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annotate libs/sratoolkit.2.8.0-centos_linux64/example/perl/mismatch-stats.pl @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 #!/usr/bin/env perl
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2 # ===========================================================================
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3 #
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4 # PUBLIC DOMAIN NOTICE
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5 # National Center for Biotechnology Information
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6 #
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7 # This software/database is a "United States Government Work" under the
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8 # terms of the United States Copyright Act. It was written as part of
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9 # the author's official duties as a United States Government employee and
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10 # thus cannot be copyrighted. This software/database is freely available
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11 # to the public for use. The National Library of Medicine and the U.S.
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12 # Government have not placed any restriction on its use or reproduction.
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13 #
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14 # Although all reasonable efforts have been taken to ensure the accuracy
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15 # and reliability of the software and data, the NLM and the U.S.
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16 # Government do not and cannot warrant the performance or results that
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17 # may be obtained by using this software or data. The NLM and the U.S.
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18 # Government disclaim all warranties, express or implied, including
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19 # warranties of performance, merchantability or fitness for any particular
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20 # purpose.
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21 #
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22 # Please cite the author in any work or product based on this material.
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23 #
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24 # ===========================================================================
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25
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26 use warnings;
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27
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28 use Data::Dumper;
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29
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30 use constant MAX_READ_COUNT => 2;
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31
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32 my %opts = (
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33 'row-range' => '-1000000',
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34 'output-type' => 'proportion'
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35 );
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36
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37 sub usage()
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38 {
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39 print <<"HELP";
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40 report BASE statistics for an SRA
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41
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42 Usage:
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43 $0 [<options>...] <accession>...
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44 options are
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45 -h | -? | --help
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46 --row-range <row-range-spec> default is first 1000000 spots
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47 --output-type <output-spec> set the type of data output
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48 count, percent, or proportion
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49 proportion is the default
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50
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51 Example:
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52 $0 --row-range "5,7,11-15,25-37" --output-type count SRR797646
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53
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54 HELP
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55 exit 0;
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56 }
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57
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58 usage if scalar @ARGV == 0;
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59 foreach (@ARGV) {
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60 usage() if (/^-h$/ || /^-\?$/ || /^--help$/);
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61 }
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62
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63 my $VDB_DUMP = `which vdb-dump` or die "Please put path to vdb-dump in PATH";
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64 chomp $VDB_DUMP;
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65
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66 my @stats = ();
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67 my $max_read = 0;
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68 my $max_len = 0;
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69
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70 sub get_index($$$)
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71 {
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72 my ($pos, $read, $base) = @_;
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73
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74 return ($pos * MAX_READ_COUNT + $read) * 6 + $base;
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75 }
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76
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77 sub resize_stats($)
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78 {
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79 my $need = get_index $_[0], MAX_READ_COUNT, 0;
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80 my $have = scalar(@stats);
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81
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82 return unless ($have < $need);
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83 splice @stats, $have, 0, map { 0 } (0..($need - $have));
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84 }
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85
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86 sub translate_base($)
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87 {
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88 return 0 if $_[0] eq '=';
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89 return 1 if $_[0] eq 'A';
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90 return 2 if $_[0] eq 'C';
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91 return 3 if $_[0] eq 'G';
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92 return 4 if $_[0] eq 'T';
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93 return 5;
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94 }
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95
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96 sub translate_base_complement($)
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97 {
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98 return 0 if $_[0] eq '=';
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99 return 1 if $_[0] eq 'T';
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100 return 2 if $_[0] eq 'G';
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101 return 3 if $_[0] eq 'C';
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102 return 4 if $_[0] eq 'A';
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103 return 5;
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104 }
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105
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106 sub expand_and_summarize($)
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107 {
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108 my ($READ_ID, $ORIENT, $MM_READ) = \split(/\t/, ${$_[0]});
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109 my $len = length $$MM_READ;
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110 my $read = $$READ_ID - 1;
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111
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112 $max_read = $read if $max_read < $read;
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113 $max_len = $len if $max_len < $len ;
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114
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115 resize_stats $len;
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116 if ($$ORIENT eq 'false') {
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117 for (my $i = 0; $i != $len; ++$i) {
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118 my $base = translate_base(substr($$MM_READ, $i, 1));
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119
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120 ++$stats[get_index($i, $read, $base)];
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121 }
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122 }
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123 else {
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124 for (my $j = 0; $j != $len; ++$j) {
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125 my $i = $len - $j - 1;
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126 my $base = translate_base_complement(substr($$MM_READ, $i, 1));
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127
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128 ++$stats[get_index($i, $read, $base)];
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129 }
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130 }
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131 }
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132
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133 sub check_aligned($)
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134 {
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135 my $aligned = 0;
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136
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137 if (`$VDB_DUMP -y "$_[0]"` =~ /Database/i) {
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138 open CMD, '-|', "$VDB_DUMP -E \"$_[0]\"" or die "$!";
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139
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140 while (defined(local $_ = <CMD>)) {
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141 chomp;
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142 if (/PRIMARY_ALIGNMENT/) {
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143 $aligned = 1;
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144 last;
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145 }
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146 }
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147 close CMD;
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148 }
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149 return $aligned;
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150 }
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151
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152 sub process($)
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153 {
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154 my $cmd = "$VDB_DUMP -f tab -C \"SEQ_READ_ID,REF_ORIENTATION,MISMATCH_READ\" -R $opts{'row-range'} -T PRIMARY_ALIGNMENT \"$_[0]\"";
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155 open CMD, '-|', $cmd or die "$!";
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156
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157 while (defined($_ = <CMD>)) {
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158 chomp;
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159 expand_and_summarize \$_;
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160 }
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161 close CMD;
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162 }
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163
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164 for (my $i = 0; $i < scalar @ARGV; ++$i) {
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165 $_ = $ARGV[$i];
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166
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167 if (/^-/) {
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168 if (/^--row-range$/) {
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169 $opts{'row-range'} = $ARGV[++$i];
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170 next;
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171 }
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172 if (/^--output-type$/) {
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173 $opts{'output-type'} = $ARGV[++$i];
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174 next;
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175 }
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176 usage();
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177 }
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178 if (check_aligned $_) {
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179 process $_;
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180 }
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181 else {
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182 print "$_ is not aligned\n";
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183 }
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184 }
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185
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186 sub format_counts($$$$)
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187 {
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188 my ($x, $cnt) = @_;
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189
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190 return $x;
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191 }
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192
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193 sub format_proportion($$$$)
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194 {
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195 my ($x, $cnt) = @_;
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196
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197 return $x/$cnt;
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198 }
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199
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200 sub format_percent($$$$)
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201 {
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202 my ($x, $cnt) = @_;
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203
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204 return int($x * 100.0/$cnt + 0.5).'%';
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205 }
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206
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207 my $format = \&format_proportion;
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208
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209 if ($opts{'output-type'} eq 'count') {
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210 $format = \&format_counts;
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211 }
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212 elsif ($opts{'output-type'} eq 'proportion') {
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213 $format = \&format_proportion;
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214 }
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215 elsif ($opts{'output-type'} eq 'percent') {
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216 $format = \&format_percent;
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217 }
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218 else {
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219 usage();
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220 }
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221
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222 printf join("\t", ('Read', 'Pos', '=', 'A', 'C', 'G', 'T', 'N'))."\n";
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223
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224 for (my $read = 0; $read <= $max_read; ++$read) {
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225 for (my $pos = 0; $pos != $max_len; ++$pos) {
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226 my $idx = get_index $pos, $read, 0;
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227 my $tot = $stats[$idx+0] + $stats[$idx+1] + $stats[$idx+2]
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228 + $stats[$idx+3] + $stats[$idx+4] + $stats[$idx+5];
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229
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230 if ($tot) {
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231 print join("\t", ($read + 1, $pos + 1,
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232 &$format($stats[$idx+0], $tot),
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233 &$format($stats[$idx+1], $tot),
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234 &$format($stats[$idx+2], $tot),
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235 &$format($stats[$idx+3], $tot),
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236 &$format($stats[$idx+4], $tot),
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237 &$format($stats[$idx+5], $tot)
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238 ))."\n";
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239 }
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240 }
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241 }