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Merge pull request #32 from Eco-Flow/nf-test-dev
Nf test dev
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| Original file line number | Diff line number | Diff line change |
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@@ -3,6 +3,6 @@ Results | |
| Go | ||
| .nextflow* | ||
| .DS_Store | ||
| .nf-test | ||
| .nf-test.log | ||
| test-results | ||
| .nf-test* | ||
| nextflow | ||
| nf-test | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| repository_type: pipeline |
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| #!/usr/bin/perl | ||
| use warnings; | ||
| use strict; | ||
| use List::Util qw(max); | ||
| use List::Util qw(min); | ||
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| my @breaks=`ls *Break_junction_information.txt`; | ||
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| #Summary of all runs: | ||
| my $outname="Trans_Inversion_junction_count.txt"; | ||
| open(my $OUT, ">", $outname) or die "Could not open $outname\n"; | ||
| #Print header of output file- see after 236 where we print this line | ||
| print $OUT "Comparison\tTranslocation_junctions\tInversion_junctions\tSame_direction_duplication_junctions\tLoop_direction_duplication_junctions\n"; | ||
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| foreach my $file (@breaks){ | ||
| chomp $file; | ||
| #Sort out which name comparison we are making | ||
| my @split_name=split(/\./, $file); | ||
| my $species1=$split_name[0]; | ||
| my $species2=$split_name[1]; | ||
| my $combName="$species1\.$species2"; | ||
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| #Initiate out file handle | ||
| my $outfile="$combName\.Classification_summary.tsv"; | ||
| open(my $out, ">", $outfile) or die "Could not open $outfile \n"; | ||
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| #Read in syntenic anchor files (produced by MScanX using the program jcvi) | ||
| my $in_break_file="$combName\.Break_junction_information.txt"; | ||
| open(my $in_break, "<", $in_break_file) or die "Could not open $in_break_file\n"; | ||
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| #Store for each syntenic blocks gene order in sp2. Needed for next script. | ||
| my $in_sp2_order="$combName\.Sp2_synteny_order.txt"; | ||
| open(my $in_order, "<", $in_sp2_order) or die "Could not open $in_sp2_order\n"; | ||
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| #First read in the synteny order file so we have a hash that tells us exactly where all the genes are location. Based on their order. | ||
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| my %gene_order_all; | ||
| my %gene_order_max; | ||
| my %gene_order_min; | ||
| my %position_to_syntenic_block; | ||
| while ( my $line1 = <$in_order> ){ | ||
| chomp $line1; | ||
| my @sp=split("\t", $line1); | ||
| my $chr=$sp[0]; | ||
| my $syn=$sp[1]; | ||
| my $list=$sp[2]; | ||
| my @array_list=split("\,", $list); | ||
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| if ($line1 =~ m/Synteny_block_number/g){ | ||
| #ignore this line, its the header | ||
| } | ||
| else{ | ||
| $gene_order_all{$chr}{$syn}=$list; | ||
| $gene_order_max{$chr}{$syn}=max(@array_list); | ||
| $gene_order_min{$chr}{$syn}=min(@array_list); | ||
| } | ||
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| #then loop through the genes in each block to assign each position to a syntenic block number | ||
| foreach my $gene_pos (@array_list){ | ||
| $position_to_syntenic_block{$chr}{$gene_pos}=$syn; | ||
| } | ||
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| } | ||
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| my $removeheader=<$in_break>; | ||
| my $odd_junction=0; | ||
| my $same_direction=0; | ||
| my $inversions=0; | ||
| my $translocations=0; | ||
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| #For each my apparetn syntenic block. | ||
| #Check first if the gene in syntenic block 1, from range min to max, are found within any other sytenic block on the same chromosome. | ||
| while ( my $line2 = <$in_break> ){ | ||
| chomp $line2; | ||
| #print "START\n$line2\n"; | ||
| my @sp=split("\t", $line2); | ||
| my $chr=$sp[0]; | ||
| my $syn1=$sp[1]; | ||
| my $syn2=$sp[2]; | ||
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| my $sta_1=$sp[3]; | ||
| my $end_1=$sp[4]; | ||
| my $sta_2=$sp[5]; | ||
| my $end_2=$sp[6]; | ||
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| my $type_original=$sp[7]; | ||
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| #calcualte direction of block | ||
| my $direction_1; | ||
| if ($sta_1 == $end_1){ | ||
| $direction_1=0; | ||
| } | ||
| elsif($sta_1 < $end_1){ | ||
| $direction_1=1; | ||
| } | ||
| else{ | ||
| $direction_1=-1; | ||
| } | ||
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| my $direction_2; | ||
| if ($sta_2 == $end_2){ | ||
| $direction_2=0; | ||
| } | ||
| elsif($sta_2 < $end_2){ | ||
| $direction_2=1; | ||
| } | ||
| else{ | ||
| $direction_2=-1; | ||
| } | ||
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| my $min_block1=$gene_order_min{$chr}{$syn1}; | ||
| my $max_block1=$gene_order_max{$chr}{$syn1}; | ||
| my $min_block2=$gene_order_min{$chr}{$syn2}; | ||
| my $max_block2=$gene_order_max{$chr}{$syn2}; | ||
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| #calculate the gene order numbers from within the two blocks: | ||
| #Didn't work, as many of the syntenic blocks have genes have genes from random chromosomes or from the same chromosome in them. Could be TEs, or indels? | ||
| #print "$min_block1 $max_block1\n"; | ||
| #for (my $i=$min_block1; $i<=$max_block1; $i++){ | ||
| # if ($position_to_syntenic_block{$chr}{$i}){ | ||
| # if ($position_to_syntenic_block{$chr}{$i} ne $syn1){ | ||
| # print "Can happen : $position_to_syntenic_block{$chr}{$i}\n"; | ||
| # } | ||
| # } | ||
| #} | ||
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| #try to calculate the smallest gap between the two blocks. | ||
| my $gap; | ||
| my $minmax=min($sta_1,$end_1)-max($sta_2,$end_2); | ||
| my $maxmin=max($sta_1,$end_1)-min($sta_2,$end_2); | ||
| if ($minmax <= $maxmin){ | ||
| $gap=$minmax; | ||
| } | ||
| else{ | ||
| $gap=$maxmin; | ||
| } | ||
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| if ($type_original eq "INVER"){ | ||
| my $junction_type; | ||
| #try to detect if its an inversion: | ||
| if ($direction_1==0 || $direction_2==0){ | ||
| $odd_junction++; | ||
| $junction_type="Odd-duplicate"; | ||
| } | ||
| elsif($direction_1==1 && $direction_2==1){ | ||
| $same_direction++; | ||
| $junction_type="Same_direction"; | ||
| } | ||
| elsif($direction_1==0 && $direction_2==0){ | ||
| $same_direction++; | ||
| $junction_type="Same_direction"; | ||
| } | ||
| else{ | ||
| #rest must be inversions: | ||
| $junction_type="Inversion"; | ||
| $inversions++; | ||
| } | ||
| print $out "$chr\t$syn1\t$syn2\t$min_block1\t$max_block1\t$sta_1\t$end_1\t$sta_2\t$end_2\t$gap\t$junction_type\n"; | ||
| } | ||
| else{ | ||
| #Then its a translocation, we cannot caluclate a gap | ||
| print $out "$chr\t$syn1\t$syn2\t$min_block1\t$max_block1\t$sta_1\t$end_1\t$sta_2\t$end_2\tNA\tTranslocation\n"; | ||
| $translocations++; | ||
| } | ||
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| } | ||
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| print $OUT "$combName\t$translocations\t$inversions\t$same_direction\t$odd_junction\n"; | ||
| print "Translocations: $translocations\nInversions: $inversions\nSame_direction_likely_duplicate: $same_direction\nOdd_direction_likely_duplicates : $odd_junction \n\#(likely duplicated, one of the syntenic block starts and ends with the same gene)\nSame_direction $same_direction \n\#Gene order in same direction (so not an inversion [or translocation]), could be caused by duplications\n\n"; | ||
| close $out; | ||
| close $in_break; | ||
| close $in_order; | ||
| } | ||
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