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bpRNA.pl
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bpRNA.pl
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#!/usr/bin/perl -w
use Graph;
use Graph::Undirected;
use strict;
#####################################################################
# 2018 Padideh Danaee,Michelle Wiley, Mason Rouches, David Hendrix #
# http://hendrixlab.cgrb.oregonstate.edu #
# ----------------------------------------------------------------- #
# MAIN #
#####################################################################
my $DEBUG = 0;
my $usage = "Usage:\n$0 <bpseq file or dot-bracket file> \n";
my $inputFile = $ARGV[0] or die $usage;
my($id,$bp,$seq);
if(isBPSeqFile($inputFile)) {
($id) = $inputFile =~ /([^\/]*?)\.bpseq/ or die "Could not parse BPSEQ filename: $inputFile\nExpected file extension \".bpseq\"";
($bp,$seq) = readBPSeqFile($inputFile);
} elsif(isDotBracketFile($inputFile)) {
($id) = $inputFile =~ /([^\/]*?)\.db/ or die "Could not parse dotbacket filename: $inputFile\nExpected file extension \".dbn\"";
($bp,$seq) = readDotBracketFile($inputFile);
} else {
die "Could not determine file type. Expecting BPSEQ or DBN (dot-bracket) file formats.";
}
if(keys %{$bp}) {
my $allSegments = getSegments($bp);
for(my $i=0;$i<@{$allSegments};$i++) {
my $w = @{$allSegments->[$i]};
print "$i $w\n" if($DEBUG);
}
my($segments,$knots,$warnings) = separateSegments($allSegments);
$bp = filterBasePairs($bp,$knots);
$segments = getSegments($bp);
my($dotbracket,$s,$k,$structureTypes,$pageNumber) = buildStructureMap($segments,$knots,$bp,$seq);
printStructureTypes($id,$seq,$dotbracket,$s,$k,$structureTypes,$pageNumber,$warnings);
} else {
my $dotbracket = "." x length($seq);
my $s = "E" x length($seq);
my $k = "N" x length($seq);
my $stFile = $id . ".st";
open(STF,">$stFile") or die "Could not open $stFile for writing.\n";
print STF "#Name: $id\n";
print STF "#Length: ", length($seq), "\n";
print STF "#PageNumber: 0\n";
print STF "$seq\n$dotbracket\n$s\n$k\n";
close(STF);
}
###############
# SUBROUTINES #
###############
sub printStructureTypes {
my($id,$seq,$dotbracket,$s,$k,$structureTypes,$pageNumber,$warnings) = @_;
$s = join("",@{$s});
$k = join("",@{$k});
my $stFile = $id . ".st";
open(STF,">$stFile") or die "Could not open $stFile for writing.\n";
print STF "#Name: $id\n";
print STF "#Length: ", length($seq), "\n";
print STF "#PageNumber: $pageNumber\n";
print STF "$warnings"; # warning contains label and newline
print STF "$seq\n$dotbracket\n$s\n$k\n";
for my $item (@{$structureTypes->{"S"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"H"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"B"}}) {
print STF "$item";
}
for my $i (sort {$a <=> $b} keys %{$structureTypes->{"I"}}) {
for my $item (@{$structureTypes->{"I"}{$i}}) {
print STF "$item";
}
}
for my $m (sort {$a <=> $b} keys %{$structureTypes->{"M"}}) {
for my $item (@{$structureTypes->{"M"}{$m}}) {
print STF "$item";
}
}
for my $item (@{$structureTypes->{"X"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"E"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"PK"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"PKBP"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"NCBP"}}) {
print STF "$item";
}
for my $item (@{$structureTypes->{"SEGMENTS"}}) {
print STF "$item";
}
close(STF);
}
sub buildStructureMap {
my($segments,$knots,$bp,$seq) = @_;
my($G,$edges) = buildSegmentGraph($seq,$bp,$segments,$knots);
my($dotbracket,$pageNumber) = computeDotBracket($segments,$knots,$seq);
my($s,$pk) = computeStructureArray($dotbracket,$bp,$seq);
my %edges;
my %pkLoops;
my %regions;
my %structureTypes;
foreach my $edge (@{$edges}) {
# $u and $v are the segment IDs
my($u,$v,$s1_pos,$s2_pos,$label) = @{$edge};
# the start and stop of edge is adjacent to segment:
my $lStart = $s1_pos+1;
my $lStop = $s2_pos-1;
my $type = "M";
$type = "H" if($u == $v);
#print "$type\n";
push(@{$edges{$type}},[$lStart,$lStop]);
#print "Loaded edge ",$#{$edges{"M"}}," from $u to $v type=$label from $lStart to $lStop\n" if $type eq "M";
}
# First, handle Multiloops
if($edges{"M"}) {
my $mG = Graph->new; # a directed graph
for(my $m=0;$m<@{$edges{"M"}};$m++) {
# this is important for X regions not adjacent to any other X regions.
$mG->add_vertex($m);
# 1-based coords
my($mStart,$mStop) = @{$edges{"M"}[$m]};
my $mSeq = substr($seq,$mStart-1,$mStop-$mStart+1);
#print "$m $mStart..$mStop $mSeq\n";
for(my $n=0;$n<@{$edges{"M"}};$n++) {
# 1-based coords
my($nStart,$nStop) = @{$edges{"M"}[$n]};
my $nSeq = substr($seq,$nStart-1,$nStop-$nStart+1);
if(loopLinked($mStart,$mStop,$nStart,$nStop,$bp)) {
#print "linking $m to $n\n";
$mG->add_edge($m,$n);
}
}
}
my $mUG = $mG->undirected_copy();
my @mCC = $mUG->connected_components();
my @multiLoops;
my @externalLoops;
# create a sorted list of multiloops.
for my $c (@mCC) {
#print "found CC of size ", scalar(@{$c}), "\n";
if(isMultiLoop($c,$mG,\%edges)) {
# sort the branches of this multiloop by position.
my @c = sort {$edges{"M"}[$a]->[0] <=> $edges{"M"}[$b]->[0]} @{$c};
push(@multiLoops,\@c);
} else {
my @c = sort {$edges{"M"}[$a]->[0] <=> $edges{"M"}[$b]->[0]} @{$c};
push(@externalLoops,\@c);
#print "found a X region\n";
}
}
@multiLoops = sort {$edges{"M"}[$a->[0]]->[0] <=> $edges{"M"}[$b->[0]]->[0]} @multiLoops;
my $mCount = 0;
for my $c (@multiLoops) {
$mCount++;
my $mp = 0;
for my $m (@{$c}) {
$mp++;
my($mStart,$mStop) = @{$edges{"M"}[$m]};
my $mLength = $mStop - $mStart + 1;
my $mSeq = substr($seq,$mStart-1,$mLength);
# define adjacet positions in 1-based
# retrieve nucleotide in 0-based
my $bp5_pos1 = $mStart-1;
my $nuc5_1 = substr($seq,$bp5_pos1-1,1);
my $bp5_pos2 = $bp->{$bp5_pos1};
my $nuc5_2 = substr($seq,$bp5_pos2-1,1);
my $bp3_pos1 = $mStop+1;
my $nuc3_1 = substr($seq,$bp3_pos1-1,1);
my $bp3_pos2 = $bp->{$bp3_pos1};
my $nuc3_2 = substr($seq,$bp3_pos2-1,1);
my @mKnots = includesKnot($mStart,$mStop,$knots);
my $PK = @mKnots ? "PK{".join(',',@mKnots)."}" : "";
push(@{$structureTypes{"M"}{$mCount}},"M$mCount.$mp $mStart..$mStop \"$mSeq\" ($bp5_pos1,$bp5_pos2) $nuc5_1:$nuc5_2 ($bp3_pos1,$bp3_pos2) $nuc3_1:$nuc3_2 $PK\n");
for my $k (@mKnots) {
push(@{$pkLoops{$k}},["M$mCount.$mp",$mStart,$mStop]);
}
########################################
# updating multiloops in %regions here #
########################################
push(@{$regions{"M"}},[$mStart,$mStop]);
# if this inequality doesn't hold, it's a branch of length 0.
if($mStart <= $mStop) {
# in a multiloop part
for(my $i=$mStart;$i<=$mStop;$i++) {
# convert to 0-based
$s->[$i-1] = "M";
}
}
}
}
for my $c (@externalLoops) {
# these need to be classified as "X" for unpaired
my $xCount = 0;
my @c = sort {$edges{"M"}[$a]->[0] <=> $edges{"M"}[$b]->[0]} @{$c};
for my $x (@c) {
my($xStart,$xStop) = @{$edges{"M"}[$x]};
my $xSeq = substr($seq,$xStart-1,$xStop-$xStart+1);
my $bp5_pos1 = $xStart-1;
my $nuc5_1 = substr($seq,$bp5_pos1-1,1);
my $bp5_pos2 = $bp->{$bp5_pos1};
my $nuc5_2 = substr($seq,$bp5_pos2-1,1);
my $bp3_pos1 = $xStop+1;
my $nuc3_1 = substr($seq,$bp3_pos1-1,1);
my $bp3_pos2 = $bp->{$bp3_pos1};
my $nuc3_2 = substr($seq,$bp3_pos2-1,1);
#print "checking $u at $uStart $uStop\n";
my @xKnots = includesKnot($xStart,$xStop,$knots);
my $PK = @xKnots ? "PK{".join(',',@xKnots)."}" : "";
if($xStart <= $xStop) {
$xCount++;
push(@{$structureTypes{"X"}},"X$xCount $xStart..$xStop \"$xSeq\" ($bp5_pos1,$bp5_pos2) $nuc5_1:$nuc5_2 ($bp3_pos1,$bp3_pos2) $nuc3_1:$nuc3_2 $PK\n");
}
for my $k (@xKnots) {
#print "visited $k uKnot";
push(@{$pkLoops{$k}},["X$xCount",$xStart,$xStop]);
}
# Check if in a multiloop part or something other than U/X
for(my $i=$xStart;$i<=$xStop;$i++) {
# convert to 0-based
die "incorrect value at $i $s->[$i-1]\n" unless($s->[$i-1] =~ /[uX]/);
}
}
}
}
# hairpins
my $hCount = 0;
if($edges{"H"}) {
#print "found H edge\n";
for(my $h=0;$h<@{$edges{"H"}};$h++) {
$hCount++;
my($hStart,$hStop) = @{$edges{"H"}[$h]};
# -1 for zero-based
my $hSeq = substr($seq,$hStart-1,$hStop-$hStart+1);
# -1 again for flanking
my $pos5 = $hStart-1;
# +1 for flanking
my $pos3 = $hStop+1;
# subtrackt 1 to get zero-based to get nucleotides flanking (closing base pair)
my $nuc1 = substr($seq,$pos5-1,1);
my $nuc2 = substr($seq,$pos3-1,1);
push(@{$regions{"H"}},[$hStart,$hStop]);
my @hKnots = includesKnot($hStart,$hStop,$knots);
my $PK = @hKnots ? "PK{".join(',',@hKnots)."}" : "";
push(@{$structureTypes{"H"}},"H$hCount $hStart..$hStop \"$hSeq\" ($pos5,$pos3) $nuc1:$nuc2 $PK\n");
#print "stored H into structureTypes\n";
for my $k (@hKnots) {
#print "visited $k hknot\n";
push(@{$pkLoops{$k}},["H$hCount",$hStart,$hStop]);
}
}
}
###################
# Extract regions #
###################
my $prevChar = "";
my $thisStart = 0;
my $thisStop = 0;
my $FIRST = 1;
####################################################
# Stems, internal loops, multiloops, hairpin loops #
####################################################
for(my $i=0;$i<@{$s};$i++) {
unless($s->[$i]) {
die "no value in \@s for $i\n"
}
if($s->[$i] ne $prevChar) {
# in a new region.
# store previous region info:
# ignore multiloops and hairpins, they are already added above
unless($prevChar =~ /[MH]/) {
# store in 1-based to be consistent with M and H above
push(@{$regions{$prevChar}},[$thisStart+1,$thisStop+1]) unless($FIRST);
}
# reset the start/stop:
$thisStart = $i;
$thisStop = $i;
$prevChar = $s->[$i];
$FIRST = 0;
} elsif(($prevChar eq "S")&&($bp->{$i+1}+1 != $bp->{$i})) {
# in a break in a stem into another stem. store in 1-based
push(@{$regions{$prevChar}},[$thisStart+1,$thisStop+1]);
$thisStart = $i;
$thisStop = $i;
$prevChar = $s->[$i];
$FIRST = 0;
} elsif(($prevChar eq "S")&&($bp->{$i} == $i+1)) {
# in a break in a stem into another stem. store in 1-based
push(@{$regions{$prevChar}},[$thisStart+1,$thisStop+1]);
$thisStart = $i;
$thisStop = $i;
$prevChar = $s->[$i];
$FIRST = 0;
} else {
# continue/extend the same region
$thisStop = $i;
}
}
# store the last region.
push(@{$regions{$prevChar}},[$thisStart+1,$thisStop+1]) unless($FIRST);
#bulges
if($regions{"B"}) {
my $bCount = 0;
foreach my $bulge (@{$regions{"B"}}) {
# 1-based
my($bStart,$bStop) = @{$bulge};
# all substr calls need 0-based, hence -1 for all:
my $bSeq = substr($seq,$bStart-1,$bStop-$bStart+1);
# 1-based positions of flanking:
my $bp5_pos1 = $bStart-1;
my $bp3_pos1 = $bStop+1;
my $bp5_nt1 = substr($seq,$bp5_pos1-1,1);
my $bp3_nt1 = substr($seq,$bp3_pos1-1,1);
my $bp5_pos2 = $bp->{$bp5_pos1};
my $bp3_pos2 = $bp->{$bp3_pos1};
my $bp5_nt2 = substr($seq,$bp5_pos2-1,1);
my $bp3_nt2 = substr($seq,$bp3_pos2-1,1);
$bCount++;
my @bKnots = includesKnot($bStart,$bStop,$knots);
my $PK = @bKnots ? "PK{".join(',',@bKnots)."}" : "";
push(@{$structureTypes{"B"}},"B$bCount $bStart..$bStop \"$bSeq\" ($bp5_pos1,$bp5_pos2) $bp5_nt1:$bp5_nt2 ($bp3_pos1,$bp3_pos2) $bp3_nt1:$bp3_nt2 $PK\n");
for my $k (@bKnots) {
push(@{$pkLoops{$k}},["B$bCount",$bStart,$bStop]);
}
}
}
if($regions{"I"}) {
my $iG = Graph::Undirected->new;
for(my $i=0;$i<@{$regions{"I"}};$i++) {
my($iStart,$iStop) = @{$regions{"I"}[$i]};
for(my $j=$i+1;$j<@{$regions{"I"}};$j++) {
my($jStart,$jStop) = @{$regions{"I"}[$j]};
if(loopLinked($iStart,$iStop,$jStart,$jStop,$bp)) {
$iG->add_edge($i,$j);
}
}
}
my @iCC = $iG->connected_components();
my @internalLoops;
for my $c (@iCC) {
my @c = sort {$regions{"I"}[$a]->[0] <=> $regions{"I"}[$b]->[0]} @{$c};
push(@internalLoops,\@c);
}
my $iCount = 0;
@internalLoops = sort {$regions{"I"}[$a->[0]]->[0] <=> $regions{"I"}[$b->[0]]->[0]} @internalLoops;
for my $c (@internalLoops) {
$iCount++;
my $componentSize = scalar(@{$c});
my $ip = 0;
for my $v (@{$c}) {
$ip++;
# 1-based positions
my($iStart,$iStop) = @{$regions{"I"}[$v]};
my $iLength = $iStop - $iStart + 1;
# subtract 1 to convert to 0-based
my $iSeq = substr($seq,$iStart-1,$iLength);
# positions in 1-based here:
my $bp5_pos1 = $iStart-1;
my $bp5_pos2 = $bp->{$bp5_pos1};
my $nuc5_1 = substr($seq,$bp5_pos1-1,1);
my $nuc5_2 = substr($seq,$bp5_pos2-1,1);
my @iKnots = includesKnot($iStart,$iStop,$knots);
my $PK = @iKnots ? "PK{".join(',',@iKnots)."}" : "";
push(@{$structureTypes{"I"}{$iCount}},"I$iCount.$ip $iStart..$iStop \"$iSeq\" ($bp5_pos1,$bp5_pos2) $nuc5_1:$nuc5_2 $PK\n");
for my $k (@iKnots) {
push(@{$pkLoops{$k}},["I$iCount.$ip",$iStart,$iStop]);
}
}
}
}
if($regions{"E"}) {
my $eCount = 0;
for(my $e=0;$e<@{$regions{"E"}};$e++) {
my($eStart,$eStop) = @{$regions{"E"}[$e]};
my $eSeq = substr($seq,$eStart-1,$eStop-$eStart+1);
$eCount++;
my @eKnots = includesKnot($eStart,$eStop,$knots);
my $PK = @eKnots ? "PK{".join(',',@eKnots)."}" : "";
push(@{$structureTypes{"E"}},"E$eCount $eStart..$eStop \"$eSeq\" $PK\n");
for my $k (@eKnots) {
push(@{$pkLoops{$k}},["E$eCount",$eStart,$eStop]);
}
}
}
#stems
my @stemList;
my %VISITED; # a hash to keep track of regions in stems that have been collected already
if($regions{"S"}) {
my $sCount = 0;
foreach my $stem (sort {$a->[0] <=> $b->[0]} @{$regions{"S"}}) {
my($sStart1,$sStop1) = @{$stem};
unless($VISITED{$sStart1}{$sStop1}) {
$sCount++;
# 1-based
my $sStart2 = $bp->{$sStop1};
my $sStop2 = $bp->{$sStart1};
# all substr calls need 0-based, hence -1 for all:
my $sSeq1 = substr($seq,$sStart1-1,$sStop1-$sStart1+1);
my $sSeq2 = substr($seq,$sStart2-1,$sStop2-$sStart2+1);
push(@{$structureTypes{"S"}},"S$sCount $sStart1..$sStop1 \"$sSeq1\" $sStart2..$sStop2 \"$sSeq2\"\n");
$VISITED{$sStart2}{$sStop2} = 1;
push(@stemList,[$sStart1,$sStop1,"S$sCount"]);
}
}
}
my $ncCount=0;
for my $i (keys %{$bp}) {
my $j = $bp->{$i};
if($i < $j) {
my $b1 = substr($seq,$i-1,1);
my $b2 = substr($seq,$j-1,1);
if(nonCanonical($b1,$b2)) {
$ncCount++;
my $thisLabel = "";
foreach my $stem (@stemList) {
my($start,$stop,$label) = @{$stem};
if(($start<=$i)&&($i<=$stop)) {
$thisLabel = $label;
}
}
die "No label found for $i,$j\n" unless($thisLabel);
push(@{$structureTypes{"NCBP"}},"NCBP$ncCount $i $b1 $j $b2 $thisLabel\n");
}
}
}
if(@{$knots}) {
for(my $k=0;$k<@{$knots};$k++) {
my $knotID = $k+1;
my @knot = @{$knots->[$k]};
my $knotSize = @knot;
my $first = shift(@knot);
my($k_5pStart,$k_3pStart) = @{$first};
my $last = @knot ? pop(@knot) : $first;
my($k_3pStop,$k_5pStop) = @{$last};
my $linkedLoops = "";
if(@{$pkLoops{$knotID}} == 2) {
@{$pkLoops{$knotID}} = sort {$a->[1] <=> $b->[1]} @{$pkLoops{$knotID}};
my($lType1,$lStart1,$lStop1) = @{$pkLoops{$knotID}[0]};
my($lType2,$lStart2,$lStop2) = @{$pkLoops{$knotID}[1]};
$linkedLoops = "$lType1 $lStart1..$lStop1 $lType2 $lStart2..$lStop2";
} else {
die "Expected two loops linked for PK$knotID\n";
}
push(@{$structureTypes{"PK"}},"PK$knotID ${knotSize}bp $k_5pStart..$k_3pStop $k_5pStop..$k_3pStart $linkedLoops\n");
push(@stemList,[$k_5pStart,$k_3pStop,"PK$knotID"]);
my $n=0;
for my $pair (@{$knots->[$k]}) {
my($k_5p,$k_3p) = @{$pair};
#print "knot $k: $k_5p $k_3p\n";
# positions in 1-based
my $b_5p = substr($seq,$k_5p-1,1);
my $b_3p = substr($seq,$k_3p-1,1);
$n++;
push(@{$structureTypes{"PKBP"}},"PK$knotID.$n $k_5p $b_5p $k_3p $b_3p\n");
# check if PKBP is non-canonical.
if(nonCanonical($b_5p,$b_3p)) {
$ncCount++;
push(@{$structureTypes{"NCBP"}},"NCBP$ncCount $k_5p $b_5p $k_3p $b_3p PK$knotID.$n\n");
}
}
}
}
for(my $i=0;$i<@{$segments};$i++) {
my $segmentID = $i+1;
my @segment = @{$segments->[$i]};
my $segSize = @segment;
my $firstPair = shift(@segment);
my($seg5pStart, $seg3pStart)= @{$firstPair};
my $lastPair = @segment ? pop(@segment) : $firstPair;
my($seg3pStop, $seg5pStop) = @{$lastPair};
my $segSeq1 = substr($seq,$seg5pStart-1,$seg3pStop-$seg5pStart+1);
my $segSeq2 = substr($seq,$seg5pStop-1,$seg3pStart-$seg5pStop+1);
push(@{$structureTypes{"SEGMENTS"}},"segment$segmentID ${segSize}bp $seg5pStart..$seg3pStop $segSeq1 $seg5pStop..$seg3pStart $segSeq2\n");
}
my @k = split(//,"N" x length($dotbracket));
for(my $i=0;$i<@{$s};$i++) {
$k[$i] = "K" if($pk->[$i]);
}
return($dotbracket,$s,\@k,\%structureTypes,$pageNumber);
}
sub buildSegmentGraph {
my($seq,$bp,$segments,$knots) = @_;
#
# 5'start 3'stop
# ACGUA
# start ||||| stop
# UGCAU
# 3'start 5'stop
#
my($firstPos,$lastPos) = getExtremePositions($bp);
my $G = Graph->new(multiedged => 1);
my @edges;
for(my $i=0;$i<@{$knots};$i++) {
my @knot1 = @{$knots->[$i]};
my $firstPair1 = shift(@knot1);
my($k1_5pStart, $k1_3pStart)= @{$firstPair1};
my $lastPair1 = @knot1 ? pop(@knot1) : $firstPair1;
my($k1_3pStop, $k1_5pStop) = @{$lastPair1};
my $k1Seq1 = substr($seq,$k1_5pStart-1,$k1_3pStop-$k1_5pStart+1);
my $k1Seq2 = substr($seq,$k1_5pStop-1,$k1_3pStart-$k1_5pStop+1);
}
if(@{$segments} > 0) {
for(my $i=0;$i<@{$segments};$i++) {
$G->add_vertex($i);
my @segment1 = @{$segments->[$i]};
my $firstPair1 = shift(@segment1);
my($s1_5pStart, $s1_3pStart)= @{$firstPair1};
my $lastPair1 = @segment1 ? pop(@segment1) : $firstPair1;
my($s1_3pStop, $s1_5pStop) = @{$lastPair1};
my $s1Seq1 = substr($seq,$s1_5pStart-1,$s1_3pStop-$s1_5pStart+1);
my $s1Seq2 = substr($seq,$s1_5pStop-1,$s1_3pStart-$s1_5pStop+1);
# get the next paired bases in each direction (see diagram above)
my $p1_5pStart = getPrevPair($s1_5pStart,$bp,$firstPos,$knots); # 1
my $n1_3pStop = getNextPair($s1_3pStop,$bp,$lastPos,$knots); # 2
my $p1_5pStop = getPrevPair($s1_5pStop,$bp,$firstPos,$knots); # 3
my $n1_3pStart = getNextPair($s1_3pStart,$bp,$lastPos,$knots); # 4
for(my $j=0;$j<@{$segments};$j++) {
my @segment2 = @{$segments->[$j]};
my $firstPair2 = shift(@segment2);
my($s2_5pStart, $s2_3pStart)= @{$firstPair2};
my $lastPair2 = @segment2 ? pop(@segment2) : $firstPair2;
my($s2_3pStop, $s2_5pStop) = @{$lastPair2};
if($n1_3pStart == $s2_5pStart) {
$G->add_edge($i,$j);
# extra label "1" is for debugging.
push(@edges,[$i,$j,$s1_3pStart,$s2_5pStart,"1"]);
#print "Connected $i to $j\n";
}
if($n1_3pStart == $s2_5pStop) {
$G->add_edge($i,$j);
push(@edges,[$i,$j,$s1_3pStart,$s2_5pStop,"2"]);
#print "Connected $i to $j\n";
}
if($n1_3pStop == $s2_5pStart) {
$G->add_edge($i,$j);
push(@edges,[$i,$j,$s1_3pStop,$s2_5pStart,"3"]);
#print "Connected $i to $j\n";
}
if($n1_3pStop == $s2_5pStop) {
$G->add_edge($i,$j);
push(@edges,[$i,$j,$s1_3pStop,$s2_5pStop,"4"]);
#print "Connected $i to $j\n";
}
}
}
}
return($G,\@edges);
}
sub computeStructureArray {
my($dotbracket,$bp,$seq) = @_;
# Takes bpseq file and adds column listing structure type of each base:
# paired "Stem" S
# Multiloop M
# Internal loop I
# Bulge B
# Hairpin loop H
# pseudoKnot K
# dangling End E
# eXternal loop X
my $knotBracket = getKnotBrackets();
my @s;
for(my $i = 0; $i < length($dotbracket); $i++) {
my $x = substr($dotbracket, $i, 1);
my $loopStructure = "";
# stem
if($x eq "(" || $x eq ")") {
$loopStructure = "S";
} elsif(($x eq ".")||($knotBracket->{$x})) {
# loops
my ($fwd,$fwdIndex) = fwdFinder($i,$dotbracket,$x,$knotBracket);
my ($bwd,$bwdIndex) = bwdFinder($i,$dotbracket,$x,$knotBracket);
my $fwdIndexPair = $bp->{$fwdIndex+1}; # returns position on RNA (1-based)
my $bwdIndexPair = $bp->{$bwdIndex+1};
my $length = $fwdIndex-$bwdIndex-1;
if($bwd eq "("){
if ($fwd eq "("){
if ($fwdIndexPair == $bwdIndexPair-1) {
$loopStructure = "B";
} else {
$loopStructure = between($fwdIndexPair-1,$bwdIndexPair-1,$dotbracket);
}
} elsif($fwd eq ")") {
$loopStructure = "H";
} elsif($fwd eq "") {
$loopStructure = "E";
} else {
$loopStructure = "What is this fwd1: $fwd";
}
} elsif ($bwd eq ")") {
if ($fwd eq "(") {
$loopStructure = "X";
} elsif ($fwd eq ")") {
if ($fwdIndexPair == $bwdIndexPair-1) {
$loopStructure = "B";
} else {
$loopStructure = between($fwdIndexPair-1,$bwdIndexPair-1,$dotbracket);
}
} elsif ($fwd eq "") {
$loopStructure = "E";
} else {
$loopStructure = "What is this fwd2: $fwd";
}
} elsif ($bwd eq "" || $bwd eq "."){
$loopStructure = "E";
} else {
$loopStructure = "What is this bwd1: $bwd";
}
}
$s[$i] = $loopStructure;
}
my @pk = split(//,"0" x length($dotbracket));
for(my $i = 0; $i < length($dotbracket); $i++) {
my $x = substr($dotbracket, $i, 1);
if($knotBracket->{$x}) {
$pk[$i] = 1;
}
}
return(\@s,\@pk);
}
sub printStructureData {
my($regions) = @_;
# collect lines for output file
my @list;
foreach my $type (keys %{$regions}) {
if(($type)&&($type ne "N")) {
my $count = 0;
foreach my $region (@{$regions->{$type}}) {
$count++;
my($start,$stop) = @{$region};
push(@list,[$start,"$id\tbpRNA\t$type\t$start\t$stop\t.\t+\t.\tID=$type$count"]);
}
}
}
my $gffFile = $id."_structure.gff";
open(GFF,">$gffFile") or die "Could not open $gffFile for writing.\n";
foreach my $region (sort {$a->[0] <=> $b->[0]} @list) {
my($start,$line) = @{$region};
print GFF "$line\n";
}
close(GFF);
}
sub isMultiLoop() {
my($c,$mG,$edges) = @_;
$,=" ";
# make copy of components
my @c = @{$c};
if(scalar(@c) == 1) {
return 0;
}
my $f = shift(@c);
my $v = $f;
while(@c) {
if(my @successors = $mG->successors($v)) {
# it should only have one successor. Reality check here.
die "Fatal error: Too many successors of multiloop part.\n$v is connectd to @successors\n" unless(@successors == 1);
my $w = shift(@successors);
my $index = -1;
for(my $i=0;$i<@c;$i++) {
if($c[$i] == $w) {
$index = $i;
}
}
if($index >= 0) {
splice(@c, $index, 1);
} else {
return 0;
}
$v = $w;
unless(my @successors = $mG->successors($v)) {
#print "leaving here 3\n";
return 0;
}
} else {
return 0;
}
}
# if here, all vertices in @c were removed.
# check if successor of last node is first node.
return 1;
}
sub computeDotBracket {
my($segments,$knots,$seq) = @_;
my $dotbracket = "." x length($seq);
## For the segments, set all pairs to parentheses
for(my $i=0;$i<@{$segments};$i++) {
foreach my $pair (@{$segments->[$i]}) {
my($l,$r) = @{$pair};
substr($dotbracket,$l-1,1) = "(";
substr($dotbracket,$r-1,1) = ")";
}
}
# loop through each base pair, update bracket
my %page;
my $n = 1;
my $unlabeledKnots = 1;
my $firstI = 0;
if(0) {
for(my $i=0;$i<@{$knots};$i++) {
#print "knot $i has ", scalar(@{$knots->[$i]}), "bp\t";
my @knot1 = @{$knots->[$i]};
my $first1 = shift(@knot1);
my($k1_5pStart,$k1_3pStart) = @{$first1};
my $last1 = @knot1 ? pop(@knot1) : $first1;
my($k1_3pStop,$k1_5pStop) = @{$last1};
#print "$k1_5pStart..$k1_3pStart\n";
}
}
while($unlabeledKnots) {
# assume no more left
$unlabeledKnots = 0;
for(my $i=0;$i<@{$knots};$i++) {
unless($page{$i}) {
$firstI = $i;
last;
}
}
$page{$firstI} = $n;
# the most 5' knot with undefined page is what everything is compared to
# start an array contaning members of this page
my @checkList = ();
push(@checkList,$firstI);
# start at next knot with undefined page
for(my $i=$firstI+1;$i<@{$knots};$i++) {
unless($page{$i}) {
# for now consider it not labeled
my $CROSSING = 0;
# if it doesn't cross, then use $n, otherwise label later.
for my $checkI (@checkList) {
if(knotsCross($knots->[$checkI],$knots->[$i])) {
# there is an unlabeled knot left.
$unlabeledKnots = 1;
$CROSSING = 1;
}
}
unless($CROSSING) {
$page{$i} = $n;
push(@checkList,$i);
}
}
}
$n++;
}
my $pageNumber = 0;
for(my $i=0;$i<@{$knots};$i++) {
my $n = $page{$i}; # page of PK. For all PKs, n > 0, where n=0 is "("
if($n > $pageNumber) {
$pageNumber = $n;
}
foreach my $pair (@{$knots->[$i]}) {
my($l,$r) = @{$pair};
my($lB,$rB) = getBrackets($n);
substr($dotbracket,$l-1,1) = $lB;
substr($dotbracket,$r-1,1) = $rB;
}
}
$pageNumber += 1; # convert to 1-based
return($dotbracket,$pageNumber);
}
sub knotsOverlap {
my($knot1,$knot2) = @_;
# treat $knot like a segment
#
# 5'start 3'stop
# ACGUA
# |||||
# UGCAU
# 3'start 5'stop
#
my @knot1 = @{$knot1};
my $first1 = shift(@knot1);
my($k1_5pStart,$k1_3pStart) = @{$first1};
my $last1 = @knot1 ? pop(@knot1) : $first1;
my($k1_3pStop,$k1_5pStop) = @{$last1};
my @knot2 = @{$knot2};
my $first2 = shift(@knot2);
my($k2_5pStart,$k2_3pStart) = @{$first2};
my $last2 = @knot2 ? pop(@knot2) : $first2;
my($k2_3pStop,$k2_5pStop) = @{$last2};
if(($k1_5pStart <= $k2_5pStart)&&($k2_5pStart <= $k1_3pStart)||
($k1_5pStart <= $k2_3pStart)&&($k2_3pStart <= $k1_3pStart)) {
return 1;
}
return 0;
}
sub knotsCross {
my($knot1,$knot2) = @_;
# treat $knot like a segment
#
# 5'start 3'stop
# ACGUA
# |||||
# UGCAU
# 3'start 5'stop
#
my @knot1 = @{$knot1};
my $first1 = shift(@knot1);
my($k1_5pStart,$k1_3pStart) = @{$first1};
my @knot2 = @{$knot2};
my $first2 = shift(@knot2);
my($k2_5pStart,$k2_3pStart) = @{$first2};
if(pkQuartet($k1_5pStart,$k1_3pStart,$k2_5pStart,$k2_3pStart)) {
return 1;
}
return 0;
}
sub loopLinked {
# 0123456789X
# ((.))((.))...
my($iStart1,$iStop1,$iStart2,$iStop2,$bp) = @_;
# here it is forced to be in order 5' to 3'
if($iStop1+1 == $bp->{$iStart2-1}) {
return 1;
}
return 0;
}
sub getKnotBrackets {
my $knots = "[]{}<>" . join("",("a".."z")) . join("",("A".."Z"));
my %knotBracket;
foreach my $c (split(//,$knots)) {
$knotBracket{$c} = 1;
}
return \%knotBracket;
}
sub getBrackets {
my($n) = @_;
die "Fatal error: too many (n>29) PKs to represent in dotbracket! $id\n" if($n >= 30);
my $left = "([{<" . join("",("A".."Z"));
my $right = ")]}>" . join("",("a".."z"));
return (substr($left,$n,1),substr($right,$n,1));
}
# Find index of the next paired base
sub fwdFinder {
my ($i,$dotbracket,$x,$knotBracket) = @_;
my $B = substr($dotbracket,$i,1);
while (($B eq ".")||($knotBracket->{$B})){
$i++;
$B = substr($dotbracket,$i,1);
if ($i >= length($dotbracket)) {
return("",$i);
}
}
return($B,$i);
}
# Find index of the previous paired base
sub bwdFinder {
my ($i,$dotbracket,$x,$knotBracket) = @_;
my $B = substr($dotbracket,$i,1);
while (($B eq ".")||($knotBracket->{$B})){
$i--;
$B = substr($dotbracket,$i,1);
if ($i < 0){
return("",$i);
}
}
return($B,$i);
}
# Determine if multiloop or internal loop
# Usage: # get to zero base
# $type = between($fwdPairIndex-1,$bwdPairIndex-1,$dotbracket);
sub between {
my ($fwdIP,$bwdIP,$dotbracket) = @_;
$fwdIP++;
while ($fwdIP < $bwdIP-1){
my $fwdP = substr($dotbracket,$fwdIP,1);
if ($fwdP eq "(" || $fwdP eq ")"){
return("X");
}
$fwdIP++;
}
return("I");
}
sub pkQuartet {
my($i,$j,$k,$l) = @_;
# assumption: i < j and k < l
if((($i < $k)&&($k < $j)&&($j < $l))||
(($i < $l)&&($l < $j)&&($k < $i))) {
return 1;
}
return 0;
}
sub getSegments {
my($bp) = @_;
#
# 5'start 3'stop
# ACG.UA
# ||| ||
# UGCAAU
# 3'start 5'stop
#
my @allSegments = ();
my($firstPos,$lastPos) = getExtremePositions($bp);
# initialize the i,j
my $i = getNextPair(0,$bp,$lastPos);
if($i) {
my $j = $bp->{$i};
# Build the first segment starting with the first basepair
# while still examining paired positions
while(($firstPos <= $i) && ($i <= $lastPos)) {
my $INSEGMENT;
my @segment = ();
if($i<$j){
push(@segment,[$i,$j]);
$INSEGMENT=1;
}
# grow the segment to include more base pairs
while($INSEGMENT) {
#print "getting nextPair for $i and prevPair of $j\n";
my $n = getNextPair($i,$bp,$lastPos);
my $p = getPrevPair($j,$bp,$firstPos);
if($n && $p) {
if($bp->{$n} == $p && $n<$p) {
# in the segment. Store these basepairs
push(@segment,[$n,$p]);
$i = $n;
$j = $p;
} else {
#print "closed - $i, $j\n";
#print "Found " . scalar(@allSegments) . " segments\n";
$INSEGMENT = 0;
push(@allSegments,\@segment);
}
} else {
$INSEGMENT = 0;
push(@allSegments,\@segment);
}
}
# go to first base pair of NEXT segment
$i = getNextPair($i,$bp,$lastPos);
$j = $bp->{$i};
}
}
# by construction, the segments should be ordered
# by the most 5' position of each segment
return \@allSegments;
}
sub filterBasePairs {
my($bp,$knots) = @_;
my %bp;
for my $i ( keys %{$bp} ) {
my $j = $bp->{$i};
unless(inKnot($i,$knots)) {
unless(inKnot($j,$knots)) {
$bp{$i} = $j;
} else {
die "filterBasePairs: $j in PK, but $i is not.\n";
}
}
}
return \%bp;
}
sub separateSegments {
my($segments) = @_;
my $warnings = "";
my %knot;
my $G = Graph::Undirected->new;
if(@{$segments} > 1) {
for(my $i=0;$i<@{$segments}-1;$i++) {
my @segment1 = @{$segments->[$i]};
my $firstPair1 = shift(@segment1);
my($s1_5pStart, $s1_3pStart)= @{$firstPair1};
#print "$i ($s1_5pStart, $s1_3pStart)\n";
for(my $j=$i+1;$j<@{$segments};$j++) {
my @segment2 = @{$segments->[$j]};
my $firstPair2 = shift(@segment2);
my($s2_5pStart, $s2_3pStart)= @{$firstPair2};
if(pkQuartet($s1_5pStart,$s1_3pStart,$s2_5pStart,$s2_3pStart)) {
$G->add_edge($i,$j);
}