Mercurial > repos > jdv > b2b_bam2consensus

annotate bam2consensus @ 1:2367d00c5182 draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:12:40 +0000
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2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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1 #!/usr/bin/env perl
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3 use strict;
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4 use warnings;
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5 use 5.012;
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6
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7 use BioX::Seq;
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8 use BioX::Seq::Stream;
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9 use BioX::Seq::Fetch;
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10 use File::Temp qw/tempfile/;
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11 use IPC::Cmd qw/can_run/;
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12 use Getopt::Long;
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13 use List::Util qw/sum max first/;
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14 use Pod::Usage;
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15 use POSIX qw/floor ceil/;
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17 #-inputs---------------------------------------------------------------------#
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18 my $fn_bam;
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19 my $fn_ref;
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20 #-outputs--------------------------------------------------------------------#
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21 my $fn_table;
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22 my $fn_consensus;
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23 my $fn_bedgraph;
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24 #-knobs----------------------------------------------------------------------#
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25 my $min_qual = 10;
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26 my $min_depth = 3;
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27 my $trim_fraction = 0.2;
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28 my $sliding_window = 30;
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29 my $bg_bin_figs = 0;
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30 my $verbose = 0;
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31
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32 my $PROGRAM = 'bam2consensus';
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33 my $VERSION = 0.004;
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34
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35 GetOptions(
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36
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37 #-inputs-----------------------------------------------------------------#
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38 'bam=s' => \$fn_bam,
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39 'ref=s' => \$fn_ref,
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40 #-outputs----------------------------------------------------------------#
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41 'table=s' => \$fn_table,
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42 'consensus=s' => \$fn_consensus,
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43 'bedgraph=s' => \$fn_bedgraph,
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44 #-knobs------------------------------------------------------------------#
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45 'min_qual=i' => \$min_qual,
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46 'min_depth=i' => \$min_depth,
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47 'trim=f' => \$trim_fraction,
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48 'window=i' => \$sliding_window,
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49 'bg_bin_figs=i' => \$bg_bin_figs,
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50 'verbose' => \$verbose,
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51 'help' => sub{ pod2usage(-verbose => 2); },
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52 'version' => sub{ print "This is $PROGRAM v$VERSION\n";exit; },
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53
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54 ) or pod2usage( -verbose => 1);
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55
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56 # check for recent version of samtools
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57 my $SAMTOOLS = can_run('samtools')
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58 // die "Samtools is required but not found\n";
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59 my $v_string = `$SAMTOOLS --version`;
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60 if ($v_string =~ /^samtools (\d+)\.(\d+)/m) {
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61 die "Requires samtools >= 1.3.0\n" if ($1 < 1 || $2 < 3);
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62 } else {
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63 die "Error parsing samtools version string\n";
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64 }
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65
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66 # check for mafft
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67 my $MAFFT = can_run('mafft')
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68 // die "MAFFT is required but not found\n";
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69
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70
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71 # misc param checking
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72 die "Error: must specify at least one output target" if (! (
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73 defined $fn_table
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74 || defined $fn_consensus
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75 || defined $fn_bedgraph
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76 ));
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77 die "Error: missing reference parameter"
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78 if (! defined $fn_ref);
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79 die "Error reading reference"
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80 if (! -r $fn_ref);
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81
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82
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83 # globals
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84 my @errors;
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85 my @lines = () if (defined $fn_table);
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86
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87 my %iupac = (
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88 A => 'A',
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89 C => 'C',
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90 G => 'G',
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91 T => 'T',
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92 AG => 'R',
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93 CT => 'Y',
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94 CG => 'S',
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95 AT => 'W',
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96 GT => 'K',
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97 AC => 'M',
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98 CGT => 'B',
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99 AGT => 'D',
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100 ACT => 'H',
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101 ACG => 'V',
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102 ACGT => 'N',
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103 );
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104
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105 my @consensi;
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106 my $bg = '';
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107
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108 my @curr_lines;
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109 my $last_chr;
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110
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111 my $last_depth = undef;
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112 my $last_loc = 0;
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113 my $bg_start = 0;
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114 my $bg_loc = 0;
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115
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116
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117 # initialize random-access sequence collection
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118 my $seqs = BioX::Seq::Fetch->new($fn_ref) or die "Error loading reference";
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119
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120
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121 # pipe from samtools mpileup command
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122 # (note: this is much faster in testing than using Perl bindings, e.g.
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123 # Bio::DB::HTS or the like)
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124
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125 $fn_bam //= '-'; # use stdin if BAM file not given
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126
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127 open my $fh, '-|', $SAMTOOLS,
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128 'mpileup',
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129 '-d' => 1000000,
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130 '-B',
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131 '-f' => $fn_ref,
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132 $fn_bam ;
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133
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134
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135
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136 LINE:
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137 while (my $line = <$fh>) {
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138
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139 chomp $line;
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140 my ($chr, @other) = split "\t", $line;
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141 $last_chr //= $chr;
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142
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143 if ($chr ne $last_chr) {
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144 process(\@curr_lines);
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145 @curr_lines = ();
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146 $last_chr = $chr;
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147 }
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148
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149 push @curr_lines, $line;
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150 }
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151
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152 process(\@curr_lines); # don't forget last call
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153
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154 # output bedgraph if asked
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155 if (defined $fn_bedgraph) {
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156 open my $fh_bedgraph, '>', $fn_bedgraph;
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157 print {$fh_bedgraph}
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158 "track type=bedGraph name=read_coverage maxHeightPixels=1000:80:20\n";
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159 print {$fh_bedgraph} $bg;
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160 close $fh_bedgraph;
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161
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162 }
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163
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164 # output fasta if asked
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165 if (defined $fn_consensus) {
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166
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167 open my $out, '>', $fn_consensus;
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168 print {$out} $_->as_fasta for (@consensi);
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169 close $out;
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170
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171 }
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172
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173 # build and process table if asked
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174 if (defined $fn_table) {
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175
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176 # calculate sliding errors
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177 my @avg_errors;
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178 my $l = scalar(@errors);
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179 $sliding_window = $l if ($l < $sliding_window);
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180 my $left = floor(($sliding_window-1)/2);
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181 my $right = ceil(($sliding_window-1)/2);
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182 my $lower = $left;
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183 my $upper = $l - $right;
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184 for my $i (0..$#errors) {
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185 my @pool;
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186 if ($i < $lower) {
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187 @pool = (@errors[0..$i-1] ,@errors[$i+1..$sliding_window-1]);
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188 }
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189 elsif ($i >= $upper) {
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190 @pool = (@errors[$l-$sliding_window..$i-1], @errors[$i+1..$l-1]);
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191 }
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192 else {
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193 @pool = (@errors[$i-$left..$i-1], @errors[$i+1..$i+$right]);
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194 }
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195 die "bad pool size @pool at $i" if (scalar(@pool)+1 != $sliding_window);
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196
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197 # calc trimmed mean
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198 @pool = sort {$a <=> $b} @pool;
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199 my $l = @pool;
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200 my @trimmed
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201 = @pool[ int($l*$trim_fraction), int($l*(1-$trim_fraction))+0.5 ];
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202 my $tm = scalar(@trimmed) > 0 ? sum(@trimmed)/scalar(@trimmed) : 'NA';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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203 push @avg_errors, $tm;
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204 }
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205
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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206 open my $fh_table, '>', $fn_table;
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207
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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208 # print table header
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209 print {$fh_table} join( "\t", (
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210 'id',
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211 'loc',
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212 'ref',
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213 'called',
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214 'total_depth',
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215 'counted_depth',
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216 'mm_rate',
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217 'A_count',
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218 'T_count',
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219 'G_count',
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220 'C_count',
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221 'N_count',
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222 'gap_count',
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223 'A_freq',
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224 'T_freq',
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225 'G_freq',
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226 'C_freq',
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227 'N_freq',
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228 'gap_freq',
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229 'A_sb',
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230 'T_sb',
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231 'G_sb',
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232 'C_sb',
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233 'bgnd_err',
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234 'insertions'
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235 ) ) . "\n";
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236
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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237 my $iter = 0;
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238 POS:
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239 for (0..$#lines) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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240 my @parts = @{ $lines[$_] };
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241 @parts[23] = sprintf '%.3f', $avg_errors[$_];
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242 print {$fh_table} join( "\t",@parts), "\n";
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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243 }
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244 close $fh_table;
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245 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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246
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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247 sub process {
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248
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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249 my $ln_ref = shift;
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250
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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251 my $last_chr;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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252 $last_depth = undef;
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253 $last_loc = 0;
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254 $bg_start = 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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255 $bg_loc = 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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256
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
257 LINE:
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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258 for my $line (@$ln_ref) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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259 chomp $line;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
260 my @parts = split "\t", $line;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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261 my $chr = $parts[0];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
262 my $loc = $parts[1];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
263 my $ref = uc $parts[2];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
264 my $depth = $parts[3];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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265 my $read_string = $parts[4];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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266 my $qual_string = $parts[5];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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267
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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268 # check that chr hasn't changed (don't supported multiple refs)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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269 $last_chr = $last_chr // $chr;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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270 if ($chr ne $last_chr) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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271 #process current, start new
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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272 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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273
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
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274 # simulate missing rows
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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275 my $t = $last_loc + 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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276 while ($t < $loc) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
277 handle_entry(
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
278 $chr,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
279 $t,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
280 $seqs->fetch_seq($chr, $t, $t),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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281 #substr($ref_seq, $t-1, 1),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
282 0,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
283 '',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
284 '',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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285 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
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286 ++$t;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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287 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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288
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
289 # send entry for handling
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
290 handle_entry(
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
291 $chr,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
292 $loc,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
293 $ref,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
294 $depth,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
295 $read_string,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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296 $qual_string,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
297 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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298
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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299 $last_loc = $loc;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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300
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
301 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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diff changeset
302
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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303 # simulate missing rows at end
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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304 my $t = $last_loc + 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
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diff changeset
305 my $l = $seqs->length($last_chr);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
306 while ($t <= $l) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
307 handle_entry(
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
308 $last_chr,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
309 $t,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
310 $seqs->fetch_seq($last_chr, $t, $t),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
311 #substr($ref_seq, $t-1, 1),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
312 0,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
313 '',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
314 '',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
315 );
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
316 ++$t;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
317 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
318
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
319 if (defined $fn_bedgraph) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
320
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
321 $bg .= join("\t", $last_chr, $bg_start, $bg_loc, $last_depth) . "\n";
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
322 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
323
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
324 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
325
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
326
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
327 sub handle_entry {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
328
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
329 my ($chr, $loc, $ref, $depth, $read_string, $qual_string) = @_;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
330
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
331 my $called = '';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
332
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
333 # handle zero-depth positions separately
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
334 if ($depth < 1) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
335 $called = 'N';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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parents:
diff changeset
336 print "Missing coverage at $chr pos $loc\n" if ($verbose);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
337 if (defined $fn_table) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
338 push @lines, [
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
339 $chr,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
340 $loc,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
341 $ref,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
342 'N',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
343 (0) x 19,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
344 undef,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
345 '',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
346 ];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
347 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
348 push @errors, 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
349 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
350
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
351 # everything else
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
352 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
353
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
354 # handle insertions
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
355 my %inserts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
356 my $insert_count = 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
357 while ($read_string =~ /\+(\d+)((??{"[ATGCNatgcnRYSWKMBDHVryswkmbdhv-]{$^N}"}))/g) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
358 $inserts{$2} += 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
359 ++$insert_count;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
360 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
361
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
362 # ...and strip extra characters
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
363 $read_string =~ s/\^.//g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
364 $read_string =~ s/[\+\-](\d+)(??{"[ATGCNatgcnRYSWKMBDHVryswkmbdhv-]{$^N}"})//g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
365 $read_string =~ s/[^\.\,\w\*]//g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
366
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
367 # simple parse check
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
368 my $l1 = length($read_string);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
369 my $l2 = length($qual_string);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
370 die "read/qual mismatch ($l1 v $l2)" if ($l1 != $l2);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
371
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
372 die "unexpected char at $chr pos $loc\n"
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
373 if ($read_string =~ /[^.,ATGCNatgcn*]/);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
374
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
375 my $lc = lc $ref;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
376 $read_string =~ s/\./$ref/g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
377 $read_string =~ s/\,/$lc/g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
378 $read_string =~ s/n/N/g;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
379
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
380 # split into arrays
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
381 my %counts = map {$_ => 0} qw/A T G C N a t g c */;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
382 my %cons_counts = map {$_ => 0} qw/A T G C N a t g c */;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
383 my @chars = split '', $read_string;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
384 my @quals = map {ord($_) - 33} split('', $qual_string);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
385
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
386 READ:
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
387 for my $i (0..$#chars) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
388 ++$cons_counts{ uc($chars[$i]) };
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
389 ++$counts{ $chars[$i] } if ($quals[$i] >= $min_qual);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
390 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
391
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
392 # calculate strand bias and collapse counts
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
393 my %sb;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
394 for my $b (qw/A T G C/) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
395 my $n = $counts{$b} + $counts{lc($b)};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
396 $sb{$b} = $n > 0
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
397 ? ($n-1)/$n*(2*max($counts{$b}/$n, ($n-$counts{$b})/$n)-1)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
398 : 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
399 $counts{$b} += $counts{lc($b)};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
400 delete $counts{lc($b)};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
401 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
402
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
403 $counts{$ref} = $counts{$ref} // 0; # some IUPAC codes not defined above
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
404 $cons_counts{$ref} = $cons_counts{$ref} // 0; # some IUPAC codes not defined above
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
405 my $mismatches = sum map {$counts{$_}} grep {$_ ne $ref} keys %counts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
406 my $counted_depth = $counts{$ref} + $mismatches;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
407 my $cons_depth = sum map {$cons_counts{$_}} keys %counts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
408 my $error_rate = $counted_depth == 0
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
409 ? 0
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
410 : sprintf '%.4f', $mismatches/$counted_depth;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
411 push @errors, $error_rate;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
412
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
413 my @insert_strings = ();
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
414 my $consensus_insert = '';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
415
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
416 #create case-insensitive insert hash
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
417 my %combined_inserts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
418 for (keys %inserts) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
419 $combined_inserts{uc($_)} += $inserts{$_};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
420 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
421
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
422 if (scalar(keys %combined_inserts) > 0) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
423 my @sorted_inserts = sort {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
424 $combined_inserts{$b} <=> $combined_inserts{$a}
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
425 || $a cmp $b
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
426 } keys %combined_inserts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
427 for (@sorted_inserts) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
428 my $f_count = $inserts{$_} // 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
429 my $r_count = $inserts{lc($_)} // 0;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
430 my $n = $combined_inserts{$_};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
431 my $sb = sprintf '%.3f', ($n-1)/$n*max($f_count/$n, ($n-$f_count)/$n);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
432 push @insert_strings, "$_($f_count,$r_count:$sb)";
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
433 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
434
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
435 # decide whether to include insert in consensus
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
436 if ($insert_count/$l1 > 0.5) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
437 my @realigned = realign(\%combined_inserts);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
438 for my $i (0..$#realigned) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
439 my @b = sort {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
440 $realigned[$i]->{$b} <=> $realigned[$i]->{$a}
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
441 } keys %{ $realigned[$i] };
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
442 if ($realigned[$i]->{$b[0]}/$l1 > 0.5) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
443 $consensus_insert .= uc $b[0];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
444 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
445 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
446 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
447
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
448 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
449 if ($cons_depth < $min_depth) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
450 $called = 'N';
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
451 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
452 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
453 my @sorted
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
454 = sort {$cons_counts{$b} <=> $cons_counts{$a}} keys %cons_counts;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
455
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
456 # get all top hits that aren't gaps
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
457 my @equal_hits = grep {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
458 $cons_counts{$_} eq $cons_counts{$sorted[0]} && $_ ne '*'
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
459 } @sorted;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
460
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
461 if (scalar(@equal_hits)) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
462 my $tag = join('',sort {$a cmp $b} @equal_hits);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
463 die "bad tag $tag" if (! defined $iupac{$tag});
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
464 $called = $iupac{$tag};
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
465 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
466 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
467 $called .= $consensus_insert;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
468
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
469 print "consensus/reference difference at $chr pos $loc (ref: $ref cons: $called)\n"
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
470 if ($verbose && $called ne $ref);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
471
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
472 if (defined $fn_table) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
473 push @lines, [
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
474 $chr,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
475 $loc,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
476 $ref,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
477 $called eq '' ? '-' : $called,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
478 $depth,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
479 $counted_depth,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
480 sprintf('%.3f',$error_rate),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
481 $counts{A},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
482 $counts{T},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
483 $counts{G},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
484 $counts{C},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
485 $counts{N},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
486 $counts{'*'},
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
487 sprintf('%.3f',$counts{A}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
488 sprintf('%.3f',$counts{T}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
489 sprintf('%.3f',$counts{G}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
490 sprintf('%.3f',$counts{C}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
491 sprintf('%.3f',$counts{N}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
492 sprintf('%.3f',$counts{'*'}/$counted_depth),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
493 sprintf('%.3f',$sb{A}),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
494 sprintf('%.3f',$sb{T}),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
495 sprintf('%.3f',$sb{G}),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
496 sprintf('%.3f',$sb{C}),
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
497 undef,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
498 join(':',@insert_strings)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
499 ];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
500 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
501 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
502
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
503 my $consensus = first {$_->id eq $chr} @consensi;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
504 if (! defined $consensus) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
505 $consensus = BioX::Seq->new('',$chr);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
506 push @consensi, $consensus;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
507 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
508 $consensus->seq .= $called;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
509
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
510 my $cons_len = length($called);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
511
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
512 # Generate bedgraph output
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
513 if (defined $fn_bedgraph && $cons_len > 0) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
514
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
515 # bin depth if requested
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
516 if ($bg_bin_figs > 0) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
517 my $divisor = 10**max(0, length($depth)-$bg_bin_figs);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
518 $depth = int($depth/$divisor) * $divisor;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
519 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
520
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
521 # output on depth change
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
522 if (! defined $last_depth || $depth != $last_depth) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
523 $bg .= join("\t",$last_chr, $bg_start, $bg_loc, $last_depth) . "\n"
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
524 if (defined $last_depth);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
525 $last_depth = $depth;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
526 $bg_start = $bg_loc;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
527 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
528
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
529 $bg_loc += $cons_len;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
530
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
531 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
532
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
533 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
534
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
535
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
536 sub realign {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
537
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
538 # calculate a local realignment at indel using MAFFT
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
539 # TODO: reimplement using native code
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
540
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
541 my ($hash) = @_;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
542
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
543 my @seqs = keys %{ $hash };
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
544 my @weights = map {$hash->{$_}} @seqs;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
545 my @scores;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
546 if (scalar(@seqs) > 1) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
547 my ($fh, $fn) = tempfile;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
548 for (0..$#seqs) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
549 my $n = $_ + 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
550 print {$fh} ">$n\n$seqs[$_]\n";
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
551 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
552 close $fh;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
553 open my $stream, '-|', $MAFFT,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
554 '--auto',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
555 '--quiet',
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
556 '--op' => 0,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
557 '--lop' => 0,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
558 $fn;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
559 my $p = BioX::Seq::Stream->new($stream);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
560 while (my $seq = $p->next_seq) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
561 my $w = shift @weights;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
562 for (0..length($seq)-1) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
563 my $base = substr $seq, $_, 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
564 next if ($base eq '-');
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
565 $scores[$_] = {} if (! defined $scores[$_]);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
566 $scores[$_]->{$base} += $w;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
567 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
568 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
569 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
570 else {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
571 my $seq = $seqs[0];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
572 my $w = $weights[0];
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
573 for (0..length($seq)-1) {
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
574 my $base = substr $seq, $_, 1;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
575 next if ($base eq '-');
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
576 $scores[$_] = {} if (! defined $scores[$_]);
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
577 $scores[$_]->{$base} += $w;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
578 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
579 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
580 return @scores;
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
581
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
582 }
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
583
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
584
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
585 __END__
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
586
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
587 =head1 NAME
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
588
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
589 bam2consensus - consensus calling (etc) from BAM alignment
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
590
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
591 =head1 SYNOPSIS
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
592
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
593 bam2consensus --bam <in.bam> --ref <in.fasta> [options] --consensus <out.fasta>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
594
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
595 =head1 DESCRIPTION
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
596
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
597 Re-calls a consensus sequence based on a BAM alignment to reference, with
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
598 various knobs and optional output formats
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
599
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
600 =head1 PREREQUISITES
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
601
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
602 Requires the following non-core Perl libraries:
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
603
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
604 =over 1
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
605
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
606 =item * BioX::Seq
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
607
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
608 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
609
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
610 as well as the following binaries:
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
611
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
612 =over 1
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
613
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
614 =item * samtools (>= 1.3.1)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
615
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
616 =item * mafft
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
617
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
618 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
619
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
620 =head1 OPTIONS
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
621
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
622 =head2 Input (required)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
623
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
624 =over 4
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
625
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
626 =item B<--bam> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
627
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
628 Path to input BAM alignments
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
629
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
630 =item B<--ref> I<filename>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
631
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
632 Path to reference sequence used to generate BAM alignments
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
633
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
634 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
635
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
636 =head2 Output (at least one is required, can specify more than one)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
637
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
638 =over 4
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
639
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
640 =item B<--consensus>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
641
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
642 Path to write consensus sequence to (as FASTA)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
643
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
644 =item B<--bedgraph>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
645
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
646 Path to write coverage file to (as bedgraph)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
647
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
648 =item B<--table>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
649
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
650 Path to write coverage file to (as tab-separated table)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
651
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
652 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
653
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
654 =head2 Configuration
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
655
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
656 =over 4
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
657
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
658 =item B<--min_qual>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
659
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
660 Minimum quality for a base to be considered in consensus calling. Default: 10.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
661
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
662 =item B<--min_depth>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
663
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
664 Minimum read depth for consensus to be called (otherwise called as "N"). Default: 3.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
665
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
666 =item B<--trim>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
667
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
668 Fraction to trim from each end when calculating trimmed mean of error window.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
669 Default: 0.2.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
670
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
671 =item B<--window>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
672
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
673 Size of sliding window used to calculate local error rates. Default: 30.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
674
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
675 =item B<--bg_bin_figs> <integer>
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
676
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
jdv
parents:
diff changeset
677 If greater than zero, the number of significant figures used to bin depths in
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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678 bedgraph output. If zero, no binning is applied. This option is useful to
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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679 reduce the size of bedgraph output by binning similar depth values when high
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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680 resolution is not important. Default: 0 (disabled).
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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681
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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682 =back
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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683
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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684 =head1 CAVEATS AND BUGS
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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685
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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686 Please submit bug reports to the issue tracker in the distribution repository.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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687
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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688 =head1 AUTHOR
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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689
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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690 Jeremy Volkening (jdv@base2bio.com)
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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691
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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692 =head1 LICENSE AND COPYRIGHT
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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693
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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694 Copyright 2014-17 Jeremy Volkening
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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695
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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696 This program is free software: you can redistribute it and/or modify
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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697 it under the terms of the GNU General Public License as published by
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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698 the Free Software Foundation, either version 3 of the License, or
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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699 (at your option) any later version.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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700
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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701 This program is distributed in the hope that it will be useful,
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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702 but WITHOUT ANY WARRANTY; without even the implied warranty of
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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703 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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704 GNU General Public License for more details.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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705
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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706 You should have received a copy of the GNU General Public License
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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707 along with this program. If not, see <http://www.gnu.org/licenses/>.
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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708
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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709 =cut
2367d00c5182 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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710