1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/d5ce1d53e611/ changeset: r5037:d5ce1d53e611 user: guru date: 2011-02-10 16:33:08 summary: Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool. affected #: 2 files (2.6 KB)

--- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Thu Feb 10 10:33:08 2011 -0500 @@ -18,7 +18,12 @@ #------------------------------------------------------------------------------- # WHICH SPUTNIK USED? my $sputnikpath = (); -$sputnikpath = "sputnik" ; +$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC"; +#print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath; +#exit if !-e $sputnikpath; +#$sputnikpath = "bx-sputnik" ; +#print "ARGV input = @ARGV\n"; +#print "ARGV input :\n mafile=$mafile\n orthfile=$orthfile\n threshold_array=$threshold_array\n species_set=$species_set\n tree_definition=$tree_definition\n separation=$separation\n"; #------------------------------------------------------------------------------- # RUNFILE #------------------------------------------------------------------------------- @@ -37,9 +42,12 @@ my $tdir = tempdir( CLEANUP => 0 ); chdir $tdir; my $dir = getcwd; +#print "current dit=$dir\n"; #------------------------------------------------------------------------------- # CREATE AXT FILES IN FORWARD AND REVERSE ORDERS IF NECESSARY my @chrfiles=(); + +#my $mafile = "/Users/ydk/work/rhesus_microsat/results/galay/align.txt"; #$ARGV[0]; my $chromt=int(rand(10000)); my $p_chr=$chromt;

@@ -54,20 +62,27 @@ push @exactspecies, $spec if $spec eq $espec; } } +#print "exactspecies=@exactspecies\n"; my $focalspec = $exactspecies[0]; my $arranged_species_set=join(".",@exactspecies); my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt"); +#print "sending to maftoAxt_multispecies: $mafile, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; maftoAxt_multispecies($mafile, $tree_definition, $chr_name, $species_set); +#print "done maf to axt conversion\n"; my $reverse_chr_name = join(".",("chr".$p_chr."r"),$arranged_species_set, "net", "axt"); artificial_axdata_inverter ($chr_name, $reverse_chr_name); +#print "reverse_chr_name=$reverse_chr_name\n"; #------------------------------------------------------------------------------- +# FIND THE CORRESPONDING CHIMP CHROMOSOME FROM FILE ORTp_chrS.TXT foreach my $direct ("reverse_direction","forward_direction"){ $p_chr=$chromt; + #print "direction = $direct\n"; $p_chr = $p_chr."r" if $direct eq "reverse_direction"; $p_chr = $p_chr if $direct eq "forward_direction"; my $config = $species_set; $config=~s/,/./g; my @orgs = split(/./,$arranged_species_set); + #print "ORGS= @orgs\n"; my @tag=@orgs; @@ -80,6 +95,7 @@ my $ptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1])."-".$threshold_array; my @sp_tags = (); + #print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n"; foreach my $sp (@tag){ push(@sp_tags, ($sp.".".$ptag)); } @@ -105,6 +121,10 @@ push(@title_queries, $title); } my $title_query = join($sep, @title_queries); + #print "title_queries=@title_queries\n"; + #print "query = >$title_query<\n"; + #print "orgs = @orgs\n"; + #------------------------------------------------------------------------------- # GET AXTNET FILES, EDIT THEM AND SPLIT THEM INTO HUMAN AND CHIMP INPUT FILES my $t1input = $pchr.".".$arranged_species_set.".net.axt"; @@ -115,6 +135,8 @@ } multi_species_t1($t1input,$tags,(join(",", @t1outputs)), $title_query); + #print "t1outputs=@t1outputs\n"; + #print "done t1\n"; #------------------------------------------------------------------------------- #START T2.PL @@ -261,6 +283,7 @@ multispecies_filtering_compound_microsats($compound_microsats, $compound_filterout, $compound_residue,$threshold_array,$threshold_array,scalar(@sp_tags)); $species_counter++; } + #print "done filtering both simple and compound microsatellites \n"; #------------------------------------------------------------------------------- @@ -289,6 +312,7 @@ } $sp_counter++; } + #print "\ndone grouping interrupted & simple microsats based on their motif size for further extention\n"; #------------------------------------------------------------------------------- # BREAK CHROMOSOME INTO PARTS OF CERTAIN NO. CONTIGS EACH, FOR FUTURE SEARCHING OF INTERRUPTED MICROSATELLITES @@ -311,6 +335,7 @@

my @unionarray = (); + #print "splist=@splist\n"; #------------------------------------------------------------------------------- # FIND INTERRUPTED MICROSATELLITES @@ -426,6 +451,7 @@ #xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx

sub maftoAxt_multispecies { + #print "in maftoAxt_multispecies : got @_\n"; my $fname=$_[0]; open(IN,"<$_[0]") or die "Cannot open $_[0]: $! \n"; my $treedefinition = $_[1]; @@ -443,6 +469,7 @@ push @exactspecies, $spec if $spec eq $espec; } } + #print "exactspecies=@exactspecies\n"; ########### my $select = 2; @@ -453,7 +480,9 @@ my @allowedset = (); @allowedset = split(/;/,allowedSetOfSpecies(join("_",@species))) if $select == 0; @allowedset = join("_",0,@species) if $select == 1; + #print "species = @species , allowedset =",join("\n", @allowedset) ," \n"; @allowedset = join("_",0,@exactspecies) if $select == 2; + #print "allowedset = @allowedset and exactspecies = @exactspecies\n"; my $start = 0; my @sequences = (); @@ -474,6 +503,7 @@ } if ($line =~ /^s /){ + # print "fields1 = $fields[1] , start = $start\n"; foreach my $sp (@species){ if ($fields[1] =~ /$sp/){ @@ -493,12 +523,14 @@ my $arrno = 0; foreach my $set (@allowedset){ if ($arranged eq $set){ + # print "$arranged == $set\n"; $stopper = 0; last; } $arrno++; } if ($stopper == 0) { + # print " accepted\n"; @titles = split ";", orderInfo(join(";", @titles), $species_counter, $arranged) if $species_counter ne $arranged; @sequences = split ";", orderInfo(join(";", @sequences), $species_counter, $arranged) if $species_counter ne $arranged; my $filteredseq = filter_gaps(@sequences); @@ -519,6 +551,7 @@ } } +# print "countermatch = $countermatch\n"; }

sub reorderSpecies{ @@ -535,6 +568,7 @@

sub filter_gaps{ my @sequences = @_; +# print "sequences sent are @sequences\n"; my $seq_length = length($sequences[0]); my $seq_no = scalar(@sequences); my $allgaps = (); @@ -557,7 +591,9 @@ for my $u (0 ... $#seq_array){ $bases = $bases.$seq_array[$u][$g]; } +# print $bases, "\n"; if ($bases eq $allgaps){ +# print "bases are $bases, position is $g \n"; for my $seq (@seq_array){ splice(@$seq , $g, 1); } @@ -580,6 +616,7 @@ sub allowedSetOfSpecies{ my @allowed_species = split(/_/,$_[0]); unshift @allowed_species, 0; +# print "allowed set = @allowed_species \n"; my @output = (); for (0 ... scalar(@allowed_species) - 4){ push(@output, join("_",@allowed_species)); @@ -626,14 +663,15 @@ my @fields = split(/\s*/,$line); $final_line = join("",reverse(@fields)); - print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; # $trycounter++; + # print "trying again....$trycounter : $final_line\n" if $final_line eq $line; # } } - print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; if ($line =~ /^[0-9]/){ - $line =~ s/chr([0-9a-b]+)/chr$1r/g; + $line =~ s/chr([A-Z0-9a-b]+)/chr$1r/g; $final_line = $line; } print OUT $final_line,"\n"; @@ -649,7 +687,7 @@ sub multi_species_t1 {

my $input1 = $_[0]; - #print "@_\n"; #<STDIN>; +# print "@_\n"; #<STDIN>; my @tags = split(/_/, $_[1]); my @outputs = split(/,/, $_[2]); my $title_query = $_[3]; @@ -1678,7 +1716,7 @@ $key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12); } else{ - print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [+|-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [+|-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; +# print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [+|-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [+|-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; } if (exists $micros{$key}){ @@ -1686,8 +1724,8 @@ delete $micros{$key}; foreach my $line (@microstring){ - print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; - print "microsat = $line" if $printer == 1; +# print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; +# print "microsat = $line" if $printer == 1; $linecounter++; my $copy_line = $line; my @mields = split(/\t/,$line); @@ -1704,7 +1742,7 @@ my @microields = split(/][a-zA-Z|-]*[/,$microsatcopy); my @inields = split(/[[a-zA-Z|-]*]/,$microsat); my $absolutstart = 1; my $absolutend = $absolutstart + ($end-$start); - print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; +# print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; shift @inields; #print "inields =@inields<\n"; $motifline =~ s/^[|]$//gs; @@ -1790,11 +1828,11 @@ if ($rightstopper == 1 && $leftstopper == 1){ print COMP $line; - print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; +# print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; next; } - print "pased initial testing phase \n" if $printer == 1; +# print "pased initial testing phase \n" if $printer == 1; my @outputs = (); my @orig_starts = (); my @orig_ends = (); @@ -1845,7 +1883,7 @@ while($lefter == 1){ $newline = left_extender($templine, $seq,$org); - print "returned line from left extender= $newline \n" if $printer == 1; +# print "returned line from left extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} @@ -1853,7 +1891,7 @@ } while($righter == 1){ $newline = right_extender($templine, $seq,$org); - print "returned line from right extender= $newline \n" if $printer == 1; +# print "returned line from right extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} if (right_extention_permission_giver($templine) eq "no") {last;} @@ -1864,7 +1902,7 @@ my @tempmotields = split(/][/,$tempfields[$motifcord]); if (scalar(@tempmotields) == 1 && $templine eq $orig_templine) { - print "scalar ( tempmotields) = 1\n" if $printer == 1; +# print "scalar ( tempmotields) = 1\n" if $printer == 1; next; } my $prevmotif = shift(@tempmotields); @@ -1877,7 +1915,7 @@ $prevmotif = $tempmot; } if ( $stopper == 1) { - print "length tempmot != length prevmotif\n" if $printer == 1; +# print "length tempmot != length prevmotif\n" if $printer == 1; next; } my $lastend = 0; @@ -1886,32 +1924,32 @@ my $left_bp = (); my $right_bp = (); # print "new startcord = $tempfields[$startcord] , new endcord = $tempfields[$endcord].. orig strts = @orig_starts and orig ends = @orig_ends\n"; for my $o (0 ... $#orig_starts){ - print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; - print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; if (($tempfields[$startcord] > $lastend) && ($tempfields[$startcord] <= $orig_ends[$o])){ # && ($tempfields[$startcord] != $fields[$startcord]) - print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; $left_captured = $o; $left_bp = $orig_ends[$o] - $tempfields[$startcord] + 1; } elsif ($tempfields[$endcord] > $lastend && $tempfields[$endcord] <= $orig_ends[$o]){ #&& $tempfields[$endcord] != $fields[$endcord]) - print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; $right_captured = $o; $right_bp = $tempfields[$endcord] - $orig_starts[$o] + 1; } $lastend = $orig_ends[$o] } - print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; +# print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; my $leftmotif = (); my $left_trashed = (); if ($tempfields[$startcord] != $fields[$startcord]) { $leftmotif = $motields[$left_captured]; - print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; +# print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; if ( $left_captured !~ /[0-9]+/) {print $line,"\n", $templine,"\n"; } $left_trashed = length($microields[$left_captured]) - $left_bp; } my $rightmotif = (); my $right_trashed = (); if ($tempfields[$endcord] != $fields[$endcord]) { - print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; +# print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; $rightmotif = $motields[$right_captured]; $right_trashed = length($microields[$right_captured]) - $right_bp; } @@ -1920,54 +1958,54 @@ $stopper = 0; my $deletioner = 0; #if($tempfields[$startcord] != $fields[$startcord]){ - print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; +# print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; if ($left_captured != 0){ - print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; +# print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; for my $e (0 ... $left_captured-1){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "after left search, deletioner = $deletioner\n" if $printer == 1; +# print "after left search, deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; next; } $deletioner = 0; #if($tempfields[$endcord] != $fields[$endcord]){ - print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; +# print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; if ($right_captured != $#microields){ - print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; +# print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; for my $e ($right_captured+1 ... $#microields){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e])) ){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { next; } @@ -1977,24 +2015,24 @@ if ($tempfields[$startcord] != $fields[$startcord] ){ #print "in left params: (length($leftmotif) == 1 && $tempfields[$startcord] != $fields[$startcord]) ... and .... $left_trashed > (1.5* length($leftmotif]) && ($tempfields[$startcord] != $fields[$startcord])\n"; if (length($leftmotif) == 1 && $left_trashed > 3){ - print "invaded left motif is long mononucleotide" if $printer == 1; +# print "invaded left motif is long mononucleotide" if $printer == 1; next; } elsif ((length($leftmotif) != 1 && $left_trashed > ( thrashallow($leftmotif)) && ($tempfields[$startcord] != $fields[$startcord]) ) ){ - print "invaded left motif too long" if $printer == 1; +# print "invaded left motif too long" if $printer == 1; next; } } if ($tempfields[$endcord] != $fields[$endcord] ){ #print "in right params: after $tempfields[$endcord] != $fields[$endcord] ..... (length($rightmotif)==1 && $tempfields[$endcord] != $fields[$endcord]) ... and ... $right_trashed > (1.5* length($rightmotif))\n"; if (length($rightmotif)==1 && $right_trashed){ - print "invaded right motif is long mononucleotide" if $printer == 1; +# print "invaded right motif is long mononucleotide" if $printer == 1; next; } elsif (length($rightmotif) !=1 && ($right_trashed > ( thrashallow($rightmotif)) && $tempfields[$endcord] != $fields[$endcord])){ - print "invaded right motif too long" if $printer == 1; +# print "invaded right motif too long" if $printer == 1; next; } @@ -2286,8 +2324,8 @@ ##print "scalar of fields = ",scalar(@fields),"\n"; if (exists ($fields[$motifcord+1])){ - print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; - <STDIN> if !exists $fields[$motifcord+1]; +# print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; +# <STDIN> if !exists $fields[$motifcord+1]; $fields[$motifcord+1] = $fields[$motifcord+1].",indel/deletion"; } else{$fields[$motifcord+1] = "indel/deletion";} @@ -2302,7 +2340,7 @@ my @seventeen=(); if (exists ($fields[$motifcord+3])){ ##print "at 608 we are doing this:length($microsat)+$intervalposs[$nikaal]\n"; - print " print fields = @fields\n " if !exists $fields[$motifcord+3]; +# print " print fields = @fields\n " if !exists $fields[$motifcord+3]; <STDIN> if !exists $fields[$motifcord+3]; my $currpos = length($microsat)+$intervalposs[$nikaal]; $fields[$motifcord+3] = $fields[$motifcord+3].",".$currpos; @@ -2596,7 +2634,7 @@ open(SUB,">$subset"); print SUB $sine; print OUT $subset,"\n"; - print $subset,"\n"; + # print $subset,"\n"; } } close OUT; @@ -2684,7 +2722,7 @@ my @microstring = @{$micros{$key}}; delete $micros{$key}; my @filteredmicrostring; - print "sequence = $sields[$sequencepos]" if $prinkter == 1; +# print "sequence = $sields[$sequencepos]" if $prinkter == 1; foreach my $line (@microstring){ $linecounter++; my $copy_line = $line; @@ -2692,7 +2730,7 @@ my $start = $fields[$startcord]; my $end = $fields[$endcord]; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; #LOOKING FOR LEFTWARD EXTENTION OF MICROSATELLITE my $newline; while(1){ @@ -2704,7 +2742,7 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_left_extention_permission_giver($line) eq "no") {last;} - print "returned line from left extender= $line \n" if $prinkter == 1; +# print "returned line from left extender= $line \n" if $prinkter == 1; } while(1){ # print "sequence = $sields[$sequencepos]\n" if $prinkter == 1; @@ -2715,9 +2753,9 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_right_extention_permission_giver($line) eq "no") {last;} - print "returned line from right extender= $line \n" if $prinkter == 1; +# print "returned line from right extender= $line \n" if $prinkter == 1; } - print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; +# print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; my @tempfields = split(/\t/,$line); if ($tempfields[$microsatcord] =~ /[/){ @@ -2744,7 +2782,7 @@

sub multiSpecies_interruptedMicrosatHunter_left_extender{ my ($line, $seq, $org) = @_; - print "left extender, like passed = $line\n" if $prinkter == 1; +# print "left extender, like passed = $line\n" if $prinkter == 1; # print "in left extender... line passed = $line and sequence is $seq\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2763,7 +2801,7 @@ } else {$firstmotif = $motif;} - print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; my $leftphase = substr($microsat, 0,length($firstmotif)); my $phaser = $leftphase.$leftphase; my @phase = split(/\s*/,$leftphase); @@ -2779,7 +2817,7 @@ my $end = $rend; my $leftseq = substr($seq, 0, $start); - print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; +# print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2788,15 +2826,15 @@ my @intervals = (); my $firstmotif_length = length($firstmotif); foreach my $phase (@phases){ - print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; - print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; +# print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; +# print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; if ($leftseq =~ /(($phase)+([a-zA-Z|-]{0,$firstmotif_length}))$/i){ - print "in left pattern\n" if $prinkter == 1; +# print "in left pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = length($leftseq)-length($trapped); my $interval = $3; my $intervalpos = index($trapped, $interval) + 1; - print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1; +# print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1;

my $extention = substr($trapped, 0, length($trapped)-length($interval)); my $leftpeep = substr($seq, 0, ($start-length($trapped))); @@ -2804,12 +2842,12 @@ for my $i (1 ... length($phase)-1){ my $overhang = substr($phase, -length($phase)+$i); - print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; +# print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; #TEMPORARY... BETTER METHOD NEEDED $leftpeep =~ s/-//g; if ($leftpeep =~ /$overhang$/i){ push(@passed_overhangs,$overhang); - print "l overhang\n" if $prinkter == 1; +# print "l overhang\n" if $prinkter == 1; } } @@ -2817,17 +2855,17 @@ my $overhang = $passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $overhang.$extention; $trapped = $overhang.$trapped; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; $trappedpos = length($leftseq)-length($trapped); } push(@extentions,$extention); - print "extentions = @extentions \n" if $prinkter == 1; +# print "extentions = @extentions \n" if $prinkter == 1;

push(@trappeds,$trapped ); push(@intervalposs,length($extention)+1); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2837,7 +2875,7 @@ ############################ my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = "[".$trappedphases[$nikaal]."]".$fields[$motifcord]; @@ -2889,14 +2927,14 @@ if ($fields[$microsatcord] =~ /[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline; }

sub multiSpecies_interruptedMicrosatHunter_right_extender{ - print "right extender\n" if $prinkter == 1; +# print "right extender\n" if $prinkter == 1; my ($line, $seq, $org) = @_; - print "in right extender... line passed = $line\n" if $prinkter == 1; +# print "in right extender... line passed = $line\n" if $prinkter == 1; # print "line = $line, sequence = ",$seq, "\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2915,7 +2953,7 @@ } else {$temp_lastmotif = $motif;} my $lastmotif = substr($microsat,-length($temp_lastmotif)); - print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; my $rightphase = substr($microsat, -length($lastmotif)); my $phaser = $rightphase.$rightphase; my @phase = split(/\s*/,$rightphase); @@ -2931,8 +2969,8 @@ my $end = $rend; my $rightseq = substr($seq, $end+1); - print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; - print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; +# print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2941,15 +2979,15 @@ my @intervals = (); my $lastmotif_length = length($lastmotif); foreach my $phase (@phases){ - print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; - print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; +# print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; if ($rightseq =~ /^(([a-zA-Z|-]{0,$lastmotif_length}?)($phase)+)/i){ - print "in right pattern\n" if $prinkter == 1; +# print "in right pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = $end+1; my $interval = $2; my $intervalpos = index($trapped, $interval) + 1; - print "trapped = $trapped, interval = $interval\n" if $prinkter == 1; +# print "trapped = $trapped, interval = $interval\n" if $prinkter == 1;

my $extention = substr($trapped, length($interval)); my $rightpeep = substr($seq, ($end+length($trapped))+1); @@ -2960,17 +2998,17 @@

for my $i (1 ... length($phase)-1){ my $overhang = substr($phase,0, $i); - print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; +# print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; if ($rightpeep =~ /^$overhang/i){ push(@passed_overhangs, $overhang); - print "r overhang\n" if $prinkter == 1; +# print "r overhang\n" if $prinkter == 1; } } if (scalar(@passed_overhangs) > 0){ my $overhang = @passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $extention.$overhang; $trapped = $trapped.$overhang; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; } push(@extentions,$extention); @@ -2979,7 +3017,7 @@ push(@trappeds,$trapped ); push(@intervalposs,$intervalpos); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2989,7 +3027,7 @@ ################################### my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = $fields[$motifcord]."[".$trappedphases[$nikaal]."]"; @@ -3032,7 +3070,7 @@ if ($fields[$microsatcord] =~ /[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline;

} @@ -3058,7 +3096,7 @@ #print "firststretch = $firststretch\n" if $prinkter == 1; } else {$firstmotif = $motif;$firststretch = $microsat;} - print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; +# print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; if (length($firststretch) < $thresholds[length($firstmotif)]){ return "no"; } @@ -3206,20 +3244,22 @@

} sub multiSpecies_interruptedMicrosatHunter_merge{ + $prinkter = 0; +# print "~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~\n"; my $line = $_[0]; - print "sent for mering: $line \n" if $prinkter ==1; +# print "sent for mering: $line \n" if $prinkter ==1; my @mields = split(/\t/,$line); my @fields = @mields; my $microsat = allCaps($fields[$microsatcord]); my $motifline = allCaps($fields[$motifcord]); my $microsatcopy = $microsat; - print "microsat = $microsat|\n" if $prinkter ==1; +# print "microsat = $microsat|\n" if $prinkter ==1; $microsatcopy =~ s/^[|]$//sg; chomp $microsatcopy; my @microields = split(/][a-zA-Z|-]*[/,$microsatcopy); my @inields = split(/[[a-zA-Z|-]*]/,$microsat); shift @inields; - print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; +# print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; $motifline =~ s/^[|]$//sg; my @motields = split(/][/,$motifline); my @firstmotifs = (); @@ -3228,7 +3268,7 @@ $firstmotifs[$i] = substr($microields[$i],0,length($motields[$i])); $lastmotifs[$i] = substr($microields[$i],-length($motields[$i])); } - print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; +# print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; my @mergelist = (); my @inter_poses = split(/,/,$fields[$interr_poscord]); my $no_of_interruptions = $fields[$no_of_interruptionscord]; @@ -3236,52 +3276,56 @@ my @interrtypes = split(/,/,$fields[$interrtypecord]); my $stopper = 0; for my $i (0 ... $#motields-1){ - print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; +# print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; if ((allCaps($lastmotifs[$i]) eq allCaps($firstmotifs[$i+1])) && (!exists $inields[$i] || $inields[$i] !~ /[a-zA-Z]/)){ $stopper = 1; push(@mergelist, ($i)."_".($i+1)); #<STDIN> if $prinkter ==1; } } - print "mergelist = @mergelist\n" if $prinkter ==1; +# print "mergelist = @mergelist\n" if $prinkter ==1; return $line if scalar(@mergelist) == 0; - print "merging @mergelist\n" if $prinkter ==1; +# print "merging @mergelist\n" if $prinkter ==1; # <STDIN> if $prinkter ==1; foreach my $merging (@mergelist){ my @sets = split(/_/, $merging); - print "sets = @sets\n" if $prinkter ==1; +# print "sets = @sets\n" if $prinkter ==1; my @tempmicro = (); my @tempmot = (); - print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; +# print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; for my $i (0 ... $sets[0]-1){ - print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; +# print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; push(@tempmicro, "[".$microields[$i]."]"); push(@tempmicro, $inields[$i]); push(@tempmot, "[".$motields[$i]."]"); - print "adding pre-motifs number $i\n" if $prinkter ==1; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "adding pre-motifs number $i\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; } - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; my $pusher = "[".$microields[$sets[0]].$microields[$sets[1]]."]"; +# print "middle is, from @motields - @sets, number 0 which is is\n"; +# print ": $motields[$sets[0]]\n"; push (@tempmicro, $pusher); push(@tempmot, "[".$motields[$sets[0]]."]"); - push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields; + push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields && exists $sets[1] && exists $inields[$sets[1]]; my $outcoming = -2; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; for my $i ($sets[1]+1 ... $#microields){ - print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; - push(@tempmicro, "[".$microields[$i]."]"); - push(@tempmicro, $inields[$i]) unless $i == $#microields; +# print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; + push(@tempmicro, "[".$microields[$i]."]") if exists $microields[$i]; + push(@tempmicro, $inields[$i]) unless $i == $#microields || !exists $inields[$i]; push(@tempmot, "[".$motields[$i]."]"); - print "adding post-motifs number $i\n" if $prinkter ==1; +# print "adding post-motifs number $i\n" if $prinkter ==1; $outcoming = $i; } +# print "____________________________________________________________________________\n"; + $prinkter = 0; $fields[$microsatcord] = join("",@tempmicro); $fields[$motifcord] = join("",@tempmot); - print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; splice(@interrtypes, $sets[0], 1); $fields[$interrtypecord] = join(",",@interrtypes); @@ -3300,7 +3344,7 @@ else{ $line = join("\t", @fields); } - print "post merging, the line is $line\n" if $prinkter ==1; +# print "post merging, the line is $line\n" if $prinkter ==1; #<STDIN> if $stopper ==1; return $line; } @@ -3411,7 +3455,7 @@ while(my $sine = <SEQ>){ #<STDIN> if $sine =~ /16349128/; next if $sine !~ /[a-zA-Z0-9]/; - print "-" x 150, "\n" if $printer == 1; +# print "-" x 150, "\n" if $printer == 1; my @sields = split(/\t/,$sine); my @merged = (); @@ -3435,7 +3479,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$fmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3457,7 +3501,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$rmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3553,7 +3597,7 @@ my @mergedSet = (); # print "set of microsats = @microstring \n"; my @microstring = map { $_->[0] } sort custom map { [$_, split /\t/ ] } @microstring0; - print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; +# print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; #<STDIN> if $printer == 1; my @tempmicrostring = @microstring; foreach my $line (@tempmicrostring){ @@ -3567,7 +3611,7 @@ } my $firstflag = 'down'; while( my $line =shift(@microstring)){ - print "-----------\nline = $line \n" if $printer == 1; +# print "-----------\nline = $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3592,9 +3636,9 @@ my $endrank = 1;

while( ($startflag eq "down") || ($endflag eq "down") ){ - print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; +# print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; if ( (($prestart < 0) && $firstflag eq "up") || (($postend > length($sequence) && $firstflag eq "up")) ){ - print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; +# print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; last; } @@ -3611,7 +3655,7 @@ chomp $startmicro; $flag = 'down'; $startrank++; - print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; delete $microend{$i}; delete $microstart{$tields[$startcord]}; $end = $tields[$endcord]; @@ -3629,7 +3673,7 @@ if ($endflag eq "down"){

for my $i ($start ... $postend){ - print "$start ----> $i -----> $postend\n" if $printer == 1; +# print "$start ----> $i -----> $postend\n" if $printer == 1; if(exists $microstart{$i} ){ chomp $microstart{$i}[0]; if(exists $compoundhash{$microstart{$i}[0]}) {next;} @@ -3640,11 +3684,11 @@ $endrank++; chomp $endmicro; $flag = 'down'; - print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; delete $microstart{$i} if exists $microstart{$i} ; delete $microend{$tields[$endcord]} if exists $microend{$tields[$endcord]}; - print "done\n" if $printer == 1; +# print "done\n" if $printer == 1; shift @microstring; $end = $tields[$endcord]; @@ -3656,25 +3700,25 @@ $flag = 'up'; $endflag = 'up'; } - print "out of the if\n" if $printer == 1; +# print "out of the if\n" if $printer == 1; } - print "out of the for\n" if $printer == 1; +# print "out of the for\n" if $printer == 1;

} # print "for next turn, flag status: startflag = $startflag and endflag = $endflag \n"; } #end while( $flag eq "down") - print "compoundlines = @compoundlines \n" if $printer == 1; +# print "compoundlines = @compoundlines \n" if $printer == 1;

if (scalar (@compoundlines) == 1){ push(@nonmerged, $line);

} if (scalar (@compoundlines) > 1){ - print "FROM CLUSTERER\n" if $printer == 1; +# print "FROM CLUSTERER\n" if $printer == 1; push(@mergedSet,merge_microsats(@compoundlines, $sequence) ); } } #end foreach my $line (@microstring){ -print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; +# print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; #<STDIN> if scalar(@mergedSet) > 0; # print "EXIT: find_clusters\n"; return (join("_",@nonmerged). "=".join("_",@mergedSet)); @@ -3711,7 +3755,7 @@ my %forPopouting = ();

while( my $line =shift(@merged)){ - print "\n MErgedline: $line \n" if $printer == 1; +# print "\n MErgedline: $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3764,7 +3808,7 @@ push(@mergedSet,join("\t",@compoundlines) ); } else { - print "FROM POPOUTER\n" if $printer == 1; +# print "FROM POPOUTER\n" if $printer == 1; push(@mergedSet, merge_microsats(@compoundlines, $sequence) ); } } @@ -3789,7 +3833,7 @@ $fields[$startcord] = $start; $fields[$endcord] = $end; $fields[$microsatcord] = reverse_micro($fields[$microsatcord]); - print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; +# print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; return join("\t",@fields); }

@@ -3823,7 +3867,7 @@ my @fmerged = (); foreach my $micro (@merged) { my @fields = split(/\t/,$micro); - if ($fields[3] =~ /chr[0-9a-z]+r/){ + if ($fields[3] =~ /chr[A-Z0-9a-z]+r/){ my $key = join("_",$fields[1], $fields[$startcord], $fields[$endcord]); # print "adding ... \n$key\n$micro\n"; push(@{$revmerged{$key}}, $micro); @@ -3853,7 +3897,7 @@ sub invert_microsat{ my $micro = $_[0]; chomp $micro; - if ($micro =~ /chr[0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} + if ($micro =~ /chr[A-Z0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} else { $micro =~ s/chr([0-9a-b]+)/chr$1r/g ; } my $sequence = $_[1]; $sequence =~ s/ //g; @@ -4032,10 +4076,10 @@ foreach my $r (@localrs){ chomp $r; my @rields = split(/\t/,$r); - print "rields = @rields\n" if $printer == 1; +# print "rields = @rields\n" if $printer == 1; my $reciprocalstart = length($sequence) - $rields[$endcord] + 1; my $reciprocalend = length($sequence) - $rields[$startcord] + 1; - print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; +# print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; my $microsat = reverse_micro(all_caps($rields[$microsatcord])); my @localcollection=(); for my $i ($reciprocalstart+1 ... $reciprocalend-1){ @@ -4055,11 +4099,11 @@ } elsif (scalar(@localcollection) == 1){ - print "f microsat = $localcollection[0]\n" if $printer == 1; +# print "f microsat = $localcollection[0]\n" if $printer == 1; my @lields = split(/\t/,$localcollection[0]); $lields[$microsatcord]=all_caps($lields[$microsatcord]); - print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; - print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; +# print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; +# print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; if ($microsat eq $lields[$microsatcord]){ chomp $localcollection[0]; print SAME $localcollection[0], "\n"; @@ -4067,19 +4111,19 @@ if ($microsat ne $lields[$microsatcord]){ chomp $localcollection[0]; my $newmicro = microsatChooser(join("\t",@lields), join("\t",@rields), $sequence); - print "newmicro = $newmicro\n" if $printer == 1; +# print "newmicro = $newmicro\n" if $printer == 1; if ($newmicro =~ /[a-zA-Z]/){ print SAME $newmicro,"\n"; } else{ print DIFF join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n"; - print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; - print "@rields\n@lields\n" if $printer == 1; +# print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; +# print "@rields\n@lields\n" if $printer == 1; } } } else{ - print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; +# print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; } } } @@ -4146,13 +4190,13 @@ my $r_purestretch = join("",@r_microields);

if ($fields[$typecord]=~/nucleotide/ && $rields[$typecord]=~/nucleotide/){ - print "now.. studying $forward\n$reverse\n" if $printer == 1; +# print "now.. studying $forward\n$reverse\n" if $printer == 1; if ($fields[$typecord] eq $rields[$typecord]){ - print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1;

if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); @@ -4202,13 +4246,13 @@ } } if ($fields[$typecord] eq "compound" && $rields[$typecord] eq "compound"){ - print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; - print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; +# print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); return invert_microsat($reverse, $sequence) if $subset_answer == 0 && length($f_purestretch) < length($r_purestretch); if ($subset_answer == 3){ @@ -4243,11 +4287,11 @@ } if ($fields[$typecord] eq "compound" && $rields[$typecord] =~ /nucleotide/){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } if ($fields[$typecord] =~ /nucleotide/ && $rields[$typecord]eq "compound"){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } } @@ -4258,7 +4302,7 @@ my $seqLength = $_[2]; my $r_start = $seqLength - $rields[$endcord] + 1; my $r_end = $seqLength - $rields[$startcord] + 1; - print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; +# print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; return "0" if $fields[$startcord] == $r_start && $fields[$endcord] == $r_end; return "1" if $fields[$startcord] <= $r_start && $fields[$endcord] >= $r_end; return "2" if $r_start <= $fields[$startcord] && $r_end >= $fields[$endcord]; @@ -4284,7 +4328,7 @@ for my $i (0 ... $#sub){ my $probe = $sub[$i].$sub[$i]; - print "probing $probe and $mega[$i]\n" if $printer == 1; +# print "probing $probe and $mega[$i]\n" if $printer == 1; if ($probe =~ /$mega[$i]/) {$subresult = 1; } else {$subresult = 0; last; } } @@ -4416,7 +4460,7 @@ # print $key, "#-#-#-#-#-#-#-#\n"; if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { my $key = join("\t",$1, $2, $3, $4, $5); - print "key = $key\n" if $prinkter == 1; +# print "key = $key\n" if $prinkter == 1; push (@{$seen{$key}},$line); $microcounter++; } @@ -4424,7 +4468,7 @@ } } # print "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; - print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; +# print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; close SPUT; #---------------------------------------------------------------------------------------------------------------- @@ -4449,7 +4493,7 @@ my $keysused = 0; while (my $line = <MATCH>) { - print colored ['magenta'], $line if $prinkter == 1; +# print colored ['magenta'], $line if $prinkter == 1; next if $line !~ /[a-zA-Z0-9]/; chomp $line; my @fields2 = split(/\t/,$line); @@ -4458,10 +4502,10 @@ if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { $matchkeysformed++; $key2 = join("\t",$1, $2, $3, $4, $5); - print "key = $key2 \n" if $prinkter == 1; +# print "key = $key2 \n" if $prinkter == 1; } else{ - print "could not make ker in SEQ : $line\n"; +# print "could not make ker in SEQ : $line\n"; next; } my $sequence = $fields2[$sequencepos]; @@ -4473,7 +4517,7 @@ delete $seen{$key2}; my @sequencearr = split(/\s*/, $sequence); - print "sequencearr = @sequencearr\n" if $prinkter == 1; +# print "sequencearr = @sequencearr\n" if $prinkter == 1; my $counter; @@ -4487,13 +4531,13 @@ my @unsorted = (); my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} for my $u (0 ... $#unsorted_raw){ my @tields = split(/\t/,$unsorted_raw[$u]); next if exists $starts{$tields[$startcord]} && exists $ends{$tields[$endcord]}; push(@unsorted, $unsorted_raw[$u]); $starts{$tields[$startcord]} = $unsorted_raw[$u]; - print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; +# print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; } my $basecounter= 0; @@ -4517,7 +4561,7 @@ if (exists $starts{$basecounter}){ my $locus = $starts{$basecounter}; - print "locus identified = $locus\n" if $prinkter == 1; +# print "locus identified = $locus\n" if $prinkter == 1; my @fields3 = split(/\t/,$locus); my $start = $fields3[$startcord]; my $end = $fields3[$endcord]; @@ -4529,14 +4573,14 @@ my $leftbrackets=(); my $rightbrackets = (); my $micro_cpy = $microsat; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; while($microsat =~ m/[/g) {push(@leftbracketpos, (pos($microsat))); $leftbrackets = join("__",@leftbracketpos);$bracket_picker='yes';} while($microsat =~ m/]/g) {push(@rightbracketpos, (pos($microsat))); $rightbrackets = join("__",@rightbracketpos);} $microsat =~ s/[[]-*]//g; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; my $human_search = join '-*', split //, $microsat; my $temp = substr($sequence, $poscounter-1); - print "with poscounter = $poscounter\n" if $prinkter == 1; +# print "with poscounter = $poscounter\n" if $prinkter == 1; my $search_result = (); my $posnow = (); while ($temp =~ /($human_search)/gi){ @@ -4725,9 +4769,9 @@ if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key = join("\t",$1, $2, $4, $5); - print "key = : $key\n" if $prinkter == 1; +# print "key = : $key\n" if $prinkter == 1; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; push (@{$single_hash{$key}},$line); } else{ @@ -4736,10 +4780,10 @@ } push @hasharr, {%single_hash}; # print "@{$single_hash{$key}} \n"; - print "done $path: counter = $counter\n" if $prinkter == 1; +# print "done $path: counter = $counter\n" if $prinkter == 1; close READ; } - #print "Done hashes\n"; +# print "Done hashes\n"; #---------------------------------------------------------------------------------------------------------------- my $question=(); #---------------------------------------------------------------------------------------------------------------- @@ -4754,22 +4798,24 @@ my %contigpath=(); my $dotcounter = 0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; $dotcounter++; - #print "." if $dotcounter % 100 ==0; - #print "\n" if $dotcounter % 5000 ==0; +# print "." if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; next if $line !~ /^[0-9]+/; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; chomp $line; my @fields2 = split(/\t/,$line); my $key2 = (); if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key2 = join("\t",$1, $2, $4, $5); } - else {print "seq line $line incompatible\n" if $prinkter == 1; next;} + else { +# print "seq line $line incompatible\n" if $prinkter == 1; + next;} @@ -4809,22 +4855,22 @@ my @currentcontigchrs=(); for my $i (0 ... $#tags){ - print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; +# print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; my @temparr = (); if (exists $hasharr[$i]{$key2}){ @temparr = @{$hasharr[$i]{$key2}}; - print "in line $line, trying to hunt for: $tags[$i]\s([a-zA-Z0-9])+\s([0-9]+)\s([0-9]+) \n" if $prinkter == 1; +# print "in line $line, trying to hunt for: $tags[$i]\s([a-zA-Z0-9])+\s([0-9]+)\s([0-9]+) \n" if $prinkter == 1; $line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/; - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; +# print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $contigstarts[$i]{$startkey}= $key2; $contigends[$i]{$endkey}= $key2; - print "confirming existance: \n" if $prinkter == 1; - print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; - print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "confirming existance: \n" if $prinkter == 1; +# print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; $currentcontigchrs[$i]=$1; $currentcontigstarts[$i]=$2; $currentcontigends[$i]=$3; @@ -4846,7 +4892,7 @@ # print "---------------------------\n"; foreach my $templine (@temparr){ - print "templine = $templine\n" if $prinkter == 1; +# print "templine = $templine\n" if $prinkter == 1; my @tields = split(/\t/,$templine); my $start = $tields[$startcord]; # - $tields[$gapcord]; my $end = $tields[$endcord]; #- $tields[$gapcord]; @@ -4870,7 +4916,7 @@ foreach my $cluster (@clusters) { my @constituenst = split(/,/,$cluster); - print "clusters returned: @constituenst\n" if $prinkter == 1; +# print "clusters returned: @constituenst\n" if $prinkter == 1; } @string = split("_",stringPainter(join("_",@string),$foundclusters)); @@ -4879,13 +4925,13 @@ } next if $stopper == 1; - print colored ['blue'],"FINAL:\n" if $prinkter == 1; +# print colored ['blue'],"FINAL:\n" if $prinkter == 1; my $finalclusters =findClusters(join("!",@string), 1); - print colored ['blue'],"----------------------\n" if $prinkter == 1; +# print colored ['blue'],"----------------------\n" if $prinkter == 1; my @clusters = split(/,/,$finalclusters); - print "@string\n" if $prinkter == 1; - print "@clusters\n" if $prinkter == 1; - print "------------------------------------------------------------------\n" if $prinkter == 1; +# print "@string\n" if $prinkter == 1; +# print "@clusters\n" if $prinkter == 1; +# print "------------------------------------------------------------------\n" if $prinkter == 1; my $clustno = 0; @@ -4921,7 +4967,7 @@ my $extremeend = largest_number(@ends); push(@contigClusterstarts, $extremestart); push(@contigClusterends, $extremeend); - print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; +# print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; foreach my $clustparts (@localclust){ my @pattern = split(/:/, $clustparts); @@ -4929,7 +4975,7 @@ push (@result, $starthash[$pattern[0]]{$pattern[1]}); } push(@contigcluster, join("\t", @result)); - print join("\t", @result),"<-result \n" if $prinkter == 1 ; +# print join("\t", @result),"<-result \n" if $prinkter == 1 ; } @@ -4940,7 +4986,7 @@ $contigclustersFirstStartOnly{$key2}=$firstclusterstart; $contigclustersLastEndOnly{$key2} = $lastclusterend; $contigclusters{$key2}=[ @contigcluster ]; - print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; +# print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; for my $i (0 ... $#tags){ #1 check if there exists adjacent alignment block wrt coordinates of this species. next if $currentcontigchrs[$i] eq "0"; #1 this means that there are no microsats in this species in this alignment block.. @@ -4951,7 +4997,7 @@ #3 adjacent alignment block is found lateron, the exact distance between the potentially #4 adjacent microsat clusters can be found here. the exact start coordinate will be used #5 immediately below. - print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; + # print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; my $species_startsubstring = substr($origsequences[$i], 0, $firstclusterstart); my $species_endsubstring = (); @@ -4959,8 +5005,8 @@ if (length ($origsequences[$i]) <= $lastclusterend+1){ $species_endsubstring = "";} else{ $species_endsubstring = substr($origsequences[$i], $lastclusterend+1);} - print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; - print "for species: $tags[$i]: \n" if $prinkter == 1; +# print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; +# print "for species: $tags[$i]: \n" if $prinkter == 1; $species_startsubstring =~ s/-| //g; $species_endsubstring =~ s/-| //g; @@ -4969,11 +5015,11 @@ - print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; - print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; - print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; +# print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; +# print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; +# print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; - print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; +# print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; } @@ -5001,7 +5047,7 @@ my $existing_removed=0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; next if $line !~ /^[0-9]+/; #print $line; chomp $line; @@ -5012,7 +5058,7 @@ } else {print "seq line $line incompatible\n"; next;} - print "KEY = : $key2\n" if $prinkter == 1; +# print "KEY = : $key2\n" if $prinkter == 1; my @currentcontigstarts=(); @@ -5024,9 +5070,9 @@ @clusters = @{$contigclusters{$key2}}; @clusterscopy=@clusters; for my $i (0 ... $#tags){ - print "in line $line, trying to hunt for: $tags[$i]\s([a-zA-Z0-9])+\s([0-9]+)\s([0-9]+) \n" if $prinkter == 1; + # print "in line $line, trying to hunt for: $tags[$i]\s([a-zA-Z0-9])+\s([0-9]+)\s([0-9]+) \n" if $prinkter == 1; if ($line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/){ - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; + # print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $currentcontigchrs[$i]=$1; @@ -5035,7 +5081,7 @@ } else { $currentcontigchrs[$i] = 0; - print "no microsat clusters for $key2\n" if $prinkter == 1; next; + # print "no microsat clusters for $key2\n" if $prinkter == 1; next; } } } # print "exists: @{$hasharr[$i]{$key2}}[0]\n"} @@ -5050,7 +5096,7 @@ next if scalar @currentcontigchrs == 0; - print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; + # print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; my %visitedcontigs=(); for my $i (0 ... $#tags){ @@ -5067,38 +5113,38 @@ my $lastclusterend = $contigclustersLastEndOnly{$key2}; my $key3 = $currentcontigchrs[$i]."_".($currentcontigstarts[$i]); - print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; +# print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; if (exists($contigends[$i]{$key3}) && !exists $visitedcontigs{$contigends[$i]{$key3}}){ $visitedcontigs{$contigends[$i]{$key3}} = $contigends[$i]{$key3}; #1 this array keeps track of adjacent contigs that we have already visited, thus saving computational time and potential redundancies# - print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; + # print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; #1 extract coordinates of the last cluster of this found alignment block - print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; - print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; - print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; - print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; +# print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; + # print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; + # print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; + # print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; my @contigclustersAllFirstStartLengthOnly_raw=@{$contigclustersFirstStartLengthOnly{$key2}}; my @contigclustersAllLastEndLengthOnly_raw=@{$contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}}; my @contigclustersAllFirstStartLengthOnly=(); my @contigclustersAllLastEndLengthOnly=(); for my $val (0 ... $#contigclustersAllFirstStartLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllFirstStartLengthOnly_raw[$val]){ push(@contigclustersAllFirstStartLengthOnly, $contigclustersAllFirstStartLengthOnly_raw[$val]) if $contigclustersAllFirstStartLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "-----\n" if $prinkter == 1; + # print "-----\n" if $prinkter == 1; for my $val (0 ... $#contigclustersAllLastEndLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllLastEndLengthOnly_raw[$val]){ push(@contigclustersAllLastEndLengthOnly, $contigclustersAllLastEndLengthOnly_raw[$val]) if $contigclustersAllLastEndLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; - print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; + # print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; + # print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; # if ($contigclustersFirstStartLengthOnly{$key2}[$i] + $contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}[$i] < 50){ if (smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly) < $CLUSTER_DIST){ @@ -5119,7 +5165,7 @@ # print " clusteringpaths $key2 -> $contigends[$i]{$key3}\n"; $founkeys_enteredcount-- if exists $foundkeys{$key2}; $existing_removed++ if exists $foundkeys{$key2}; - print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; +# print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; delete $foundkeys{$key2} if exists $foundkeys{$key2}; $complete_transfered++; } @@ -5165,13 +5211,13 @@ my $pathed_count=0; foreach my $key2 (keys %foundkeys){ #print "x" x 60, "\n"; - print "x" if $dotcounter % 100 ==0; - print "\n" if $dotcounter % 5000 ==0; +# print "x" if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; $founkeys_count++; my $key = $key2; - print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; +# print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; if ($clusteringpaths{$key} eq $key){ - print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; +# print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; $nopath_count++; delete $foundkeys{$key2}; print ORTH join ("\n",@{$contigclusters{$key2}}),"\n"; @@ -5180,43 +5226,43 @@ my @pool=(); my $key3=(); $pathed_count++; - print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; - print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; if ($clusteringpathsRev{$key} eq "0") { next; } else{ my $yek3 = $clusteringpathsRev{$key}; my $yek = $key; - print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; +# print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; while ($yek3 ne "0"){ - print "$yek->$yek3," if $prinkter == 1; +# print "$yek->$yek3," if $prinkter == 1; $yek = $yek3; $yek3 = $clusteringpathsRev{$yek}; } - print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; +# print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; $key3 = $clusteringpaths{$yek}; $key = $yek; } - print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; +# print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; while($key ne $key3){ - print "KEEY $key->$key3\n" if $prinkter == 1; - print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; +# print "KEEY $key->$key3\n" if $prinkter == 1; +# print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; if (scalar(@{$contigclusters{$key}}) > 0) {push @pool, @{$contigclusters{$key}}; print "now pool = @pool\n" if $prinkter == 1;} delete $foundkeys{$key3}; $key=$key3; $key3=$clusteringpaths{$key}; } - print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; +# print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; my @firstcontig= @{$contigclusters{$key}}; delete $foundkeys{$key2} if exists $foundkeys{$key2} ; delete $foundkeys{$key} if exists $foundkeys{$key}; unshift @pool, pop @firstcontig; - print join("\t",@pool),"\n" if $prinkter == 1; +# print join("\t",@pool),"\n" if $prinkter == 1; print ORTH join ("\n",@firstcontig),"\n" if scalar(@firstcontig) > 0; print ORTH join ("\t",@pool),"\n"; # join(); @@ -5224,7 +5270,7 @@ } #close (NORTH); - print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; +# print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; close (BO); close (ORTH); close (OUTP);

--- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Thu Feb 10 10:33:08 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0"> +<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1"><description> for multiple (>2) species alignments</description><command interpreter="perl"> multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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