Mercurial > repos > nml > filter_spades_repeats
annotate filter_spades_repeats.pl @ 0:90957420cc07 draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
author | nml |
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date | Thu, 12 Oct 2017 15:04:45 -0400 |
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rev | line source |
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0
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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1 #!/usr/bin/env perl |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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2 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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3 use strict; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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4 use Getopt::Long; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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5 use Bio::SeqIO; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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6 use Pod::Usage; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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7 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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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); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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9 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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10 GetOptions( |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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11 'c|coverage-cutoff=s' => \$coverage_co, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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12 'l|length-cutoff=s' => \$length_co, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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13 'e|coverage-length-cutoff=s' => \$coverage_length_co, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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14 'r|repeat_cutoff=s' => \$repeat_co, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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changeset
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15 'i|input=s' => \$fasta_file, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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16 't|tab=s' => \$tab_file, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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changeset
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17 'f|filtered-out=s' => \$out_filtered, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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18 'o|output-repeats=s' => \$out_repeats, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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19 'u|output-norepeats=s' => \$out_norepeats, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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20 'n|filtered-repeats=s' => \$filtered_repeats, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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21 's|summary=s' => \$summary_out, |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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22 'h|help' => \$help |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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23 ); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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24 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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25 pod2usage(-verbose => 2) if ($help); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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26 print "A fasta file is required. Please enter a fasta file using the -i flag.\n" if (!$fasta_file); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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27 print "A spades tabs file is required. Please enter a tabs file using the -t flag\n" if (!$tab_file); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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28 pod2usage(1) unless $fasta_file && $tab_file; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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29 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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30 if (!$coverage_co) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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31 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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32 $coverage_co = 0.33; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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33 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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34 if (!$length_co) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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35 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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36 $length_co = 1000; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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37 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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38 if (!$coverage_length_co) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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39 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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40 $coverage_length_co = 5000; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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41 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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42 if (!$repeat_co) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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43 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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44 $repeat_co = 1.75; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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45 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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46 if (!$out_filtered) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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47 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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48 $out_filtered = "Discarded_sequences.fasta"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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49 print "Discarded sequences will be printed out to $out_filtered\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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50 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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51 if (!$out_repeats) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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52 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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53 $out_repeats = "Filtered_sequences_with_repeats.fasta"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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54 print "Filtered sequences with repeats will be printed out to $out_repeats\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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55 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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56 if (!$out_norepeats) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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57 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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58 $out_norepeats = "Filtered_sequences_no_repeats.fasta"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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59 print "Filtered sequences without repeats will be printed out to $out_norepeats\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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60 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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61 if (!$filtered_repeats) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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62 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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63 $filtered_repeats = "Repeat_sequences.fasta"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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64 print "Repeat sequences will be printed out to $filtered_repeats\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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65 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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66 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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67 die ("No tab file specified") unless ($tab_file); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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68 die ("No fasta file specified") unless ($fasta_file); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
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69 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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70 ##Read tab file and discard rows with comments |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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71 open TAB, '<', $tab_file or die "Could not open tab file: $?"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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72 open SEQIN, '<', $fasta_file or die "Could not open tab file: $?"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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73 open SEQOUT_REP, '>', $out_repeats or die "Could not open file for writing: $?"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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74 open SEQOUT_NOREP, '>', $out_norepeats or die "Could not open file for writing: $?"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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75 open SEQOUT_FILT, '>', $out_filtered if ($out_filtered); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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76 open SEQOUT_FILT_REP, '>', $filtered_repeats or die "Could not open file for writing: $?"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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77 open SUMMARY, '>', $summary_out if ($summary_out); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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78 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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79 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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80 my $avg_coverage = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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81 my $num_contigs = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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82 my $cutoff_coverage; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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83 my $cutoff_repeats; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
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84 my @stats; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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85 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
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86 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
87 while (<TAB>) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
88 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
89 chomp; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
90 push @stats, $_ unless (/^#/); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
91 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
92 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
93 #Calculate average coverage. |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
94 foreach my $stat(@stats) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
95 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
96 my ($length, $coverage); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
97 (undef,$length, $coverage) = split(/\t+/, $stat); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
98 die "length or coverage not defined at $stat\n" unless ($length && ($coverage ne '' && $coverage >= 0)); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
99 if ($length >= $coverage_length_co) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
100 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
101 $avg_coverage = $avg_coverage + $coverage; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
102 $num_contigs++; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
103 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
104 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
105 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
106 $avg_coverage = $avg_coverage / $num_contigs; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
107 $cutoff_coverage = $avg_coverage * $coverage_co; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
108 $cutoff_repeats = $avg_coverage * $repeat_co; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
109 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
110 print SUMMARY "Filter SPAdes repeats Results Summary\n======================================\n\n" if ($summary_out); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
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); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
112 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
113 print SUMMARY "Calculations:\nAverage coverage: $avg_coverage\nCoverage cutoff: $cutoff_coverage\nRepeat cutoff: $cutoff_repeats\n\nFile headers:\n" if ($summary_out); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
114 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
115 my ($header, $seq_id, $seq); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
116 my $repeated = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
117 my $valid = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
118 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
119 #Summary strings: |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
120 my $discarded = ""; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
121 my $repeats = ""; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
122 my $filtered_rep = ""; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
123 my $filtered_norep = ""; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
124 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
125 while (my $line = <SEQIN>) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
126 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
127 if ($line =~ />/) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
128 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
129 chomp $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
130 #Get the sequence name to compare against tab file |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
131 $header = $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
132 $seq_id = $line =~ /(\w+)_length/; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
133 $seq = ""; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
134 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
135 my $stat = shift @stats; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
136 die "Less rows in tab than sequences in seq file" unless $stat; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
137 my($name, $length, $coverage) = split(/\t+/, $stat); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
138 die "name or length not defined at $stat\n" unless ($name && $length); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
139 die "coverage is not defined at $stat\n" unless ($coverage ne '' && $coverage >= 0); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
140 die "Unmatched names $header and $name\n" unless ($header =~ /$name/i); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
141 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
142 #Entry passes the length and coverage cutoffs? |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
143 if ($length >= $length_co && $coverage >= $cutoff_coverage) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
144 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
145 $valid = 1; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
146 #Repeats |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
147 if ($coverage >= $cutoff_repeats) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
148 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
149 my $num_repeats = int($coverage/$avg_coverage); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
150 $header = $header."(".$num_repeats." copies)"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
151 print SEQOUT_REP $header,"\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
152 $filtered_rep = $filtered_rep.$header."\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
153 print SEQOUT_FILT_REP $header, "\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
154 $repeats = $repeats.$header."\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
155 $repeated = 1; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
156 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
157 else |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
158 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
159 print SEQOUT_REP $header, "\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
160 $filtered_rep = $filtered_rep.$header."\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
161 print SEQOUT_NOREP $header, "\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
162 $filtered_norep = $filtered_norep.$header."\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
163 $repeated = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
164 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
165 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
166 elsif ($out_filtered) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
167 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
168 $valid = 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
169 print SEQOUT_FILT $header,"\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
170 $discarded = $discarded.$header."\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
171 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
172 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
173 else |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
174 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
175 if ($valid) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
176 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
177 print SEQOUT_REP $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
178 if (!$repeated) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
179 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
180 print SEQOUT_NOREP $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
181 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
182 else |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
183 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
184 print SEQOUT_FILT_REP $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
185 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
186 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
187 elsif ($out_filtered) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
188 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
189 print SEQOUT_FILT $line; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
190 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
191 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
192 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
193 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
194 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
195 close TAB; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
196 close SEQIN; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
197 close SEQOUT_REP; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
198 close SEQOUT_NOREP; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
199 close SEQOUT_FILT; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
200 close SEQOUT_FILT_REP; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
201 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
202 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
203 #Get summary info: |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
204 if ($summary_out) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
205 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
206 print SUMMARY "Filtered sequences (with repeats):\n$filtered_rep\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
207 print SUMMARY "Filtered sequences (no repeats):\n$filtered_norep\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
208 print SUMMARY "Repeat sequences:\n$repeats\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
209 if ($out_filtered) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
210 { |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
211 print SUMMARY "Discarded sequences:\n$discarded\n"; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
212 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
213 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
214 close SUMMARY; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
215 } |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
216 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
217 die "More rows in stats file than sequences in the fasta file\n" if (scalar(@stats) > 0); |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
218 exit 0; |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
219 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
220 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
221 __END__ |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
222 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
223 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
224 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
225 =head1 NAME |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
226 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
227 filter_spades_repeats.pl - Filters contigs or scaffolds based on contig length and detects contigs/scaffolds with very high coverage. |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
228 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
229 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
230 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
231 =head1 USAGE |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
232 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
233 filter_spades_output.pl -i <contigs/scaffolds input> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
234 -t <stats input> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
235 -o <output fasta with repeats> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
236 -u <output fasta without repeats> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
237 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
238 Optional: |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
239 -c <coverage cutoff ratio> (default 0.33) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
240 -l <length cutoff> (default: 1000) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
241 -e <length cutoff for average coverage calculation> (default: 5000) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
242 -r <repeat cutoff ratio> (default (1.75) |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
243 -n <filtered repeated sequences> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
244 -f <discarded sequences> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
245 -s <output summary file> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
246 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
247 For more information: |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
248 -h |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
249 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
250 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
251 =head1 INPUT |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
252 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
253 =over 8 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
254 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
255 =item B<-i>B<--input> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
256 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
257 Contigs/Scaffolds fasta file. |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
258 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
259 =item B<-t>B<--tab> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
260 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
261 The tabular output file from SPAdes. This file should have the following format: |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
262 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
263 #name length coverage |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
264 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
265 NODE_1 31438 24.5116 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
266 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
267 NODE_2 31354 2316.96 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
268 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
nml
parents:
diff
changeset
|
269 NODE_3 26948 82.3294 |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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270 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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271 =item B<-o>B<--output-repeats> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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272 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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273 Output fasta file including the contigs marked as repeated. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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274 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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275 =item B<-u>B<--output-norepeats> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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276 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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277 Output fasta file excluding the contigs marked as repeated. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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278 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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279 =item B<-c>B<--coverage-cutoff> |
90957420cc07
planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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280 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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281 Mininum coverage ratio. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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282 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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283 coverage_theshold = average_coverage * minimum_coverage_ratio. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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284 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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285 Any contigs/scaffolds with coverage below the coverage_theshold will be eliminated. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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286 |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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287 =item B<-l>B<--length-cutoff> |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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288 |
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289 Mininum length. Contigs below this length will be eliminated. |
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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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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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planemo upload for repository https://github.com/phac-nml/galaxy_tools/ commit 8ea19b9db8a5d861466adf3bf4e01928d3d1ca38
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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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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 |