Mercurial > repos > brasset_jensen > srnapipe
diff lib/sRNAPipe/align.pm @ 64:967512924317 draft
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
| author | brasset_jensen |
|---|---|
| date | Mon, 28 Jan 2019 11:57:15 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/align.pm Mon Jan 28 11:57:15 2019 -0500 @@ -0,0 +1,551 @@ +package sRNAPipe::align; + +use strict; +use warnings; +use File::Basename; +use String::Random; + +use FindBin; +use lib "$FindBin::Bin/../lib"; +use sRNAPipe::Rcall qw ( histogram ); + +use Exporter; +our @ISA = qw( Exporter ); +our @EXPORT = qw( &rpms_rpkm_te &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam ); + +sub to_build +{ + my ( $toBuildTabP, $log, $newdir ) = @_; + + foreach my $pairs ( @{ $toBuildTabP } ) + { + if ( $pairs->[0] == 1 ) + { + my $sym = $newdir.basename(${$pairs->[1]}).'_symlink.fa'; + symlink( ${$pairs->[1]}, $sym ); + ${$pairs->[1]} = $sym; + build_index ( ${$pairs->[1]}, $log ); + } + } +} + +sub build_index +{ + my $to_index = shift; + my $log = shift; + my $index_log = $to_index.'_index.err'; + `bwa index '$to_index' 2> '$index_log'`; + print $log "Creating index for $to_index\n"; +} + +sub get_unique +{ + my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_; + + my $fout = $col_prefix.'_all_mappers.fastq'; + my $funi = $col_prefix.'_unique_mappers.fastq'; + my $frej = $col_prefix.'_unmapped.fastq'; + + my $repartition = $out_prefix.'distribution.txt'; + my $png_rep = $out_prefix.'distribution.png'; + my ( %duplicates, %genome_hits) ; + + #alignement to the first reference + my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report ); + my $ref_fai = $return[4]; + my $mappers = $return[5]; + my $mappers_uni = $return[6]; + my $size_mappedHashR = $return[7]; + + if ( $details == 1 ) + { + #print number of duplicates and hits number + my ($pourcentage, $total) =(0,0); + + $total += $_ foreach values %{$size_mappedHashR}; + open (my $rep, '>'.$repartition) || die "cannot create $repartition $!\n"; + print $rep "size\tnumber\tpercentage\n"; + foreach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR})) + { + $pourcentage = 0; + $pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0; + + print $rep "$k\t$size_mappedHashR->{$k}\t"; + printf $rep "%.2f\n",$pourcentage; + } + + histogram($size_mappedHashR, $png_rep, $total); + + + my $dup = $out_prefix.'dup_mapnum.txt'; + my $dup_u = $out_prefix .'dup_unique.txt'; + my $dup_r = $out_prefix .'dup_nonmapp.txt'; + open(my $tab,">".$dup) || die "cannot open output txt file\n"; + open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n"; + open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n"; + print $tab "sequence\tcount\tmapnum\n"; + print $tab_u "sequence\tcount\n"; + print $tab_r "sequence\tcount\n"; + foreach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates) + { + $duplicates{$k} = 0 unless exists($duplicates{$k}); + $genome_hits{$k} = 0 unless exists($genome_hits{$k}); + if ($genome_hits{$k} != 0) { print $tab $k."\t".$duplicates{$k}."\t".$genome_hits{$k}."\n"; } + else {print $tab_r $k."\t".$duplicates{$k}."\n";} + if ($genome_hits{$k} == 1) { print $tab_u $k."\t".$duplicates{$k}."\n"; } + } + close $dup; close $dup_r; close $dup_u; + } + return ( $ref_fai, $mappers, $mappers_uni ); +} + +sub sam_parse +{ + my ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ; + my ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size); + $mappers = $mappersUnique = $reads = 0; + + open my $fic, '<', $sam || die "cannot open $sam $!\n"; + open my $accepted, '>', $fastq_accepted || die "cannot create $fastq_accepted $! \n"; + open my $unique, '>', $fastq_accepted_unique || die "cannot create $fastq_accepted_unique $! \n"; + open my $rejected, '>', $fastq_rejected || die "cannot create $fastq_rejected $! \n"; + open my $sam_uni, '>', $sam_unique || die "cannot create $sam_unique $! \n"; + my $sequence = ''; + while(<$fic>) + { + chomp $_; + if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) + { + if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) + { + $size{$1} = $2; + $unique_number{$1} = 0; + $number{$1} = 0; + $numberNM{$1} = 0; + $numberM{$1} = 0; + } + print $sam_uni $_."\n"; + next; + } + $reads++; + my @line = split (/\t/,$_); + $sequence = $line[9]; + if ($line[1] & 16) + { + $sequence =reverse($sequence); + $sequence =~ tr/atgcuATGCU/tacgaTACGA/; + } + if ($line[1] == 16 || $line[1] == 0) + { + my $len = length($sequence); + $size_num{$len} ++; + $size_num_spe{$line[2]}{$len}++; + $mappers ++; + + ${$best_hit_number_hashR}{$sequence} = $1 if ($line[13] =~ /X0:i:(\d*)/ || $line[14] =~/X0:i:(\d*)/ ); + ${$duplicate_hashR}{$sequence}++; + $number{$line[2]}++; + $numberSens{$line[2]}++ if $line[1] == 0 ; + $numberReverse{$line[2]}++ if $line[1] == 16 ; + print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; + + if ($line[11] eq "XT:A:U") + { + $unique_number{$line[2]}++; + $mappersUnique++; + print $unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; + print $sam_uni $_."\n"; + } + if ($_ =~ /.*XM:i:(\d+).*/) + { + if ($1 == 0){$numberNM{$line[2]}++;}else{$numberM{$line[2]}++;} + } + } + else + { + ${$best_hit_number_hashR}{$sequence} = 0; + ${$duplicate_hashR}{$sequence}++; + print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; + } + } + close $fic; close $accepted; close $unique; close $rejected; close $sam_uni; + + print $report "Parsing $sam file\n"; + print $report "\treads: $reads\n"; + print $report "\tmappers: $mappers\n"; + print $report "\tunique mappers: $mappersUnique\n"; + print $report "-----------------------------\n"; + return (\%number, \%unique_number, \%numberSens, \%numberReverse, \%size, $mappers, $mappersUnique, \%size_num, \%size_num_spe, \%numberNM, \%numberM ); +} + +sub get_hash_alignment +{ + my ($index, $mismatches, $accept, $reject, $outA, $outR, $fastq, $number_of_cpus, $name, $sam, $report, $fai_f) = @_ ; + my ($reads, $mappers, $unmapped) = (0,0,0); + my $accep_unique; + BWA_call ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ); + + open my $fic, '<', $sam || die "cannot open $sam $!\n"; + open my $accepted, '>', $outA || die "cannot open $outA\n" if $accept == 1; + open my $rejected, '>', $outR || die "cannot open $outR\n" if $reject == 1; + open my $fai, '>', $fai_f || die "cannot open $fai_f\n" if $fai_f; + #if ($name eq "snRNAs") { + # open ( $accep_unique, ">".$1."-unique.fastq") if $outR =~ /(.*)\.fastq/; + #} + my $sequence = ''; + while(<$fic>) + { + chomp $_; + if( $_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) + { + if ($fai_f && $_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) + { + print $fai $1."\t".$2."\n"; + } + next; + } + $reads++; + my @line = split (/\t/,$_); + $sequence = $line[9]; + if ($line[1] & 16) + { + $sequence =reverse($sequence); + $sequence =~ tr/atgcuATGCU/tacgaTACGA/; + } + if ($line[1] & 16 || $line[1] == 0) + { + $mappers ++; + if ($accept == 1 ) + { + print $accepted "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; + # print $accep_unique "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if ($name eq "snRNAs" && $line[11] eq "XT:A:U"); + } + } + else + { + print $rejected "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n" if $reject == 1; + $unmapped++; + } + } + # close $accep_unique if ($name eq "bonafide_reads"); + close $fic; + close $accepted if $accept == 1; + close $rejected if $reject ==1; + close $fai if $fai_f; + print $report "\treads: $reads\n"; + print $report "\tmappers: $mappers\n"; + print $report "\tunmapped: $unmapped\n"; + print $report "-----------------------------\n"; + return ($mappers, $unmapped); +} + +sub sam_count +{ + my $sam = shift; + my ( %number, %size ); + + open my $fic, '<', $sam || die "cannot open $sam file $!\n"; + while(<$fic>) + { + chomp $_; + if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) + { + if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) + { + $size{$1} = $2; + $number{$1} = 0; + } + } + else + { + my @line = split (/\t/,$_); + if ( $line[1] & 16 || $line[1] == 0 ) + { + $number{$line[2]}++; + } + } + } + close $fic; + return ( \%number, \%size ); +} + +sub sam_count_mis +{ + + my $sam = shift; + my ( %number, %numberNM, %numberM, %size); + + open my $fic, '<', $sam || die "cannot open $sam file $!\n"; + while(<$fic>) + { + chomp $_; + if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) + { + if ($_ =~ /\@SQ\tSN:(.*)\tLN:(\d*)/) + { + $size{$1} = $2; + $number{$1} = [0,0,0,0,0,0,0]; + $numberNM{$1} = [0,0,0,0,0,0,0]; + $numberM{$1} = [0,0,0,0,0,0,0]; + } + } + else + { + my @line = split (/\t/,$_); + my @seq = split //, $line[9]; + if ( $line[1] == 16 || $line[1] == 0 ) + { + $number{ $line[2] }->[0]++; + if ($line[1] == 0) + { + $number{$line[2]}->[1]++; + $number{$line[2]}->[3]++ if $seq[0] eq 'T'; + $number{$line[2]}->[5]++ if $seq[9] eq 'A'; + } + else + { + $number{$line[2]}->[2]++; + $number{$line[2]}->[4]++ if $seq[9] eq 'A'; + $number{$line[2]}->[6]++ if $seq[0] eq 'T'; + } + if ($_ =~ /.*XM:i:(\d+).*/) + { + if ( $1 == 0 ) + { + $numberNM{$line[2]}->[0]++; + if ($line[1] == 0) + { + $numberNM{$line[2]}->[1]++; + $numberNM{$line[2]}->[3]++ if $seq[0] eq 'T'; + $numberNM{$line[2]}->[5]++ if $seq[9] eq 'A'; + } + else + { + $numberNM{$line[2]}->[2]++; + $numberNM{$line[2]}->[4]++ if $seq[9] eq 'A'; + $numberNM{$line[2]}->[6]++ if $seq[0] eq 'T'; + } + } + else + { + $numberM{$line[2]}->[0]++; + if ($line[1] == 0) + { + $numberM{$line[2]}->[1]++; + $numberM{$line[2]}->[3]++ if $seq[0] eq 'T'; + $numberM{$line[2]}->[5]++ if $seq[9] eq 'A'; + } + else + { + $numberM{$line[2]}->[2]++; + $numberM{$line[2]}->[4]++ if $seq[9] eq 'A'; + $numberM{$line[2]}->[6]++ if $seq[0] eq 'T'; + } + } + } + } + } + } + return (\%number, \%size, \%numberNM, \%numberM ); +} + +sub rpms_rpkm_te +{ + my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_; + open(my $out, ">".$out_file) || die "cannot open normalized file $! \n"; + print $out "ID\treads counts\tRPKM"; + print $out "\tper million of piRNAs" if ($piRNA_number != 0); + print $out "\tper million of miRNAs" if ($miRNA_number != 0); + print $out "\tper million of bonafide reads" if ($bonafide_number != 0); + print $out "\tsense reads counts\treverse reads counts"; + print $out "\t% of sense 1U\t% of sense 10A\t% of reverse 1U\t% of reverse 10A\n"; + foreach my $k ( sort keys %{$counthashR} ) + { + my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0); + + $rpkm = ( $counthashR->{$k}->[0] * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ; + print $out $k."\t".$counthashR->{$k}->[0]."\t"; printf $out "%.2f",$rpkm; + + if ($piRNA_number != 0 ) + { + $pirna = ( $counthashR->{$k}->[0] * 1000000) / $piRNA_number; + printf $out "\t%.2f",$pirna; + } + if ($miRNA_number != 0 ) + { + $mirna = ( $counthashR->{$k}->[0] * 1000000) / $miRNA_number; + printf $out "\t%.2f",$mirna; + } + if ($bonafide_number != 0 ) + { + $bonafide = ( $counthashR->{$k}->[0] * 1000000) / $bonafide_number; + printf $out "\t%.2f",$bonafide; + } + + print $out "\t".$counthashR->{$k}->[1]."\t".$counthashR->{$k}->[2] ; + my $S1U = 0; + $S1U = $counthashR->{$k}->[3] / $counthashR->{$k}->[1] * 100 if $counthashR->{$k}->[1] != 0; + my $R1U = 0; + $R1U = $counthashR->{$k}->[6] / $counthashR->{$k}->[2] * 100 if $counthashR->{$k}->[2] != 0; + my $S10A = 0; + $S10A = $counthashR->{$k}->[5] / $counthashR->{$k}->[1] * 100 if $counthashR->{$k}->[1] != 0; + my $R10A = 0; + $R10A = $counthashR->{$k}->[4] / $counthashR->{$k}->[2] * 100 if $counthashR->{$k}->[2] != 0; + print $out "\t".$S1U."\t".$S10A."\t".$R1U."\t".$R10A; + + print $out "\n"; + } + close $out; +} + + +sub sam_to_bam_bg +{ + my ( $sam, $scale, $number_of_cpus ) = @_; + my ( $bam_sorted, $bedgraphM, $bedgraphP, $view_err, $sort_err ) = ( '', '', '', '', '' ); + if ( $sam =~ /(.*?).sam$/ ) + { + $bam_sorted = $1.'_sorted.bam'; + $bedgraphP= $1.'_plus.bedgraph'; + $bedgraphM = $1.'_minus.bedgraph'; + $view_err = $1.'_view.err'; + $sort_err = $1.'_sort.err'; + } + `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; + `bedtools genomecov -scale $scale -strand + -bga -ibam '$bam_sorted' > '$bedgraphP'`; + `bedtools genomecov -scale $scale -strand - -bga -ibam '$bam_sorted' > '$bedgraphM'`; +} + +sub sam_sorted_bam +{ + my ( $sam, $number_of_cpus ) = @_; + my ( $bam_sorted, $view_err, $sort_err ) = ( '', '', '' ); + if ( $sam =~ /(.*?).sam$/ ) + { + $bam_sorted = $1.'_sorted.bam'; + $view_err = $1.'_view.err'; + $sort_err = $1.'_sort.err'; + + } + `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`; +} + +sub BWA_call +{ + my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_; + my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 ); + print $report "-----------------------------\n"; + print $report "bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam'\n"; + `bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam' `; +} + +sub rpms_rpkm +{ + my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_; + open(my $out, ">".$out_file) || die "cannot open normalized file $! \n"; + print $out "ID\treads counts\tRPKM"; + print $out "\tper million of piRNAs" if ($piRNA_number != 0); + print $out "\tper million of miRNAs" if ($miRNA_number != 0); + print $out "\tper million of bonafide reads" if ($bonafide_number != 0); + print $out "\n"; + foreach my $k ( sort keys %{$counthashR} ) + { + my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0); + + $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ; + print $out $k."\t".$counthashR->{$k}."\t"; printf $out "%.2f",$rpkm; + + if ($piRNA_number != 0 ) + { + $pirna = ( $counthashR->{$k} * 1000000) / $piRNA_number; + printf $out "\t%.2f",$pirna; + } + if ($miRNA_number != 0 ) + { + $mirna = ( $counthashR->{$k} * 1000000) / $miRNA_number; + printf $out "\t%.2f",$mirna; + } + if ($bonafide_number != 0 ) + { + $bonafide = ( $counthashR->{$k} * 1000000) / $bonafide_number; + printf $out "\t%.2f",$bonafide; + } + print $out "\n"; + } + close $out; +} + +sub extract_sam +{ + my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_; + + open my $s_in, '<', $sam_in || die "cannot open $sam_in file $!\n"; + + open my $f_out, '>', $fastq_out || die "cannot create $fastq_out $!\n"; + open my $f_uni_out, '>', $fastq_uni_out || die "cannot create $fastq_uni_out $!\n"; + + open my $s_out, '>', $sam_out || die "cannot create $sam_out file $!\n" if defined ($hashRef); + open my $s_uni_out, '>', $sam_uni_out || die "cannot create $sam_uni_out file $!\n"; + + my $sequence = ''; + while(<$s_in>) + { + if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ) + { + print $s_out $_ if defined ($hashRef); + print $s_uni_out $_; + next; + } + my @line = split (/\t/,$_); + $sequence = $line[0]; + if ( (! defined ($hashRef) )|| ( exists $hashRef->{$sequence} && $hashRef->{$sequence} == 1 ) ) + { + my $arn = $line[9]; + if ($line[1] & 16) + { + $arn =reverse($arn); + $arn =~ tr/atgcuATGCU/tacgaTACGA/; + } + + if ( ( $line[1] == 16 || $line[1] == 0 ) ) + { + print $f_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ; + print $s_out $_ if defined ($hashRef); + if ( $line[11] eq "XT:A:U" ) + { + print $f_uni_out "\@".$line[0]."\n".$arn."\n+\n".$line[10]."\n" ; + print $s_uni_out $_ ; + } + } + } + } + close $s_in; close $s_out if defined ($hashRef); + close $s_uni_out; close $f_out; close $f_uni_out; +} + +sub get_fastq_seq +{ + my $fastq = shift; + my %hash; my $cmp = 0; + + open my $fic, '<', $fastq || die "cannot open input file $! \n"; + while(<$fic>) + { + chomp $_; + $cmp++; + if ($cmp % 4 == 1) + { + die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); + if ($_ =~ /^\@(.*)\s.*/) { $hash{$1} = 1;} + elsif ($_ =~ /^\@(.*)/) { $hash{$1} = 1;} + } + elsif ($cmp % 4 == 3 ) + { + die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; + } + } + close $fic; + return \%hash; +} + +1;