Mercurial > repos > romaingred > pirna_pipeline

comparison bin/html.pm @ 32:0cffda6c3d1a draft

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Uploaded
author romaingred
date Tue, 28 Nov 2017 09:08:02 -0500
parents a8a6e346893f
children dfe259eb1e6b
comparison
equal deleted inserted replaced
31:241aa6141cac 32:0cffda6c3d1a
64 fut($h,'Genome',$HG); 64 fut($h,'Genome',$HG);
65 carousel2($h,$UniG, $NonUniG,$dir_root); 65 carousel2($h,$UniG, $NonUniG,$dir_root);
66 footer($h); 66 footer($h);
67 close $h; 67 close $h;
68 68
69 open $h, '>', $prefix.'-exons.html' || die "cannot create $prefix-exons.html $!\n"; 69 open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n";
70 header($h); 70 header($h);
71 navbar ( $h, $list_mainTabP, $current ); 71 navbar ( $h, $list_mainTabP, $current );
72 fut($h,'Exons',$Hex); 72 fut($h,'transcripts',$Hex);
73 footer($h); 73 footer($h);
74 close $h; 74 close $h;
75 } 75 }
76 76
77 sub ppp_page 77 sub ppp_page
185 <div class=\"span6\"> 185 <div class=\"span6\">
186 <h2>bonafide reads</h2> 186 <h2>bonafide reads</h2>
187 reads of size between $min and $max<br>with no mi, sn, t and r RNAs 187 reads of size between $min and $max<br>with no mi, sn, t and r RNAs
188 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p> 188 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
189 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p> 189 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
190 <p><a class=\"btn\" href=\"$name-bonafide_reads-exons.html\">Exons</a></p> 190 <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">transcripts</a></p>
191 <div class=\"row-fluid\"> 191 <div class=\"row-fluid\">
192 <div class=\"span6\"> 192 <div class=\"span6\">
193 <h2>siRNAs</h2> 193 <h2>siRNAs</h2>
194 bonafide reads of size between $simin and $simax 194 bonafide reads of size between $simin and $simax
195 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p> 195 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
196 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p> 196 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
197 <p><a class=\"btn\" href=\"$name-siRNAs-exons.html\">Exons</a></p> 197 <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">transcripts</a></p>
198 </div> 198 </div>
199 <div class=\"span6\"> 199 <div class=\"span6\">
200 <h2>piRNAs</h2> 200 <h2>piRNAs</h2>
201 bonafide reads of size between $pimin and $pimax 201 bonafide reads of size between $pimin and $pimax
202 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p> 202 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
203 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p> 203 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
204 <p><a class=\"btn\" href=\"$name-piRNAs-exons.html\">Exons</a></p> 204 <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">transcripts</a></p>
205 </div> 205 </div>
206 </div> 206 </div>
207 </div> 207 </div>
208 <div class=\"span6\"> 208 <div class=\"span6\">
209 <h2>miRNAs</h2> 209 <h2>miRNAs</h2>
210 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p> 210 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
211 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p> 211 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
212 <p><a class=\"btn\" href=\"$name-miRNAs-exons.html\">Exons</a></p> 212 <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">transcripts</a></p>
213 </div> 213 </div>
214 </div> 214 </div>
215 </div> 215 </div>
216 "; 216 ";
217 } 217 }
235 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; } 235 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
236 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; } 236 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
237 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; } 237 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
238 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; } 238 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
239 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; } 239 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
240 elsif ( $f =~ /exons_sorted\.bam$/) { $Hex{'exons mappers (sorted bam)'} = $f;} 240 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
241 elsif ( $f =~ /exons_unique_sorted\.bam$/) { $Hex{'exons unique mappers (sorted bam)'} = $f;} 241 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
242 elsif ( $f =~ /exons_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;} 242 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;}
243 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; } 243 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
244 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; } 244 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
245 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; } 245 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
246 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; } 246 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
247 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; } 247 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
744 744
745 sub get_distri_exon 745 sub get_distri_exon
746 { 746 {
747 my ($dir, $name) = @_; 747 my ($dir, $name) = @_;
748 my (@out,@group); 748 my (@out,@group);
749 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-exons-*distribution-*.png'; 749 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
750 @group = glob $group; 750 @group = glob $group;
751 foreach (my $g =0; $g <= $#group; $g++) 751 foreach (my $g =0; $g <= $#group; $g++)
752 { 752 {
753 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-exons-.*distribution-.*\.png)/ ) 753 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
754 { 754 {
755 my $tmp = $1; 755 my $tmp = $1;
756 push @out, $1; 756 push @out, $1;
757 } 757 }
758 } 758 }