_1460 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
759 TATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
760 >FUOMOGO01AWOTU length=54 xy=0255_0800 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
761 ATATATATATATATATATATATATATATATATATATATATATATATATATAGTA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
762 >FUOMOGO01A11TC length=66 xy=0316_1054 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
763 ATATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
764 CGTACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
765 >FUOMOGO01ASRJP length=401 xy=0210_2019 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
766 TATATATATATATATATATATATATATATATATATATATATATATATATATATAGTATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
767 AGTAGTAGTAGTATATATATATATATATATATATATATATATATATATATATATATATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
768 ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
769 ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
770 ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
771 ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
772 ATATATATATATATATATATATATATATATATATATATATA
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
773 >FUOMOGO01AU1ZH length=67 xy=0236_2363 region=1 run=R_2009_04_23_17_54_06_
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
774 TATATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGT
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
775 ACGTACG
ad2b274663f8 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit 3f9ae719338c7c8db81d645b8ee09727e2d9ce23
nml
parents:
diff changeset
776 =cut