Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate scripts/filter_spades_repeats.pl @ 5:fd9093b9368f draft
planemo upload commit 9af296d380b81335353ebfb8bb6de831e1fbebe1
author | iss |
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date | Thu, 19 Oct 2023 20:27:22 +0000 |
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1 #!/usr/bin/env perl |
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2 |
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3 use strict; |
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4 use Getopt::Long; |
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5 use Bio::SeqIO; |
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6 use Pod::Usage; |
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7 |
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8 my ($fasta_file, $tab_file, $coverage_co, $length_co, $repeat_co, $out_filtered, $out_repeats, $out_norepeats,$coverage_length_co, $summary_out, $filtered_repeats, $help); |
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9 |
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10 GetOptions( |
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11 'c|coverage-cutoff=s' => \$coverage_co, |
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12 'l|length-cutoff=s' => \$length_co, |
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13 'e|coverage-length-cutoff=s' => \$coverage_length_co, |
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14 'r|repeat_cutoff=s' => \$repeat_co, |
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15 'i|input=s' => \$fasta_file, |
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16 't|tab=s' => \$tab_file, |
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17 'f|filtered-out=s' => \$out_filtered, |
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18 'o|output-repeats=s' => \$out_repeats, |
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19 'u|output-norepeats=s' => \$out_norepeats, |
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20 'n|filtered-repeats=s' => \$filtered_repeats, |
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21 's|summary=s' => \$summary_out, |
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22 'h|help' => \$help |
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23 ); |
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24 |
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25 pod2usage(-verbose => 2) if ($help); |
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26 print "A fasta file is required. Please enter a fasta file using the -i flag.\n" if (!$fasta_file); |
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27 print "A spades tabs file is required. Please enter a tabs file using the -t flag\n" if (!$tab_file); |
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28 pod2usage(1) unless $fasta_file && $tab_file; |
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29 |
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30 if (!$coverage_co) |
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31 { |
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32 $coverage_co = 0.33; |
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33 } |
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34 if (!$length_co) |
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35 { |
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36 $length_co = 1000; |
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37 } |
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38 if (!$coverage_length_co) |
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39 { |
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40 $coverage_length_co = 5000; |
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41 } |
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42 if (!$repeat_co) |
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43 { |
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44 $repeat_co = 1.75; |
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45 } |
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46 if (!$out_filtered) |
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47 { |
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48 $out_filtered = "Discarded_sequences.fasta"; |
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49 print "Discarded sequences will be printed out to $out_filtered\n"; |
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50 } |
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51 if (!$out_repeats) |
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52 { |
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53 $out_repeats = "Filtered_sequences_with_repeats.fasta"; |
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54 print "Filtered sequences with repeats will be printed out to $out_repeats\n"; |
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55 } |
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56 if (!$out_norepeats) |
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57 { |
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58 $out_norepeats = "Filtered_sequences_no_repeats.fasta"; |
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59 print "Filtered sequences without repeats will be printed out to $out_norepeats\n"; |
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60 } |
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61 if (!$filtered_repeats) |
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62 { |
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63 $filtered_repeats = "Repeat_sequences.fasta"; |
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64 print "Repeat sequences will be printed out to $filtered_repeats\n"; |
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65 } |
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66 |
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67 die ("No tab file specified") unless ($tab_file); |
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68 die ("No fasta file specified") unless ($fasta_file); |
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69 |
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70 ##Read tab file and discard rows with comments |
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71 open TAB, '<', $tab_file or die "Could not open tab file: $?"; |
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72 open SEQIN, '<', $fasta_file or die "Could not open tab file: $?"; |
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73 open SEQOUT_REP, '>', $out_repeats or die "Could not open file for writing: $?"; |
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74 open SEQOUT_NOREP, '>', $out_norepeats or die "Could not open file for writing: $?"; |
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75 open SEQOUT_FILT, '>', $out_filtered if ($out_filtered); |
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76 open SEQOUT_FILT_REP, '>', $filtered_repeats or die "Could not open file for writing: $?"; |
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77 open SUMMARY, '>', $summary_out if ($summary_out); |
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78 |
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79 |
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80 my $avg_coverage = 0; |
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81 my $num_contigs = 0; |
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82 my $cutoff_coverage; |
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83 my $cutoff_repeats; |
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84 my @stats; |
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85 |
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86 |
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87 while (<TAB>) |
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88 { |
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89 chomp; |
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90 push @stats, $_ unless (/^#/); |
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91 } |
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92 |
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93 #Calculate average coverage. |
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94 foreach my $stat(@stats) |
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95 { |
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96 my ($length, $coverage); |
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97 (undef,$length, $coverage) = split(/\t+/, $stat); |
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98 die "length or coverage not defined at $stat\n" unless ($length && ($coverage ne '' && $coverage >= 0)); |
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99 if ($length >= $coverage_length_co) |
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100 { |
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101 $avg_coverage = $avg_coverage + $coverage; |
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102 $num_contigs++; |
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103 } |
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104 } |
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105 |
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106 $avg_coverage = $avg_coverage / $num_contigs; |
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107 $cutoff_coverage = $avg_coverage * $coverage_co; |
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108 $cutoff_repeats = $avg_coverage * $repeat_co; |
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109 |
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110 print SUMMARY "Filter SPAdes repeats Results Summary\n======================================\n\n" if ($summary_out); |
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111 print SUMMARY "Paramaters used:\nLength cutoff for calcularing average cutoff: $coverage_length_co\nCoverage cutoff ratio: $coverage_co\nRepeat cutoff ratio: $repeat_co\nLength cutoff: $length_co\n\n" if ($summary_out); |
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112 |
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113 print SUMMARY "Calculations:\nAverage coverage: $avg_coverage\nCoverage cutoff: $cutoff_coverage\nRepeat cutoff: $cutoff_repeats\n\nFile headers:\n" if ($summary_out); |
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114 |
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115 my ($header, $seq_id, $seq); |
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116 my $repeated = 0; |
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117 my $valid = 0; |
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118 |
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119 #Summary strings: |
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120 my $discarded = ""; |
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121 my $repeats = ""; |
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122 my $filtered_rep = ""; |
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123 my $filtered_norep = ""; |
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124 |
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125 while (my $line = <SEQIN>) |
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126 { |
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127 if ($line =~ />/) |
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128 { |
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129 chomp $line; |
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130 #Get the sequence name to compare against tab file |
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131 $header = $line; |
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132 $seq_id = $line =~ /(\w+)_length/; |
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133 $seq = ""; |
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134 |
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135 my $stat = shift @stats; |
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136 die "Less rows in tab than sequences in seq file" unless $stat; |
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137 my($name, $length, $coverage) = split(/\t+/, $stat); |
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138 die "name or length not defined at $stat\n" unless ($name && $length); |
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139 die "coverage is not defined at $stat\n" unless ($coverage ne '' && $coverage >= 0); |
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140 die "Unmatched names $header and $name\n" unless ($header =~ /$name/i); |
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141 |
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142 #Entry passes the length and coverage cutoffs? |
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143 if ($length >= $length_co && $coverage >= $cutoff_coverage) |
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144 { |
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145 $valid = 1; |
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146 #Repeats |
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147 if ($coverage >= $cutoff_repeats) |
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148 { |
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149 my $num_repeats = int($coverage/$avg_coverage); |
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150 $header = $header."(".$num_repeats." copies)"; |
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151 print SEQOUT_REP $header,"\n"; |
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152 $filtered_rep = $filtered_rep.$header."\n"; |
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153 print SEQOUT_FILT_REP $header, "\n"; |
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154 $repeats = $repeats.$header."\n"; |
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155 $repeated = 1; |
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156 } |
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157 else |
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158 { |
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159 print SEQOUT_REP $header, "\n"; |
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160 $filtered_rep = $filtered_rep.$header."\n"; |
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161 print SEQOUT_NOREP $header, "\n"; |
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162 $filtered_norep = $filtered_norep.$header."\n"; |
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163 $repeated = 0; |
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164 } |
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165 } |
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166 elsif ($out_filtered) |
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167 { |
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168 $valid = 0; |
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169 print SEQOUT_FILT $header,"\n"; |
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170 $discarded = $discarded.$header."\n"; |
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171 } |
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172 } |
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173 else |
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174 { |
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175 if ($valid) |
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176 { |
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177 print SEQOUT_REP $line; |
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178 if (!$repeated) |
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179 { |
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180 print SEQOUT_NOREP $line; |
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181 } |
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182 else |
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183 { |
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184 print SEQOUT_FILT_REP $line; |
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185 } |
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186 } |
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187 elsif ($out_filtered) |
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188 { |
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189 print SEQOUT_FILT $line; |
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190 } |
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191 } |
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192 |
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193 } |
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194 |
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195 close TAB; |
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196 close SEQIN; |
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197 close SEQOUT_REP; |
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198 close SEQOUT_NOREP; |
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199 close SEQOUT_FILT; |
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200 close SEQOUT_FILT_REP; |
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201 |
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202 |
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203 #Get summary info: |
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204 if ($summary_out) |
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205 { |
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206 print SUMMARY "Filtered sequences (with repeats):\n$filtered_rep\n"; |
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207 print SUMMARY "Filtered sequences (no repeats):\n$filtered_norep\n"; |
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208 print SUMMARY "Repeat sequences:\n$repeats\n"; |
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209 if ($out_filtered) |
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210 { |
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211 print SUMMARY "Discarded sequences:\n$discarded\n"; |
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212 } |
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213 |
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214 close SUMMARY; |
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215 } |
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216 |
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217 die "More rows in stats file than sequences in the fasta file\n" if (scalar(@stats) > 0); |
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218 exit 0; |
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219 |
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220 |
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221 __END__ |
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222 |
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223 |
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224 |
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225 =head1 NAME |
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226 |
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227 filter_spades_repeats.pl - Filters contigs or scaffolds based on contig length and detects contigs/scaffolds with very high coverage. |
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228 |
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229 |
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230 |
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231 =head1 USAGE |
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232 |
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233 filter_spades_output.pl -i <contigs/scaffolds input> |
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234 -t <stats input> |
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235 -o <output fasta with repeats> |
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236 -u <output fasta without repeats> |
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237 |
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238 Optional: |
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239 -c <coverage cutoff ratio> (default 0.33) |
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240 -l <length cutoff> (default: 1000) |
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241 -e <length cutoff for average coverage calculation> (default: 5000) |
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242 -r <repeat cutoff ratio> (default (1.75) |
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243 -n <filtered repeated sequences> |
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244 -f <discarded sequences> |
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245 -s <output summary file> |
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246 |
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247 For more information: |
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248 -h |
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249 |
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250 |
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251 =head1 INPUT |
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252 |
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253 =over 8 |
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254 |
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255 =item B<-i>B<--input> |
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256 |
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257 Contigs/Scaffolds fasta file. |
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258 |
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259 =item B<-t>B<--tab> |
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260 |
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261 The tabular output file from SPAdes. This file should have the following format: |
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262 |
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263 #name length coverage |
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264 |
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265 NODE_1 31438 24.5116 |
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266 |
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267 NODE_2 31354 2316.96 |
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268 |
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269 NODE_3 26948 82.3294 |
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270 |
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271 =item B<-o>B<--output-repeats> |
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272 |
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273 Output fasta file including the contigs marked as repeated. |
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274 |
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275 =item B<-u>B<--output-norepeats> |
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276 |
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277 Output fasta file excluding the contigs marked as repeated. |
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278 |
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279 =item B<-c>B<--coverage-cutoff> |
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280 |
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281 Mininum coverage ratio. |
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282 |
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283 coverage_theshold = average_coverage * minimum_coverage_ratio. |
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284 |
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285 Any contigs/scaffolds with coverage below the coverage_theshold will be eliminated. |
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286 |
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287 =item B<-l>B<--length-cutoff> |
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288 |
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289 Mininum length. Contigs below this length will be eliminated. |
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290 |
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291 =item B<-e>B<--coverage-length-cutoff> |
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292 |
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293 Minimum length to use for average coverage calculations. |
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294 |
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295 =item B<-r>B<--repeat-cutoff> |
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296 |
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297 Minimum repeats ratio. |
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298 |
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299 repeat_threshold = average_coverage * repeat_ratio. |
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300 |
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301 Any contigs with coverage below this threshold will be considered to be repeated |
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302 |
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303 |
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304 =item B<-f>B<--filtered-out> |
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305 |
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306 If specified, filtered out sequences will be written to this file. |
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307 |
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308 =item B<-s>B<--summary> |
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309 |
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310 A summary of results |
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311 |
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312 =back |
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313 =cut |