void g_geneseq( VariantGroup & vars , void * p )
{
Out & pout = Out::stream( "gsview" );
Opt_geneseq * aux = (Opt_geneseq*)p;
Out * rout = aux->R_plot ? &Out::stream( "gsview.R" ) : NULL ;
if ( aux->R_plot ) geneseq_define_Rfunc( rout );
Region region = g.locdb.get_region( PLINKSeq::DEFAULT_LOC_GROUP() , vars.name() ) ;
if ( region.subregion.size() == 0 ) return;
int s = region.subregion[0].meta.get1_int( PLINKSeq::TRANSCRIPT_STRAND() ) ;
bool positive_strand = s > 0 ;
if ( s == 0 ) Helper::halt( "no strand info" );
//
// get list of all 'events' (variants, intron/exon boundaries, reference variants)
//
std::set<int> events;
std::map<int,const Variant*> evars;
std::map<int,int> elocstart;
std::map<int,int> elocstop;
std::map<int,int> cds_num;
std::map<int,const RefVariant*> erefvars;
for (int v=0; v<vars.size(); v++)
{
int pos = positive_strand ? vars(v).position() : -vars(v).position() ;
events.insert( vars(v).position() ) ;
evars[ vars(v).position() ] = &vars(v);
}
//
// enumerate CDS exons first
//
int num_cds_exons = 0;
int cds_bp = 0;
int genomic_start = 0;
int genomic_stop = 0;
for (int s = 0 ; s < region.subregion.size(); s++)
{
// only consider CDS exons
if ( ! region.subregion[s].CDS() ) continue;
cds_num[s] = num_cds_exons;
int pos1 = region.subregion[s].start.position();
int pos2 = region.subregion[s].stop.position();
if ( genomic_start == 0 ) genomic_start = pos1;
if ( pos2 > genomic_stop ) genomic_stop = pos2;
// track start & stop CDS (and record exon #)
elocstart[ pos1 ] = num_cds_exons;
elocstop[ pos2 ] = num_cds_exons;
++num_cds_exons;
// total CDS extent in base-pairs
cds_bp += region.subregion[s].stop.position() - region.subregion[s].start.position() + 1;
}
//
// reference variant
//
std::set<RefVariant> rvars = g.refdb.lookup( region , aux->ref );
std::set<RefVariant>::iterator i = rvars.begin();
while ( i != rvars.end() )
{
// for now, just place 'start' of reference-variant events
//int pos = positive_strand ? i->start() : - i->start() ;
int pos = i->start();
events.insert( pos );
erefvars[ pos ] = &(*i);
++i;
// std::cout << "found " << pos << "\n";
}
pout << vars.name() << " | "
<< g.locdb.alias( vars.name() , false ) << " | "
<< num_cds_exons << " CDS exons | "
<< ( positive_strand ? "+ve strand | " : "-ve strand | " )
<< vars.size() << " variants | ";
if ( rvars.size() > 0 )
pout << rvars.size() << " refvars | ";
pout << region.coordinate() << " | "
<< ( region.stop.position() - region.start.position() + 1 )/1000.0 << " kb | "
<< cds_bp << " coding bases\n";
//
// attach LOCDB
//
LocDBase * locdb = g.resolve_locgroup( PLINKSeq::DEFAULT_LOC_GROUP() ) ;
if ( ! locdb ) return;
int gid = locdb->lookup_group_id( PLINKSeq::DEFAULT_LOC_GROUP() );
if ( gid == 0 ) return;
//
// Translate to AA sequence
//
Annotate::setDB( locdb , &g.seqdb );
std::string aa = Annotate::translate_reference( region , false );
//
// Protein feature/domain annotations
//
std::map<int,std::string> pdm; //protein domain map
if ( aux->protdb )
{
std::set<Feature> features = aux->protdb->fetch( vars.name() );
bool all_prot = aux->protdom.find( "*" ) != aux->protdom.end()
|| aux->protdom.find( "ALL" ) != aux->protdom.end()
|| aux->protdom.find( "all" ) != aux->protdom.end();
std::set<Feature>::iterator ii = features.begin();
while ( ii != features.end() )
{
if ( all_prot || aux->protdom.find( ii->source_id ) != aux->protdom.end() )
{
// Subtract 1 to have 0-based aa coordinates:
for (int aa = ii->pstart - 1; aa <= ii->pstop - 1; aa++)
{
if ( pdm[aa] != "" ) pdm[aa] += " ";
pdm[ aa ] += ii->source_id + "::" + ii->feature_id + ":" + ii->feature_name + " ";
}
}
++ii;
}
}
//
// Display full AA sequence, with 1-codon padding either side
//
int pmin = genomic_start ;
int pmax = genomic_stop ;
if ( ! positive_strand )
{
int t = pmin;
pmin = pmax;
pmax = t;
}
pmin += positive_strand ? -9 : +9 ;
pmax += positive_strand ? +9 : -9 ;
int step = positive_strand ? +1 : -1;
//
// codon position, cycle 0,1,2
// transcript CDS should always start at 0
//
int cpos = 0;
int gpos = 0;
// will always start just before CDS, but in 'printable' region, thus:::
bool cds = false;
bool printing = true;
int exon = 0;
int exon0 = 0;
int last_exon = 0;
bool split_codon = false;
std::string codon = "";
std::string prt_codon = "";
std::string prt_intronic = "";
int chr = region.start.chromosome();
int apos = 0;
std::string refannot = "";
std::string varannot = "";
bool has_evar = false;
int stop_here = positive_strand ? pmax+1 : pmax-1;
std::stringstream ss;
for ( int bp = pmin ; bp != pmax+step ; bp += step )
{
const int searchbp = bp;
//
// Are we entering or leaving a printable region?
// (cpos-adjusted start, to make sure we are always in-sync)
//
if ( positive_strand )
{
if ( elocstart.find( searchbp + 9 + cpos ) != elocstart.end() )
{
printing = true;
// space a new one
if ( ! aux->only_variant_sites ) pout << "\n";
}
else if ( elocstop.find( searchbp - ( 7 + (3 - cpos) ) ) != elocstop.end() ) printing = false;
}
else
{
if ( elocstop.find( searchbp - ( 9 + cpos ) ) != elocstop.end() )
{
printing = true;
// space a new one
if ( ! aux->only_variant_sites ) pout << "\n";
}
else if ( elocstart.find( searchbp + 7 + (3-cpos) ) != elocstart.end() ) printing = false;
}
//
// hitting first position in a new CDS?
//
if ( ( positive_strand && elocstart.find( searchbp ) != elocstart.end() ) ||
( (!positive_strand) && elocstop.find( searchbp ) != elocstop.end() ) )
{
cds = true;
// track exon number
exon = positive_strand ? elocstart[ searchbp ] : elocstop[ searchbp ];
exon0 = exon;
if ( ! positive_strand ) exon = num_cds_exons - (exon+1) ;
}
//
// Have we gone one past the end of a current exon?
//
if ( cds )
if ( ( positive_strand && elocstop.find( searchbp - step ) != elocstop.end() )
||
( (!positive_strand) && elocstart.find( searchbp - step ) != elocstart.end() )
)
{
cds = false;
// track last exon code, for use printing introns
last_exon = exon+1;
if ( positive_strand )
{
if ( elocstop[ searchbp - step ] != exon ) plog.warn("internal inconsistency");
}
else
{
if ( elocstart[ searchbp - step ] != exon0 ) plog.warn("internal inconsistency");
}
//
// are we ending a CDS mid-frame?
//
if ( cpos == 1 )
{
split_codon = true;
//prt_codon = ".";
}
else if ( cpos == 2 )
{
split_codon = true;
//prt_codon = "..";
}
}
if ( bp == stop_here ) { continue; }
//
// append variant information
//
if ( printing && evars.find( searchbp ) != evars.end() )
{
const Variant * pvar = evars.find( searchbp )->second;
has_evar = true;
std::stringstream ss2;
ss2 << "[" ;
int case_count = 0 , case_tot = 0;
int control_count = 0 , control_tot = 0;
bool ma, control_ma;
if ( aux->pheno )
{
ma = pvar->n_minor_allele( &case_count , &case_tot , NULL , CASE );
control_ma = pvar->n_minor_allele( &control_count , &control_tot , NULL , CONTROL );
}
else
ma = pvar->n_minor_allele( &case_count , &case_tot );
// always report non-ref
if ( ! ma ) case_count = case_tot - case_count;
if ( ! control_ma ) control_count = control_tot - control_count;
// print minor/major allele(s)
if ( cpos == 0 )
ss2 << "" << pvar->alternate() << "..";
else if ( cpos == 1 )
ss2 << "." << pvar->alternate() << ".";
else
ss2 << ".." << pvar->alternate() ;
if ( aux->pheno )
ss2 << "|A/U=" << case_count << ":" << control_count ;
else
ss2 << "|MAC=" << case_count ;
ss2 << "|";
// always use PSEQ engine for annotation
// if ( pvar->meta.has_field( PLINKSeq::META_ANNOT() ) )
// ss2 << pvar->meta.get1_string( PLINKSeq::META_ANNOT() );
// {
// else
bool exonic = Annotate::annotate( (Variant&)*pvar , region );
// pull out correct transcript annotation
std::vector<std::string> annot = pvar->meta.get_string( PLINKSeq::ANNOT_TYPE() );
std::vector<std::string> annot_trans = pvar->meta.get_string( PLINKSeq::ANNOT_GENE() );
std::vector<std::string> annot_prot = pvar->meta.get_string( PLINKSeq::ANNOT_PROTEIN() );
std::string a = ".";
std::string ap = ".";
if ( annot.size() == annot_trans.size() && annot.size() == annot_prot.size() )
{
for( int i=0;i<annot.size(); i++)
{
if ( annot_trans[i] == vars.name() )
{
a = annot[i]; ap = annot_prot[i];
}
}
}
ss2 << a ;
if ( exonic )
{
ss2 << "|" << ap;
}
ss2 << "]";
if ( varannot != "" ) varannot += " ";
varannot += ss2.str();
}
//
// append ref-variant information
//
if ( printing && erefvars.find( searchbp ) != erefvars.end() )
{
const RefVariant * refvar = erefvars.find( searchbp )->second;
std::stringstream ss2;
ss2 << *refvar;
if ( refannot != "" ) refannot += " ";
refannot += ss2.str();
}
// cpos == 2 <==> last base in codon (since still on 0-based base count within exon: 0,1,2), so only annotate once
// [Can change to 'cpos == 0' if want to annotate the first part of the 'split codon' instead of the last part]:
if ( printing && aux->protdb && cds && cpos == 2 && pdm.find( apos ) != pdm.end() )
{
refannot += pdm[ apos ];
}
//
// Only show CDS
//
if ( printing )
{
if ( gpos == 0 )
if ( cds )
ss << "exon " << exon+1 << ( exon < 9 ? " " : "" ) << " " << Helper::chrCode( chr ) << ":" << searchbp;
else
{
if ( last_exon == 0 )
ss << "intron */1 " << ( exon < 9 ? " " : "" );
else if ( exon == num_cds_exons - 1 )
ss << "intron " << last_exon << "/* " << ( exon < 9 ? " " : "" );
else
ss << "intron " << last_exon << "/" << last_exon+1 << " " << ( exon < 9 ? " " : "" );
ss << Helper::chrCode( chr ) << ":" << searchbp;
}
}
if ( printing )
{
++gpos;
if ( cds )
{
codon += g.seqdb.lookup( chr , bp ) ;
prt_codon += g.seqdb.lookup( chr , bp ) ;
prt_intronic += ".";
++cpos;
}
else
{
prt_codon += ".";
prt_intronic += g.seqdb.lookup( chr , bp ) ;
}
//
// Print row
//
if ( gpos == 3 )
{
gpos = 0;
std::string aa_code = cds && cpos == 3 ? aa.substr( apos++ , 1 ) : ( split_codon ? ">" : "." ) ;
std::string aa_name = cds && cpos == 3 ? Annotate::aa[ aa_code ] : ( split_codon ? ">>>" : " . " );
ss << "\t" << prt_intronic << " " << prt_codon
<< " " << aa_code << " " << aa_name << " " << ( cds ? Helper::int2str(apos) : ( split_codon ? "> " : ". " ) )
<< "\t" << (refannot == "" ? "." : refannot )
<< "\t" << (varannot == "" ? "." : varannot )
<< "\n";
// print?
if ( (!aux->only_variant_sites) || has_evar )
pout << ss.str();
// reset all codon-specific stuff
if ( ! split_codon ) codon = "";
prt_codon = "";
prt_intronic = "";
refannot = "";
varannot = "";
has_evar = false;
split_codon = false;
// and clear stream
ss.str( std::string() );
}
}
if ( gpos == 3 ) gpos = 0;
if ( cpos == 3 ) cpos = 0;
}
//
// Create R plot?
//
if ( aux->R_plot )
{
//
// Upfront stuff
//
*rout << "## Populate data-structures for " << vars.name() << "\n"
<< "\n"
<< "transname = \"" << vars.name() << "\"\n"
<< "genename = \"" << g.locdb.alias( vars.name() , false ) << "\"\n"
<< "chrcode = \"" << Helper::chrCode( vars(0).chromosome() ) << "\"\n"
<< "refname = \"" << ( aux->ref ? args.as_string( "ref" ) : "" ) << "\"\n"
<< "var <- list();ref <- list();dom <- list();exon <- list() \n"
<< "# main transcript \n"
<< "trans <<- c( " << region.start.position() << " , " << region.stop.position() << ") \n"
<< "# strand for main (and only) transcript (+1, -1, 0) \n"
<< " strand <<- " << ( positive_strand ? "+1" : "-1" ) << "\n"
<< "# determine border \n"
<< " translen <<- trans[2] - trans[1] + 1 \n"
<< " total <<- round(c( trans[1] - 1000 , trans[2] + 1000 ) ) \n"
<< " totallen <<- total[2] - total[1] + 1 \n"
<< " ## exon structure \n";
//
// look at all CDS exons
//
int exc = 1;
for (int s = 0 ; s < region.subregion.size(); s++)
{
if ( ! region.subregion[s].CDS() ) continue;
*rout << " exon[[" << exc << "]] <- c( " << region.subregion[s].start.position() << " , " << region.subregion[s].stop.position() << " ) \n";
++exc;
}
*rout << " cdslength <<- " << cds_bp << " \n";
//
// non-CDS exons
//
exc = 1;
*rout << "exon_notcds <- list() \n";
for (int s = 0 ; s < region.subregion.size(); s++)
{
if ( ! region.subregion[s].exon() ) continue;
*rout << " exon_notcds[[" << exc << "]] <- c( " << region.subregion[s].start.position() << " , " << region.subregion[s].stop.position() << " ) \n";
++exc;
}
//
// All other overlapping transcripts
//
std::string g_chr_code = Helper::chrCode( region.start.chromosome() );
int g_chr = region.start.chromosome();
int g_bp1 = region.start.position();
int g_bp2 = region.stop.position();
std::set<Region> others = g.locdb.get_regions( g.locdb.lookup_group_id( PLINKSeq::DEFAULT_LOC_GROUP() ) , g_chr , g_bp1 , g_bp2 );
*rout << "others <- list() \n";
if ( others.size() > 0 )
{
int cnt1 = 1;
std::set<Region>::iterator ii = others.begin();
while ( ii != others.end() )
{
// for this transcript, exclude self
if ( ii->subregion.size() > 0 && ii->name != vars.name() )
{
*rout << "others[[" << cnt1 << "]] <- list( name = \"" << ii->name << "\" , \n ";
*rout << "exon_cds = list( " ;
int cnt2 = 1;
for (int s = 0 ; s < ii->subregion.size(); s++)
{
if ( ii->subregion[s].CDS() ) { *rout << (cnt2>1?",":"") << " c( " << ii->subregion[s].start.position() << " , " << ii->subregion[s].stop.position() << " ) \n"; ++cnt2; }
}
*rout << " ) , \n";
*rout << "exon_notcds = list( " ;
cnt2 = 1;
for (int s = 0 ; s < ii->subregion.size(); s++)
if ( ii->subregion[s].exon() ) { *rout << (cnt2>1?",":"") << " c( " << ii->subregion[s].start.position() << " , " << ii->subregion[s].stop.position() << " ) \n"; ++cnt2; }
*rout << " ) \n";
*rout << " ) \n";
++cnt1;
}
++ii;
}
}
//
// Variants;
//
*rout << " ## variants, with MAC (by cases), with annotation \n";
for (int v=0;v<vars.size();v++)
{
std::string annot = ".";
std::string annotdet = ".";
int cnta , cntu;
int case_count = 0 , case_tot = 0;
int control_count = 0 , control_tot = 0;
bool ma, control_ma;
Variant * pvar = &vars(v);
if ( aux->pheno )
{
ma = pvar->n_minor_allele( &case_count , &case_tot , NULL , CASE );
control_ma = pvar->n_minor_allele( &control_count , &control_tot , NULL , CONTROL );
}
else
ma = pvar->n_minor_allele( &case_count , &case_tot );
// always report non-ref
if ( ! ma ) case_count = case_tot - case_count;
if ( ! control_ma ) control_count = control_tot - control_count;
if ( ! aux->pheno )
{
cntu = -ma;
}
else
{
cnta = case_count;
cntu = control_count;
}
bool exonic = Annotate::annotate( (Variant&)*pvar , region );
// pull out correct transcript annotation
std::vector<std::string> annot_func = pvar->meta.get_string( PLINKSeq::ANNOT_TYPE() );
std::vector<std::string> annot_trans = pvar->meta.get_string( PLINKSeq::ANNOT_GENE() );
std::vector<std::string> annot_prot = pvar->meta.get_string( PLINKSeq::ANNOT_PROTEIN() );
if ( annot_func.size() == annot_trans.size() && annot_func.size() == annot_prot.size() )
{
for( int i=0;i<annot_func.size(); i++)
{
if ( annot_trans[i] == vars.name() )
{
annot = annot_func[i];
annotdet = annot_prot[i];
}
}
}
*rout << "var[[" << v+1 << "]] <- list( pos = c( " << vars(v).position() << " , " << vars(v).stop()
<< " ) , name = \"" << vars(v).name()
<< "\" , annot = \"" << annot << "\" , annotdet = \"" << annotdet
<< "\" , a = " << cnta << " , u = " << cntu << " ) \n";
}
//
// Reference variants
//
if ( aux->ref )
{
*rout << "## Reference variants\n";
*rout << "ref[[1]] <- list( group = \"" << args.as_string( "ref" ) << "\" , det = list() ) \n";
std::set<RefVariant>::iterator i = rvars.begin();
int rfc = 1;
while ( i != rvars.end() )
{
int pos = i->start();
*rout << "ref[[1]]$det[[" << rfc++ << "]] <- list( pos = c( " << i->start() << " , " << i->stop() << " ) , name = \"" << i->name() << "\" ) \n";
++i;
}
}
//
// Protein domains
//
if ( aux->protdb )
{
// just repeat this lookup from above for now...
*rout << "## Protein domains \n";
std::set<Feature> features = aux->protdb->fetch( vars.name() );
bool all_prot = aux->protdom.find( "*" ) != aux->protdom.end()
|| aux->protdom.find( "ALL" ) != aux->protdom.end()
|| aux->protdom.find( "all" ) != aux->protdom.end();
int pdct = 1;
std::map<std::string,int> sourcemap;
std::map<std::string,int> sourcecnt;
std::set<Feature>::iterator ii = features.begin();
while ( ii != features.end() )
{
if ( all_prot || aux->protdom.find( ii->source_id ) != aux->protdom.end() )
{
if ( sourcemap.find( ii->source_id ) == sourcemap.end() )
{
int t = sourcemap.size() + 1 ;
sourcemap[ ii->source_id ] = t;
*rout << "dom[[" << t << "]] <- list( group = \"" << ii->source_id << "\" , det = list() ) \n";
}
// 1-based count
*rout << "dom[[" << sourcemap[ ii->source_id ] << "]]$det[[" << ++sourcecnt[ ii->source_id ]
<< "]] <- list( name = \"" << ii->feature_id << ":" << ii->feature_name << "\" , "
<< "pos = c( " << ii->gstart << " , " << ii->gstop << " ) , aa = c( " << ii->pstart << " , " << ii->pstop << " ) ) \n ";
}
++ii;
}
}
// Perform actual plot, redircted to PDF
*rout << "\n\n#create plot\n"
<< "pdf( width = 14 , height = 10 , file=\"plot" << vars.name() << ".pdf\") \n "
<< "doplot() \n"
<< "dev.off() \n\n"
<< "#---------------------------------------------------------------------------\n\n\n";
}
pout << "------------------------------------------------------------\n\n";
}
