int main(int argc,char ** argv)
{
GenoVarSet * s;
PackAln * pal;
AlnBlock * alb;
DPRunImpl * dpri;
SnpMatch * snpm;
int i;
GenomePara * p;
MouseSNPMatch * forward;
MouseSNPMatch * backward;
FILE * ifp;
dpri = new_DPRunImpl_from_argv(&argc,argv);
strip_out_standard_options(&argc,argv,show_help,show_version);
ifp = openfile(argv[1],"r");
assert(ifp != NULL);
s = read_sanger_genotype_file(ifp);
p = new_GenomePara(0.95,0.01);
fprintf(stdout,"Score for match %d, score for mismatch %d\n",p->match,p->mismatch);
for(i=0;i < s->len ;i++) {
snpm = new_SnpMatch(s->chr[i],s,"DBA","PWK","CAST","WSB");
/* show_SnpMatchStats(snpm,stdout); */
backward = backward_logsum_MouseSNPMatch(p,snpm,dpri);
forward = forward_logsum_MouseSNPMatch(p,snpm,dpri);
fprintf(stdout,"Backward score is %d\n",
MouseSNPMatch_EXPL_SPECIAL(backward,0,-1,0));
fprintf(stdout,"Forward score is %d Backward score is %d\n",MouseSNPMatch_EXPL_SPECIAL(forward,0,forward->lenj-1,1),
MouseSNPMatch_EXPL_SPECIAL(backward,0,-1,0));
}
}
int main(int argc,char ** argv)
{
DnaMatchPara * para;
HitListOutputImpl * hitoutput;
HitList * hitlist;
Sequence * reference;
Sequence * swap;
Sequence * trans;
SequenceSet * amplimers;
int show_hitlist = 0;
int show_swapped = 1;
hitoutput = new_HitListOutputImpl_from_argv(&argc,argv);
para = new_DnaMatchPara_from_argv(&argc,argv);
strip_out_boolean_def_argument(&argc,argv,"hitlist",&show_hitlist);
strip_out_boolean_def_argument(&argc,argv,"swapped",&show_hitlist);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
reference = read_fasta_file_Sequence(argv[1]);
amplimers = read_fasta_SequenceSet_file(argv[2]);
hitlist = HitList_from_Sequence_SequenceSet_DNA(reference,amplimers,para);
if( show_hitlist ) {
show_HitList_HitListOutputImpl(hitoutput,hitlist,stdout);
}
swap = swapped_Sequence(reference,hitlist);
trans = translate_swapped(swap);
if( show_swapped ) {
write_fasta_Sequence(swap,stdout);
write_fasta_Sequence(trans,stdout);
}
}
int main(int argc,char ** argv)
{
DnaProfileEnginePara * dpep;
DnaProfileNode * root;
DnaProfileSet * set;
FILE * ifp;
boolean is_four = FALSE;
dpep = new_DnaProfileEnginePara_from_argv(&argc,argv);
is_four = strip_out_boolean_argument(&argc,argv,"bfour");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
ifp = openfile(argv[1],"r");
if( ifp == NULL ) {
fatal("could not open file %s",argv[1]);
}
if( is_four ) {
root = balanced_4_Sequence_fasta_stream(ifp);
} else {
root = simple_cascade_Sequence_fasta_stream(ifp);
}
populate_DnaProfileNode_from_root(root,dpep);
/*set = filter_DnaProfileSet(root->set,0,0);*/
show_DnaProfileSet(root->set,dpep->rm,stdout);
return 0;
}
int main(int argc,char ** argv)
{
int i;
char * temp;
build_defaults();
strip_out_standard_options(&argc,argv,show_help,show_version);
potential_file = strip_out_assigned_argument(&argc,argv,"pg");
pal_file = strip_out_assigned_argument(&argc,argv,"pal_file");
if( (temp = strip_out_assigned_argument(&argc,argv,"gap")) != NULL )
gap_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"g")) != NULL )
gap_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"ext")) != NULL )
ext_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"e")) != NULL )
ext_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"matrix")) != NULL )
matrix_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"m")) != NULL )
matrix_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"s")) != NULL )
qstart_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"t")) != NULL )
qend_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"u")) != NULL )
tstart_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"v")) != NULL )
tend_str = temp;
if( (strip_out_boolean_argument(&argc,argv,"trev")) == TRUE )
reverse = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"[no]newgene")) == TRUE )
use_new_stats = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"tfor")) == TRUE ){
if( reverse == TRUE ) {
warn("You have specified both trev and tfor. Treating as both");
do_both = TRUE;
reverse = FALSE;
} else {
reverse = FALSE;
}
}
if( (temp = strip_out_assigned_argument(&argc,argv,"insert")) != NULL ) {
if( strcmp(temp,"flat") == 0 ) {
flat_insert = TRUE;
} else {
flat_insert = FALSE;
}
}
if( (strip_out_boolean_argument(&argc,argv,"both")) == TRUE )
do_both = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"fembl")) == TRUE )
is_embl = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"tabs")) == TRUE )
target_abs = TRUE;
pseudo = strip_out_boolean_argument(&argc,argv,"pseudo");
if( (temp = strip_out_assigned_argument(&argc,argv,"codon")) != NULL )
codon_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"gene")) != NULL )
gene_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"alg")) != NULL )
alg_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"kbyte")) != NULL )
kbyte_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"subs")) != NULL )
subs_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"indel")) != NULL )
indel_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"cfreq")) != NULL )
cfreq_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"splice")) != NULL ) {
warn("deprecated command line option -splice. use -splice_gtag now");
splice_string = temp;
}
if( (temp = strip_out_assigned_argument(&argc,argv,"init")) != NULL )
startend_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"null")) != NULL )
null_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"intron")) != NULL )
intron_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"alln")) != NULL )
allN_string = temp;
if( (strip_out_boolean_argument(&argc,argv,"hmmer")) == TRUE )
use_tsm = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"intie")) == TRUE )
use_tied_model = TRUE;
if( (temp = strip_out_assigned_argument(&argc,argv,"hname")) != NULL )
hmm_name = temp;
if( (strip_out_boolean_argument(&argc,argv,"pretty")) != FALSE )
show_pretty = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"gff")) != FALSE )
show_gff = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"diana")) != FALSE )
show_diana = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"embl")) != FALSE )
show_embl = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"genes")) != FALSE )
show_pretty_gene = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"genesf")) != FALSE )
show_supp_gene = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"para")) != FALSE )
show_para = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"trans")) != FALSE )
show_trans = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pep")) != FALSE )
show_pep = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"cdna")) != FALSE )
show_cdna = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"sum")) != FALSE )
show_match_sum = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"alb")) != FALSE )
show_AlnBlock = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"ace")) != FALSE )
show_ace = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pal")) != FALSE )
show_PackAln = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"gener")) != FALSE )
show_gene_plain = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"over")) != FALSE )
show_overlap = TRUE;
if( (temp = strip_out_assigned_argument(&argc,argv,"divide")) != NULL )
divide_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"block")) != NULL )
main_block_str = temp;
dpri = new_DPRunImpl_from_argv(&argc,argv);
gmp = new_GeneModelParam_from_argv(&argc,argv);
ppp = new_PhasedProteinPara_from_argv(&argc,argv);
gwrp = new_GeneWiseRunPara_from_argv(&argc,argv);
strip_out_remaining_options_with_warning(&argc,argv);
if( argc != 3 ) {
warn("Wrong number of arguments (expect 2)!\n");
if( argc > 1 ){
warn("Arg line looked like (after option processing)");
for(i=1;i<argc;i++) {
fprintf(stderr," %s\n",argv[i]);
}
}
show_short_help();
}
if( show_embl == FALSE && show_diana == FALSE && show_gff == FALSE && show_overlap == FALSE && show_pretty_gene == FALSE && show_match_sum == FALSE && show_ace == FALSE && show_gene_plain == FALSE && show_pretty == FALSE && show_AlnBlock == FALSE && show_PackAln == FALSE && show_pep == FALSE ) {
show_pretty = TRUE;
show_para = TRUE;
}
dna_seq_file = argv[2];
if( use_tsm == FALSE)
protein_file = argv[1];
else
hmm_file = argv[1];
if( build_objects() == FALSE)
fatal("Could not build objects!");
if( show_para == TRUE) {
show_parameters();
}
if( build_alignment() == FALSE)
fatal("Could not build alignment!");
if( show_output() == FALSE)
fatal("Could not show alignment. Sorry!");
if( do_both == TRUE) {
reverse_target();
if( build_alignment() == FALSE)
fatal("Could not build alignment!");
if( show_output() == FALSE)
fatal("Could not show alignment. Sorry!");
}
free_temporary_objects();
free_io_objects();
return 0;
}
int main(int argc,char ** argv)
{
Sequence * gen;
Genomic * genomic;
CodonTable * ct = NULL;
GenomeEvidenceSet * ges = NULL;
RandomCodonScore * rcs;
FILE * ifp = NULL;
ComplexSequence * cs = NULL;
ComplexSequenceEvalSet * cses = NULL;
AlnBlock * alb;
PackAln * pal;
GenomicRegion * gr;
int i;
Protein * trans;
cDNA * cdna;
int kbyte = 10000;
int stop_codon_pen = 200;
int start_codon_pen = 30;
int new_gene = 5000;
int switch_cost = 100;
int smell = 8;
DPRunImpl * dpri = NULL;
EstEvidence * est;
boolean show_trans = TRUE;
boolean show_cdna = FALSE;
boolean show_genes = TRUE;
boolean show_alb = FALSE;
boolean show_pal = FALSE;
boolean show_gff = TRUE;
boolean show_debug = FALSE;
boolean show_geneu = TRUE;
char * divide_string = "//";
strip_out_boolean_def_argument(&argc,argv,"geneutr",&show_geneu);
strip_out_boolean_def_argument(&argc,argv,"genes",&show_genes);
strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);
strip_out_boolean_def_argument(&argc,argv,"gff",&show_gff);
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal);
strip_out_boolean_def_argument(&argc,argv,"debug",&show_debug);
strip_out_boolean_def_argument(&argc,argv,"cdna",&show_cdna);
strip_out_integer_argument(&argc,argv,"stop",&stop_codon_pen);
strip_out_integer_argument(&argc,argv,"start",&start_codon_pen);
strip_out_integer_argument(&argc,argv,"gene",&new_gene);
strip_out_integer_argument(&argc,argv,"switch",&switch_cost);
strip_out_integer_argument(&argc,argv,"smell",&smell);
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
ct = read_CodonTable_file("codon.table");
gen = read_fasta_file_Sequence(argv[1]);
ifp = openfile(argv[2],"r");
ges = read_est_evidence(ifp,ct);
for(i=0;i<ges->len;i++) {
est = (EstEvidence *) ges->geu[i]->data;
est->in_smell = smell;
}
rcs= RandomCodonScore_alloc();
for(i=0;i<125;i++) {
if( is_stop_codon(i,ct) ) {
rcs->codon[i] = -1000000;
} else {
rcs->codon[i] = 0;
}
/* fprintf(stderr,"Got %d for %d\n",rcs->codon[i],i); */
}
cses = default_genomic_ComplexSequenceEvalSet();
cs = new_ComplexSequence(gen,cses);
pal = PackAln_bestmemory_GenomeWise9(ges,cs,-switch_cost,-new_gene,-start_codon_pen,-stop_codon_pen,rcs,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_GenomeWise9(pal);
genomic = Genomic_from_Sequence(gen);
gr = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_GeneWise(gr,1,gen->len,alb,gen->name,0,NULL);
if( show_genes ) {
show_pretty_GenomicRegion(gr,0,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_gff ) {
show_GFF_GenomicRegion(gr,gen->name,"genomwise",stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_trans ) {
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,stdout);
}
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_cdna ) {
for(i=0;i<gr->len;i++) {
cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]);
write_fasta_Sequence(cdna->baseseq,stdout);
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_geneu ) {
show_utr_exon_genomewise(alb,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_alb ) {
mapped_ascii_AlnBlock(alb,id,1,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_debug ) {
debug_genomewise(alb,ges,ct,gen,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_pal ) {
show_simple_PackAln(pal,stdout);
fprintf(stdout,"%s\n",divide_string);
}
return 0;
}
int main(int argc,char ** argv)
{
int i;
char * temp;
build_defaults();
bootstrap_HMMer2();
strip_out_standard_options(&argc,argv,show_help,show_version);
if( (temp = strip_out_assigned_argument(&argc,argv,"gap")) != NULL )
gap_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"g")) != NULL )
gap_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"ext")) != NULL )
ext_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"e")) != NULL )
ext_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"matrix")) != NULL )
matrix_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"m")) != NULL )
matrix_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"s")) != NULL )
qstart_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"t")) != NULL )
qend_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"aln")) != NULL )
aln_number_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"codon")) != NULL )
codon_file = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"alg")) != NULL )
alg_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"aalg")) != NULL )
aln_alg_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"cut")) != NULL )
search_cutoff_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"ecut")) != NULL )
evalue_search_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"subs")) != NULL )
subs_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"indel")) != NULL )
indel_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"init")) != NULL )
startend_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"alln")) != NULL )
allN_string = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"null")) != NULL )
null_string = temp;
if( (strip_out_boolean_argument(&argc,argv,"dnas")) == TRUE )
use_single_dna = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"dnadb")) == TRUE )
use_single_dna = FALSE;
if( (strip_out_boolean_argument(&argc,argv,"tfor")) == TRUE )
do_forward_only = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"flati")) == TRUE )
flat_insert = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"hmmer")) == TRUE )
use_tsm = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pfam2")) == TRUE )
use_pfam1 = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pfam")) == TRUE )
use_pfam2 = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"protein")) == TRUE )
use_single_pro = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"prodb")) == TRUE )
use_db_pro = TRUE;
if( (temp = strip_out_assigned_argument(&argc,argv,"hname")) != NULL )
hmm_name = temp;
if( (strip_out_boolean_argument(&argc,argv,"nohis")) != FALSE )
show_histogram = FALSE;
if( (strip_out_boolean_argument(&argc,argv,"pretty")) != FALSE )
show_pretty = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pep")) != FALSE )
show_pep = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"mul")) != FALSE )
make_anchored_aln = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"para")) != FALSE )
show_para = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"sum")) != FALSE )
show_match_sum = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"alb")) != FALSE )
show_AlnBlock = TRUE;
if( (strip_out_boolean_argument(&argc,argv,"pal")) != FALSE )
show_PackAln = TRUE;
if( (temp = strip_out_assigned_argument(&argc,argv,"divide")) != NULL )
divide_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"block")) != NULL )
main_block_str = temp;
if( (temp = strip_out_assigned_argument(&argc,argv,"report")) != NULL )
report_str = temp;
dbsi = new_DBSearchImpl_from_argv(&argc,argv);
dpri = new_DPRunImpl_from_argv(&argc,argv);
strip_out_remaining_options_with_warning(&argc,argv);
if( argc != 3 ) {
warn("Wrong number of arguments (expect 2)!\n");
if( argc > 1 ){
warn("Arg line looked like (after option processing)");
for(i=1;i<argc;i++) {
fprintf(stderr," %s\n",argv[i]);
}
}
show_short_help();
}
if( show_pretty == FALSE && show_AlnBlock == FALSE && show_PackAln == FALSE && show_pep == FALSE ) {
show_pretty = TRUE;
show_para = TRUE;
}
if( use_db_pro == FALSE && use_single_pro == FALSE && use_tsm == FALSE && use_pfam1 == FALSE && use_pfam2 == FALSE ) {
use_single_pro = TRUE;
}
if( use_single_pro == TRUE || use_tsm == TRUE ) {
if( use_single_dna == TRUE )
fatal("one on one search. Shouldn't you use pcwise?");
search_mode = PC_SEARCH_S2DB;
} else {
if( use_single_dna == TRUE )
search_mode = PC_SEARCH_DB2S;
else
search_mode = PC_SEARCH_DB2DB;
}
if( evalue_search_str != NULL && search_mode != PC_SEARCH_S2DB ) {
fatal("Trying to set a evalue cutoff on a non evalue based search. you can only use evalues in a protein HMM vs DNA database search (sorry!)");
}
if( make_anchored_aln == TRUE && search_mode != PC_SEARCH_S2DB ) {
fatal("Trying to make an anchored alignment and not in single search mode");
}
if( make_anchored_aln == TRUE) {
do_complete_analysis = TRUE;
}
/* pick up remaining args and do it */
dna_seq_file = argv[2];
protein_file = argv[1];
if( build_objects() == FALSE)
fatal("Could not build objects!");
if( build_db_objects() == FALSE)
fatal("Could not build database-ready objects!");
show_header(stdout);
if( search_db() == FALSE)
warn("Could not search database");
show_output();
free_objects();
return 0;
}
int main (int argc,char ** argv)
{
MappedCloneSet * trusted;
MappedCloneSet * weak;
MappedCloneMatch * match;
FILE * in;
int kbyte = 10000;
PackAln * pal;
AlnBlock * alb;
int spread = 30;
boolean show_alb = 0;
boolean show_pal = 0;
boolean show_zip = 1;
boolean show_path = 0;
char * alg_string = "local";
char * temp;
char * divide_string = "//";
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal);
strip_out_boolean_def_argument(&argc,argv,"zip",&show_zip);
strip_out_boolean_def_argument(&argc,argv,"path",&show_path);
strip_out_integer_argument(&argc,argv,"wgap",&query_gap_start);
strip_out_integer_argument(&argc,argv,"wext",&query_gap_extend);
strip_out_integer_argument(&argc,argv,"wswitch",&query_switch_cost);
strip_out_integer_argument(&argc,argv,"tgap",&target_gap_start);
strip_out_integer_argument(&argc,argv,"text",&target_gap_extend);
strip_out_integer_argument(&argc,argv,"match",&match_score);
strip_out_integer_argument(&argc,argv,"mismatch",&mismatch_score);
temp =strip_out_assigned_argument(&argc,argv,"alg");
if( temp != NULL ) {
alg_string = temp;
}
strip_out_integer_argument(&argc,argv,"spread",&spread);
strip_out_integer_argument(&argc,argv,"kbyte",&kbyte);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
in = fopen(argv[1],"r");
if( in == NULL ) {
fatal("Unable to open %s",argv[1]);
}
trusted = read_MappedCloneSet(in);
/* fprintf(stderr,"first start %d\n",trusted->clone[0]->start);*/
in = fopen(argv[2],"r");
if( in == NULL ) {
fatal("Unable to open %s",argv[2]);
}
change_max_BaseMatrix_kbytes(kbyte);
weak = read_MappedCloneSet(in);
synchronise_MappedCloneSets(trusted,weak);
/* fprintf(stderr,"score for 2,2 is %d\n",MappedCloneSet_match(weak,trusted,2,2,0,10,-5)); */
match = new_MappedCloneMatch(weak,trusted,match_score,mismatch_score);
fprintf(stderr,"Match matrix calculated\n");
if( strcmp(alg_string,"global") == 0 ) {
pal = PackAln_bestmemory_CloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL);
alb = convert_PackAln_to_AlnBlock_CloneWise(pal);
} else if ( strcmp(alg_string,"local") == 0 ) {
pal = PackAln_bestmemory_LocalCloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL);
alb = convert_PackAln_to_AlnBlock_LocalCloneWise(pal);
} else {
/* keep gcc happy */
pal = NULL;
alb = NULL;
fatal("Not a proper algorithm string %s",alg_string);
}
if( show_path ) {
extended_path(alb,weak,trusted,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_zip ) {
debug_zip(alb,weak,trusted,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_alb ) {
mapped_ascii_AlnBlock(alb,id,1,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_pal ) {
show_simple_PackAln(pal,stdout);
fprintf(stdout,"%s\n",divide_string);
}
return 0;
}
int main(int argc,char **argv)
{
FiveStateFrameSet * frame;
FiveStateModel * fsm;
FiveStateScore * fss;
RandomModel * rm;
ProteinDB * proteindb;
DBSearchImpl * dbsi;
Hscore * hs;
double gathering_cutoff = 0.0;
double bits;
int i;
dbsi = new_DBSearchImpl_from_argv(&argc,argv);
strip_out_float_argument(&argc,argv,"ga",&gathering_cutoff);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
rm = default_RandomModel();
frame = read_FiveStateFrameSet_file(argv[1],"block.str");
if( frame == NULL )
fatal("Unable to make FiveStateModel from context %s, block.str file",argv[1]);
fsm = FiveStateModel_from_FiveStateFrameSet(frame);
/* dump_FiveStateModel(fsm,stdout); */
fsm->name = stringalloc(argv[1]);
fold_RandomModel_into_FiveStateModel(fsm,rm);
/* converts probabilities to integers for calculation */
fss = FiveStateScore_from_FiveStateModel(fsm);
proteindb = single_fasta_ProteinDB(argv[2]);
if( proteindb== NULL )
fatal("Unable to make proteindb from %s",argv[2]);
hs = std_score_Hscore(Probability2Score(gathering_cutoff)-10,-1);
search_FiveStateProtein(dbsi,hs,fss,proteindb);
fprintf(stdout,"\n\n#High Score list\n");
fprintf(stdout,"#Protein ID DNA Str ID Bits Evalue\n");
fprintf(stdout,"--------------------------------------------------------------------------\n");
for(i=0;i<hs->len;i++) {
bits = Score2Bits(hs->ds[i]->score);
if( bits < gathering_cutoff ) {
break;
}
fprintf(stdout,"Protein %-20sDNA [%c] %-24s %.2f\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits);
}
}
int main(int argc,char ** argv)
{
int type = ALIGN_NORMAL;
DPRunImpl * dpri = NULL;
HitList * hl;
HitListOutputImpl * hloi;
Sequence * query;
Sequence * target;
Sequence * target_rev;
PairwiseShortDna * two;
LocalCisHitSet * set;
LocalCisHitSet * greedy_set;
LocalCisHitScore * lchs;
LocalCisHitSetPara * setpara;
MotifMatrixPara * mmp;
MotifMatrixScore * mms;
TransFactorMatchSet * tfms_query = NULL;
TransFactorMatchSet * tfms_target = NULL;
TransFactorMatchSet * tfms_target_rev = NULL;
int qstart = -1;
int qend = -1;
int tstart = -1;
int tend = -1;
int i;
char * temp;
DnaMatrix * dm;
DnaProbMatrix * dmp;
TransFactorBuildPara * tfbp;
TransFactorMatchPara * tfmp;
TransFactorSet * tfs;
char * motif_library = NULL;
int use_laurence = FALSE;
int use_ben = FALSE;
dmp = DnaProbMatrix_from_match(0.75,NMaskType_BANNED);
assert(dmp);
flat_null_DnaProbMatrix(dmp);
dm = DnaMatrix_from_DnaProbMatrix(dmp);
dpri = new_DPRunImpl_from_argv(&argc,argv);
hloi = new_HitListOutputImpl_from_argv(&argc,argv);
setpara = new_LocalCisHitSetPara_from_argv(&argc,argv);
mmp = new_MotifMatrixPara_from_argv(&argc,argv);
tfbp = new_TransFactorBuildPara_from_argv(&argc,argv);
tfmp = new_TransFactorMatchPara_from_argv(&argc,argv);
strip_out_integer_argument(&argc,argv,"s",&qstart);
strip_out_integer_argument(&argc,argv,"t",&qend);
strip_out_integer_argument(&argc,argv,"u",&tstart);
strip_out_integer_argument(&argc,argv,"v",&tend);
temp = strip_out_assigned_argument(&argc,argv,"motiflib");
if( temp != NULL ) {
motif_library = stringalloc(temp);
}
use_laurence = strip_out_boolean_argument(&argc,argv,"lr");
use_ben = strip_out_boolean_argument(&argc,argv,"ben");
temp = strip_out_assigned_argument(&argc,argv,"align");
if( temp != NULL ) {
if( strcmp(temp,"motif") == 0 ) {
type = ALIGN_MOTIF;
} else if ( strcmp(temp,"normal") == 0 ) {
type = ALIGN_NORMAL;
} else {
fatal("cannot recognise string %s as align type",temp);
}
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
query = read_fasta_file_Sequence(argv[1]);
target = read_fasta_file_Sequence(argv[2]);
for(i=0;i<query->len;i++) {
query->seq[i] = toupper(query->seq[i]);
}
assert(query != NULL);
assert(target != NULL);
target_rev = reverse_complement_Sequence(target);
mms = MotifMatrixScore_from_MotifMatrixPara(mmp);
if( type == ALIGN_MOTIF ) {
if( motif_library == NULL ) {
fatal("Wanted to align with motif but not motif library. Must use -motiflib");
}
if( use_laurence == TRUE ) {
tfs = read_laurence_TransFactorSet_file(motif_library);
} else if( use_ben == TRUE ) {
tfs = read_ben_IUPAC_TransFactorSet_file(motif_library);
} else {
tfs = read_TransFactorSet_file(motif_library);
}
build_TransFactorSet(tfs,tfbp);
tfms_query = calculate_TransFactorMatchSet(query,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_query);
tfms_target = calculate_TransFactorMatchSet(target,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_target);
tfms_target_rev = calculate_TransFactorMatchSet(target_rev,tfs,tfmp);
sort_by_start_TransFactorMatchSet(tfms_target);
fprintf(stdout,"Motif Set: %d in query and %d in target\n",tfms_query->len,tfms_target->len);
}
if( qstart == -1 ) {
qstart = 0;
}
if( qend == -1 ) {
qend = query->len;
}
if( tstart == -1 ) {
tstart = 0;
}
if( tend == -1 ) {
tend = target->len;
}
two = query_to_reverse_target(query,target,dm,qstart,qend,tstart,tend);
set = make_LocalCisHitSet(query,target,target_rev,two->forward,two->reverse,setpara,lchs,tfms_query,tfms_target,tfms_target_rev,mms,type == ALIGN_MOTIF ? 1 : 0,dpri);
greedy_set = greedy_weed_LocalCisHitSet(set,setpara);
hl = HitList_from_LocalCisHitSet(greedy_set);
show_HitList_HitListOutputImpl(hloi,hl,stdout);
return 0;
}
int main(int argc,char ** argv)
{
DPRunImpl * dpri = NULL;
ScanWiseHSPImpl * scani = NULL;
HSP2HitListImpl * hsp2hiti = NULL;
HitListOutputImpl * hloi = NULL;
ProteinIndexConstructor * pic = NULL;
HSPScanInterface * hsi;
HSPScanInterfacePara * para;
SearchStatInterface * ssi;
SearchStatInterface * ssl;
SeqLookupLoadPara * slp;
HSPset2HitPairPara * hsp2hit;
CompMat * mat;
SequenceDB * db;
Sequence * seq;
int ret;
int i;
int effective_db_size = 300000;
int kk;
int count = 0;
LinearHSPmanager * lm;
HitList * hl;
boolean use_mott = 1;
boolean trunc_best_hsp = 0;
boolean verbose = 0;
static struct rusage use;
struct timeval t0, t1;
gettimeofday(&t0, NULL);
dpri = new_DPRunImpl_from_argv(&argc,argv);
dpri->memory = DPIM_Explicit;
scani = new_ScanWiseHSPImpl_from_argv(&argc,argv);
hsp2hiti = new_HSP2HitListImpl_from_argv(&argc,argv);
hloi = new_HitListOutputImpl_from_argv(&argc,argv);
slp = new_SeqLookupLoadPara_from_argv(&argc,argv);
pic = new_ProteinIndexConstructor_from_argv(&argc,argv);
hsp2hit = new_HSPset2HitPairPara_from_argv(&argc,argv);
para = new_HSPScanInterfacePara_from_argv(&argc,argv);
verbose = strip_out_boolean_argument(&argc,argv,"verbose") ;
strip_out_boolean_def_argument(&argc,argv,"mott",&use_mott);
strip_out_boolean_def_argument(&argc,argv,"besthsp",&trunc_best_hsp);
strip_out_integer_argument(&argc,argv,"dbsize",&effective_db_size);
#ifdef SCAN_CORBA
sorb = get_Wise2Corba_Singleton(&argc,argv,"orbit-local-orb");
#endif
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
/* ugly, but we don't want to bounce matrices around the network... */
mat = read_Blast_file_CompMat("BLOSUM62.bla");
erroroff(REPORT);
hsi = new_HSPScanInterface_from_ScanWiseHSPImpl(scani,pic,slp);
ssi = new_Mott_SearchStatInterface();
ssl = new_lookup_SearchStatInterface(40,2.3);
if( verbose ) {
info("contacted database");
}
db = single_fasta_SequenceDB(argv[1]);
if( db == NULL ) {
fatal("Could not open sequence db...\n");
}
for(seq = init_SequenceDB(db,&ret); seq != NULL;seq = get_next_SequenceDB(db) ) {
count++;
for(i=0;i<seq->len;i++) {
if( !isalpha(seq->seq[i]) ) {
fatal("Sequence position %d [%c] is not valid",i,seq->seq[i]);
}
seq->seq[i] = toupper(seq->seq[i]);
}
info("Processing %s",seq->name);
getrusage(RUSAGE_SELF,&use);
/* info("Before query %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
lm = (*hsi->scan_query)(hsi->data,seq,para);
fprintf(stderr,"Got linear manager is %d entries\n",lm->len);
if( lm->mat == NULL ) {
lm->mat = hard_link_CompMat(mat);
}
getrusage(RUSAGE_SELF,&use);
/*
info("After query %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
sort_LinearHSPmanager(lm,compare_HSPset_score);
if( trunc_best_hsp == 1 ) {
for(kk=1;kk<lm->len;kk++) {
free_HSPset(lm->set[kk]);
lm->set[kk] = NULL;
}
lm->len = 1;
}
getrusage(RUSAGE_SELF,&use);
/*
info("After sort %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
hl = HitList_from_HSP_HSP2HitListImpl(hsp2hiti,lm,dpri,hsp2hit);
getrusage(RUSAGE_SELF,&use);
/*
info("After conversion %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
free_LinearHSPmanager(lm);
if( use_mott == 1 ) {
apply_SearchStat_to_HitList(hl,ssi,effective_db_size);
} else {
for(kk=0;kk<hl->len;kk++) {
hl->pair[kk]->bit_score = hl->pair[kk]->raw_score / 2.0;
}
}
sort_HitList_by_score(hl);
show_HitList_HitListOutputImpl(hloi,hl,stdout);
getrusage(RUSAGE_SELF,&use);
/*
info("After output %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
free_HitList(hl);
free_Sequence(seq);
}
free_DPRunImpl(dpri);
free_HSPScanInterface(hsi);
gettimeofday(&t1, NULL);
fprintf(stderr, "[client stats] queries, time (s): %d %f\n",
count,
(t1.tv_sec - t0.tv_sec) +
(t1.tv_usec - t0.tv_usec) * 1e-6);
return 0;
}
int main(int argc,char ** argv)
{
int i;
DPRunImpl * dpri = NULL;
GeneModelParam * gmp = NULL;
GeneModel * gm = NULL;
Sequence * seq;
RandomCodon * rc;
RandomModelDNA * rmd;
RandomCodonScore * rcs;
ComplexSequenceEval * splice5;
ComplexSequenceEval * splice3;
ComplexSequenceEvalSet * cses;
ComplexSequence * cseq;
SyExonScore * exonscore;
PackAln * pal;
AlnBlock * alb;
Genomic * genomic;
GenomicRegion * gr;
Protein * trans;
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
gmp = new_GeneModelParam_from_argv(&argc,argv);
ct= read_CodonTable_file("codon.table");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) {
fatal("Could not build gene model");
}
seq = read_fasta_file_Sequence(argv[1]);
assert(seq);
cses = new_ComplexSequenceEvalSet_from_GeneModel(gm);
cseq = new_ComplexSequence(seq,cses);
rc = flat_RandomCodon(ct);
rmd = RandomModelDNA_std();
fold_in_RandomModelDNA_into_RandomCodon(rc,rmd);
rcs = RandomCodonScore_from_RandomCodon(rc);
exonscore = SyExonScore_flat_model(200,250,0.1,0.1);
/*
for(i=0;i<cseq->length;i++) {
fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]);
}
exit(0);
*/
/*
show_RandomCodonScore(rcs,stdout);
for(i=3;i<seq->len;i++) {
fprintf(stdout,"seq %d is %c with score %d\n",i,aminoacid_from_seq(ct,seq->seq+i-2),rcs->codon[CSEQ_GENOMIC_CODON(cseq,i)]);
}
exit(0);
*/
pal = PackAln_bestmemory_StatWise10(exonscore,cseq,rcs,Probability2Score(1.0/10.0),Probability2Score(1.0/10.0),NULL,dpri);
alb = convert_PackAln_to_AlnBlock_StatWise10(pal);
mapped_ascii_AlnBlock(alb,id,1,stdout);
genomic = Genomic_from_Sequence(seq);
gr = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_GeneWise(gr,1,seq->len,alb,"bollocks",0,NULL);
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,stdout);
}
}
return 0;
}
int main(int argc,char ** argv)
{
int i;
DPRunImpl * dpri = NULL;
GeneModelParam * gmp = NULL;
GeneModel * gm = NULL;
FILE * ifp;
SeqAlign * al;
PairBaseSeq * pbs;
ComplexSequenceEval * splice5;
ComplexSequenceEval * splice3;
ComplexSequence * cseq;
CompMat * score_mat;
CompProb * comp_prob;
RandomModel * rm;
PairBaseCodonModelScore * codon_score;
PairBaseModelScore* nonc_score;
PairBaseCodonModelScore * start;
PairBaseCodonModelScore * stop;
SyExonScore * exonscore;
PackAln * pal;
AlnBlock * alb;
Genomic * genomic;
GenomicRegion * gr;
GenomicRegion * gr2;
Protein * trans;
StandardOutputOptions * std_opt;
ShowGenomicRegionOptions * sgro;
char * dump_packaln = NULL;
char * read_packaln = NULL;
FILE * packifp = NULL;
boolean show_trans = 1;
boolean show_gene_raw = 0;
ct = read_CodonTable_file(codon_table);
/*
score_mat = read_Blast_file_CompMat("blosum62.bla");
comp_prob = CompProb_from_halfbit(score_mat);
*/
rm = default_RandomModel();
comp_prob = read_Blast_file_CompProb("wag85");
fold_column_RandomModel_CompProb(comp_prob,rm);
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
gmp = new_GeneModelParam_from_argv(&argc,argv);
std_opt = new_StandardOutputOptions_from_argv(&argc,argv);
sgro = new_ShowGenomicRegionOptions_from_argv(&argc,argv);
dump_packaln = strip_out_assigned_argument(&argc,argv,"dump");
read_packaln = strip_out_assigned_argument(&argc,argv,"recover");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) {
fatal("Could not build gene model");
}
codon_score = make_PairBaseCodonModelScore(comp_prob);
nonc_score = make_PairBaseModelScore();
splice5 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice5score);
splice3 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice3score);
if((ifp = openfile(argv[1],"r")) == NULL ) {
fatal("Could not open file %s",argv[1]);
}
al = read_fasta_SeqAlign(ifp);
assert(al);
assert(al->len == 2);
assert(al->seq[0]->len > 0);
assert(al->seq[1]->len > 0);
/* write_fasta_SeqAlign(al,stdout);*/
pbs = new_PairBaseSeq_SeqAlign(al);
if( read_packaln == NULL ) {
cseq = ComplexSequence_from_PairBaseSeq(pbs,splice5,splice3);
}
start = make_start_PairBaseCodonModelScore(ct);
stop = make_stop_PairBaseCodonModelScore(ct);
/* show_PairBaseCodonModelScore(stop,ct,stdout); */
/*
for(i=0;i<pbs->anchor->len;i++) {
printf("%3d %c For %-6d %-6d %c Rev %-6d %-6d\n",i,pbs->anchor->seq[i],
CSEQ_PAIR_5SS(cseq,i),CSEQ_PAIR_3SS(cseq,i),
char_complement_base(pbs->anchor->seq[i]),
CSEQ_REV_PAIR_5SS(cseq,i),CSEQ_REV_PAIR_3SS(cseq,i));
}
*/
/* show_ComplexSequence(cseq,stdout);
*/
exonscore = SyExonScore_flat_model(100,150,0.1,1.0);
/*
for(i=0;i<cseq->length;i++) {
fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]);
}
exit(0);
*/
if( read_packaln != NULL ) {
packifp = openfile(read_packaln,"r");
if( packifp == NULL ) {
fatal("File %s is unopenable - ignoring dump command",dump_packaln);
} else {
pal = read_simple_PackAln(packifp);
}
} else {
pal = PackAln_bestmemory_SyWise20(exonscore,cseq,codon_score,nonc_score,start,stop,Probability2Score(1.0/100.0),Probability2Score(1.0/10000.0),Probability2Score(1.0/10.0),NULL,dpri);
}
alb = convert_PackAln_to_AlnBlock_SyWise20(pal);
if( dump_packaln != NULL ) {
packifp = openfile(dump_packaln,"w");
if( packifp == NULL ) {
warn("File %s is unopenable - ignoring dump command",dump_packaln);
} else {
show_simple_PackAln(pal,packifp);
}
}
show_score_sequence(alb,pbs,nonc_score,stdout);
/*
show_StandardOutputOptions(std_opt,alb,pal,"//",stdout);
*/
genomic = Genomic_from_Sequence(al->seq[0]);
gr = new_GenomicRegion(genomic);
gr2 = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_new(gr,alb);
show_GenomicRegionOptions(sgro,gr,ct,"//",stdout);
return 0;
}
int main(int argc,char ** argv)
{
Sequence * cdna;
Sequence * gen;
Sequence * active_gen;
Sequence * active_cdna;
int i;
int dstart = -1;
int dend = -1;
int cstart = -1;
int cend = -1;
CodonTable * ct = NULL;
CodonMatrixScore * cm = NULL;
RandomCodon * rndcodon = NULL;
RandomCodonScore * rndcodonscore = NULL;
DnaMatrix * dm = NULL;
DPRunImpl * dpri = NULL;
GeneModel * gm;
GeneModelParam * gmp;
GeneStats * gs;
GeneParser21 * gp21;
GeneParser21Score * gp21s;
GeneParser4Score * gp;
ComplexSequenceEvalSet * cdna_cses;
ComplexSequenceEvalSet * gen_cses;
ComplexSequence * cs_cdna;
ComplexSequence * cs_gen;
Genomic * gent;
GenomicRegion * gr;
CompMat * cmat;
CompProb * cprob;
char * matfile = "blosum62.bla";
Protein * trans;
PackAln * pal;
AlnBlock * alb;
FILE * ofp = stdout;
dpri = new_DPRunImpl_from_argv(&argc,argv);
gmp = new_GeneModelParam_from_argv(&argc,argv);
strip_out_integer_argument(&argc,argv,"u",&dstart);
strip_out_integer_argument(&argc,argv,"v",&dend);
strip_out_integer_argument(&argc,argv,"s",&cstart);
strip_out_integer_argument(&argc,argv,"t",&cend);
strip_out_standard_options(&argc,argv,show_help,show_version);
ct = read_CodonTable_file(codon_file);
cmat = read_Blast_file_CompMat(matfile);
cprob = CompProb_from_halfbit(cmat);
cm = naive_CodonMatrixScore_from_prob(ct,cprob);
gm = GeneModel_from_GeneModelParam(gmp);
cdna = read_fasta_file_Sequence(argv[1]);
gen = read_fasta_file_Sequence(argv[2]);
if( dstart != -1 || dend != -1 ) {
if( dstart == -1 ) {
dstart = 1;
}
if( dend == -1 ) {
dend = gen->len;
}
active_gen = magic_trunc_Sequence(gen,dstart,dend);
} else {
active_gen = hard_link_Sequence(gen);
}
if( cstart != -1 || cend != -1 ) {
if( cstart == -1 ) {
cstart = 1;
}
if( cend == -1 ) {
cend = gen->len;
}
active_cdna = magic_trunc_Sequence(gen,cstart,cend);
} else {
active_cdna = hard_link_Sequence(gen);
}
rndcodon = RandomCodon_from_raw_CodonFrequency(gm->codon,ct);
fold_in_RandomModelDNA_into_RandomCodon(rndcodon,gm->rnd);
rndcodonscore = RandomCodonScore_from_RandomCodon(rndcodon);
assert(active_cdna);
assert(active_gen);
cdna_cses = default_cDNA_ComplexSequenceEvalSet();
gen_cses = new_ComplexSequenceEvalSet_from_GeneModel(gm);
cs_cdna = new_ComplexSequence(active_cdna,cdna_cses);
cs_gen = new_ComplexSequence(active_gen,gen_cses);
gp21 = std_GeneParser21();
GeneParser21_fold_in_RandomModelDNA(gp21,gm->rnd);
gp21s = GeneParser21Score_from_GeneParser21(gp21);
gp = GeneParser4Score_from_GeneParser21Score(gp21s);
dm = identity_DnaMatrix(Probability2Score(halfbit2Probability(1)),Probability2Score(halfbit2Probability(-1)));
assert(cs_cdna);
assert(cs_gen);
assert(gp);
assert(rndcodonscore);
assert(dm);
assert(dpri);
/* show_CodonMatrixScore(cm,ct,ofp);*/
pal = PackAln_bestmemory_CdnaWise10(cs_cdna,cs_gen,gp,cm,rndcodonscore,dm,
Probability2Score(halfbit2Probability(-12)),
Probability2Score(halfbit2Probability(-2)),
Probability2Score(halfbit2Probability(-5)),
Probability2Score(halfbit2Probability(0)),
NULL,
dpri);
alb = convert_PackAln_to_AlnBlock_CdnaWise10(pal);
gent = Genomic_from_Sequence(gen);
assert(gent);
gr = new_GenomicRegion(gent);
assert(gr);
add_Genes_to_GenomicRegion_GeneWise(gr,active_gen->offset,active_gen->end,alb,cdna->name,0,NULL);
mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp);
show_pretty_GenomicRegion(gr,0,ofp);
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(ofp,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,ofp);
}
}
}
