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| #!/usr/bin/perlq | ||
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| ###### | ||
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| use Getopt::Long; | ||
| use Pod::Usage; | ||
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| my $refseq; # gene annotation - UCSC | ||
| my $output; # length of sequence read | ||
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| GetOptions('r=s'=>\$refseq,'b=s'=>\$bamlist,'o=s'=>\$output); | ||
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| if((!($refseq))||(!($output))||(!($bamlist))){ | ||
| pod2usage(); | ||
| } | ||
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| open FP, "$bamlist"; | ||
| while(<FP>) { | ||
| chomp(); | ||
| if(!(/\.bam/)) { | ||
| print "BAM file are invalid!\n"; | ||
| exit(1); | ||
| } | ||
| print "loading $_ ...\n" | ||
| } | ||
| close FP; | ||
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| my %exonstarts; | ||
| my %exonends; | ||
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| my %tran2chr; | ||
| my %tran2strand; | ||
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| my %knownGene = (); | ||
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| open FP, "$refseq"; | ||
| while(<FP>) { | ||
| chomp(); | ||
| my @a = split("\t"); | ||
| next if !($a[2] eq "exon"); | ||
| my $chr = $a[0]; | ||
| my $gene; | ||
| my $trans; | ||
| my $exstart = $a[3] - 1; | ||
| my $exend = $a[4]; | ||
| my $info = $a[8]; | ||
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| if(/gene_name/) { | ||
| my @b = split("gene_name", $info); | ||
| my @c = split("\"", $b[1]); | ||
| $gene = $c[1]; | ||
| } else { | ||
| my @b = split("gene_id", $info); | ||
| my @c = split("\"", $b[1]); | ||
| $gene = $c[1]; | ||
| } | ||
| my @d = split("transcript_id", $info); | ||
| my @e = split("\"", $d[1]); | ||
| $trans = $e[1]; | ||
| $tran2chr{$trans} = $chr; | ||
| $tran2strand{$trans} = $a[6]; | ||
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| $exonstarts{$gene}{$trans} = $exonstarts{$gene}{$trans}.$exstart.";"; | ||
| $exonends{$gene}{$trans} = $exonends{$gene}{$trans}.$exend.";"; | ||
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| #print "$gene\t$trans\n"; | ||
| } | ||
| close FP; | ||
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| foreach my $gene (keys %exonstarts) { | ||
| foreach my $trans (keys %{$exonstarts{$gene}}) { | ||
| my @sss = split(";", $exonstarts{$gene}{$trans}); | ||
| my @eee = split(";", $exonends{$gene}{$trans}); | ||
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| my @sss_sort = sort {$a <=> $b} @sss; | ||
| my @eee_sort = sort {$a <=> $b} @eee; | ||
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| my $starts; | ||
| my $ends; | ||
| foreach my $i (0..$#sss_sort) { | ||
| $starts = $starts.$sss_sort[$i].","; | ||
| $ends = $ends.$eee_sort[$i].","; | ||
| } | ||
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| $knownGene{$gene}{$trans}{"chrom"} = $tran2chr{$trans}; | ||
| $knownGene{$gene}{$trans}{"strand"} = $tran2strand{$trans}; | ||
| $knownGene{$gene}{$trans}{"txStart"} = $sss_sort[0]; | ||
| $knownGene{$gene}{$trans}{"txEnd"} = $eee_sort[$#eee]; | ||
| $knownGene{$gene}{$trans}{"exonCount"} = $#sss + 1; | ||
| $knownGene{$gene}{$trans}{"exonStarts"} = $starts; | ||
| $knownGene{$gene}{$trans}{"exonEnds"} = $ends; | ||
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| } | ||
| } | ||
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| my $number_genes = scalar keys %knownGene; | ||
| print "$number_genes genes are being processed...\n"; | ||
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| #open(REF, $ref | ||
| open (RRR, ">$output"); | ||
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| ########## load isoform annotation | ||
| my %isoGene = (); | ||
| my %isoStart = (); | ||
| my %isoEnd = (); | ||
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| foreach my $name (keys %knownGene ) | ||
| { | ||
| foreach my $tran (keys %{$knownGene{$name}}) | ||
| { | ||
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| my $i_start = $knownGene{$name}{$tran}{"txStart"}; | ||
| my $i_end = $knownGene{$name}{$tran}{"txEnd"}; | ||
| $isoGene{$name} = $isoGene{$name}.$tran.","; | ||
| if($isoStart{$name} == NULL ) | ||
| {$isoStart{$name} = $i_start;} | ||
| else | ||
| { | ||
| if($isoStart{$name} > $i_start){ $isoStart{$name} = $i_start; } | ||
| } | ||
| if($isoEnd{$name} == NULL ) | ||
| {$isoEnd{$name} = $i_end;} | ||
| else | ||
| { | ||
| if($isoEnd{$name} < $i_end){ $isoEnd{$name} = $i_end;} | ||
| } | ||
| } | ||
| } | ||
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| ################## process isoform information | ||
| foreach my $ID (keys %isoGene ) | ||
| { | ||
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| my @genename = split(/,/, $isoGene{$ID}); | ||
| my $size = @genename; | ||
| my $i_chrom = $knownGene{$ID}{$genename[0]}{"chrom"}; | ||
| my $i_strand = $knownGene{$ID}{$genename[0]}{"strand"}; | ||
| my $i_start = $isoStart{$ID}; | ||
| my $i_end = $isoEnd{$ID}; | ||
| my %ISO_Index = (); | ||
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| if($size >1) ### you can specify the number of the isoform per gene here | ||
| { | ||
| print RRR "$ID\t$i_chrom\t$i_strand\t$i_start\t$i_end\t"; | ||
| for(my $j=0; $j<= $#genename; $j++) | ||
| { | ||
| my $name = $genename[$j]; | ||
| print RRR "tran_$j,"; | ||
| my @start = split(/,/, $knownGene{$ID}{$name}{"exonStarts"}); | ||
| my @end = split(/,/, $knownGene{$ID}{$name}{"exonEnds"}); | ||
| for (my $ijk=0; $ijk<= $#start; $ijk++) | ||
| { | ||
| my $sss = $start[$ijk]; | ||
| my $eee = $end[$ijk]; | ||
| for (my $abc=$sss; $abc<=$eee; $abc++) | ||
| {$ISO_Index{$abc}{$j} = 1;} | ||
| } # ijk | ||
| } # j | ||
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| print RRR "\n"; | ||
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| my %NEW_EXON =(); | ||
| my $CCC =0; | ||
| my $pre_POS = $i_start-10; | ||
| my @pre_Index = (); | ||
| for(my $j=0; $j <= $#genename; $j++) | ||
| {$pre_Index{$j}=0;} | ||
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| for my $ijk (sort {$a<=>$b} keys %ISO_Index) | ||
| { | ||
| my $tot =0; | ||
| my @cur_Index=(); | ||
| for(my $j=0; $j<=$#genename; $j++) | ||
| { | ||
| my $name = $genename[$j]; | ||
| my $value = exists $ISO_Index{$ijk}{$j} ? $ISO_Index{$ijk}{$j} : 0; | ||
| $cur_Index[$j] = $value; | ||
| if($cur_Index[$j] != $pre_Index[$j]) | ||
| {$tot = $tot +1;} | ||
| } | ||
| my $move = $ijk - $pre_POS; | ||
| if($move != 1) | ||
| { | ||
| $NEW_EXON{$CCC}{"start"} = $ijk; | ||
| $NEW_EXON{$CCC}{"Index"} = [@cur_Index]; | ||
| if($CCC > 0) | ||
| { | ||
| $NEW_EXON{$CCC-1}{"end"} = $pre_POS; | ||
| } | ||
| @pre_Index = @cur_Index; | ||
| $CCC = $CCC+1; | ||
| } | ||
| else{ | ||
| if($tot >0) | ||
| { | ||
| $NEW_EXON{$CCC}{"start"} = $ijk; | ||
| $NEW_EXON{$CCC-1}{"end"} = $ijk-1; | ||
| $NEW_EXON{$CCC}{"Index"} = [@cur_Index]; | ||
| @pre_Index = @cur_Index; | ||
| $CCC = $CCC+1; | ||
| } | ||
| } | ||
| $pre_POS = $ijk; | ||
| } # ijk | ||
| $NEW_EXON{$CCC-1}{"end"} = $i_end; | ||
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| ### print data structure | ||
| for my $CCC (sort {$a<=>$b} keys %NEW_EXON) | ||
| { | ||
| print RRR "$ID\t$i_chrom\t$i_strand\t"; | ||
| my $sss = $NEW_EXON{$CCC}{"start"}; | ||
| print RRR "$sss\t"; | ||
| my $eee = $NEW_EXON{$CCC}{"end"}; | ||
| print RRR "$eee\t"; | ||
| my $Read_C = 0; | ||
| #for (my $abc=$sss; $abc<=$eee; $abc++) | ||
| #{ | ||
| # my $value = exists $genome{$i_chrom}{$abc} ? $genome{$i_chrom}{$abc} : 0; | ||
| # $Read_C =$Read_C+$value; | ||
| #} | ||
| #print RRR "$Read_C\t"; | ||
| my @index_get = $NEW_EXON{$CCC}{"Index"}; | ||
| for my $INDEX ( 0 .. $#{$NEW_EXON{$CCC}{"Index"}}){ | ||
| my $index_get = $NEW_EXON{$CCC}{"Index"}[$INDEX]; | ||
| print RRR "$index_get,"; } | ||
| print RRR "\n"; | ||
| #print "haha\n"; | ||
| } ### for CCC | ||
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| } # if size | ||
| } #i : Cluster ID -1 | ||
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| close(SAM); | ||
| close(REF); | ||
| close(RRR); | ||
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| =head1 SYNOPSIS | ||
| -r ---RefSeqAnnotation file | ||
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| -o ---The file name that you want to save the results |
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