static void tfscan_print_hits(AjPList *l,
ajint hits, AjPReport outf,
const AjPTable t,
const AjPSeq seq, ajuint minlength,
const AjPTable btable)
{
ajint i;
EmbPMatMatch m;
const AjPStr acc = NULL;
const AjPStr bf = NULL;
AjPFeattable ftable = NULL;
AjPFeature gf = NULL;
AjPStr type = ajStrNewC("SO:0000235");
AjPStr tmpstr = NULL;
ftable = ajFeattableNewSeq(seq);
/*ajFmtPrintF(outf,"TFSCAN of %s from %d to %d\n\n",ajStrGetPtr(name),
begin,end);*/
for(i=0;i<hits;++i)
{
ajListPop(*l,(void **)&m);
acc = ajTableFetchS(t, m->seqname);
if(m->len >= minlength)
{
/*ajFmtPrintF(outf,"%-20s %-8s %-5d %-5d %s\n",
ajStrGetPtr(m->seqname),
ajStrGetPtr(acc),m->start,
m->start+m->len-1,ajStrGetPtr(s));*/
if(m->forward)
gf = ajFeatNew(ftable, ajUtilGetProgram(), type,
m->start,
m->start+m->len-1,
(float) m->score,
'+',0);
else
gf = ajFeatNew(ftable, ajUtilGetProgram(), type,
m->start,
m->start+m->len-1,
(float) m->score,
'-',0);
ajFmtPrintS(&tmpstr, "*acc %S", acc);
ajFeatTagAddSS(gf, NULL, tmpstr);
bf = ajTableFetchS(btable, m->seqname);
ajFmtPrintS(&tmpstr, "*factor %S", bf);
ajFeatTagAddSS(gf, NULL, tmpstr);
}
embMatMatchDel(&m);
}
ajReportWrite(outf, ftable, seq);
ajFeattableDel(&ftable);
ajStrDel(&tmpstr);
ajStrDel(&type);
return;
}
int main(int argc, char **argv)
{
AjPFile inf = NULL;
AjPFile inf2 = NULL;
AjPFeattable tab = NULL;
AjPReport report = NULL;
AjPSeq sequence = NULL;
AjPStr redatanew = NULL;
AjPStr str = NULL;
AjPStr regexp = NULL;
AjPStr temp = NULL;
AjPStr text = NULL;
AjPStr docdata = NULL;
AjPStr data = NULL;
AjPStr accession = NULL;
AjPStr name = NULL;
EmbPPatMatch match = NULL;
AjPStr savereg = NULL;
AjPStr fthit = NULL;
AjBool full;
AjBool prune;
ajint i;
ajint number;
ajint start;
ajint end;
ajint length;
ajint zstart;
ajint zend;
const char *p;
ajint seqlength;
AjPStr tmpstr = NULL;
AjPStr tailstr = NULL;
AjPFeature gf;
embInit("patmatmotifs", argc, argv);
ajStrAssignC(&fthit, "SO:0001067");
savereg = ajStrNew();
str = ajStrNew();
regexp = ajStrNew();
temp = ajStrNew();
data = ajStrNew();
accession = ajStrNew();
text = ajStrNew();
name = ajStrNew();
sequence = ajAcdGetSeq("sequence");
report = ajAcdGetReport("outfile");
full = ajAcdGetBoolean("full");
prune = ajAcdGetBoolean("prune");
ajSeqFmtUpper(sequence); /* prosite regexs are all upper case */
tab = ajFeattableNewSeq(sequence);
ajStrAssignC(&tailstr, "");
seqlength = ajStrGetLen(str);
str = ajSeqGetSeqCopyS(sequence);
redatanew = ajStrNewC("PROSITE/prosite.lines");
docdata = ajStrNewC("PROSITE/");
inf = ajDatafileNewInNameS(redatanew);
if(!inf)
ajFatal("Either EMBOSS_DATA undefined or PROSEXTRACT needs running");
ajFmtPrintAppS(&tmpstr, "Full: %B\n", full);
ajFmtPrintAppS(&tmpstr, "Prune: %B\n", prune);
ajFmtPrintAppS(&tmpstr, "Data_file: %F\n", inf);
ajReportSetHeaderS(report, tmpstr);
while(ajReadlineTrim(inf, ®exp))
{
p=ajStrGetPtr(regexp);
if(*p && *p!=' ' && *p!='^')
{
p=ajSysFuncStrtok(p," ");
ajStrAssignC(&name,p);
if(prune)
if(ajStrMatchCaseC(name,"myristyl") ||
ajStrMatchCaseC(name,"asn_glycosylation") ||
ajStrMatchCaseC(name,"camp_phospho_site") ||
ajStrMatchCaseC(name,"pkc_phospho_site") ||
ajStrMatchCaseC(name,"ck2_phospho_site") ||
ajStrMatchCaseC(name,"tyr_phospho_site"))
{
for(i=0;i<4;++i)
ajReadlineTrim(inf, ®exp);
continue;
}
p=ajSysFuncStrtok(NULL," ");
ajStrAssignC(&accession,p);
}
if(ajStrPrefixC(regexp, "^"))
{
p = ajStrGetPtr(regexp);
ajStrAssignC(&temp,p+1);
ajStrAssignC(&savereg,p+1);
match = embPatMatchFind(temp, str, ajFalse, ajFalse);
number = embPatMatchGetNumber(match);
for(i=0; i<number; i++)
{
seqlength = ajStrGetLen(str);
start = 1+embPatMatchGetStart(match, i);
end = 1+embPatMatchGetEnd(match, i);
length = embPatMatchGetLen(match, i);
gf = ajFeatNew(tab, NULL, fthit, start, end,
(float) length, ' ', 0);
ajFmtPrintS(&tmpstr, "*motif %S", name);
ajFeatTagAddSS(gf, NULL, tmpstr);
if(start-5<0)
zstart = 0;
else
zstart = start-5;
if(end+5> seqlength)
zend = end;
else
zend = end+5;
ajStrAssignSubS(&temp, str, zstart, zend);
}
if(full && number)
{
ajStrAssignC(&redatanew,ajStrGetPtr(docdata));
ajStrAppendC(&redatanew,ajStrGetPtr(accession));
inf2 = ajDatafileNewInNameS(redatanew);
if(!inf2)
continue;
/*
** Insert Prosite documentation from files made by
** prosextract.c
*/
ajFmtPrintAppS(&tailstr, "Motif: %S\n", name);
ajFmtPrintAppS(&tailstr, "Count: %d\n\n", number);
while(ajReadlineTrim(inf2, &text))
ajFmtPrintAppS(&tailstr, "%S\n", text);
ajFmtPrintAppS(&tailstr, "\n***************\n\n");
ajFileClose(&inf2);
}
embPatMatchDel(&match);
}
}
ajReportSetTailS(report,tailstr);
ajReportWrite(report, tab, sequence);
ajReportDel(&report);
ajFeattableDel(&tab);
ajStrDel(&temp);
ajStrDel(®exp);
ajStrDel(&savereg);
ajStrDel(&str);
ajStrDel(&data);
ajStrDel(&docdata);
ajStrDel(&text);
ajStrDel(&redatanew);
ajStrDel(&accession);
ajSeqDel(&sequence);
ajStrDel(&tailstr);
ajStrDel(&fthit);
ajStrDel(&name);
ajStrDel(&tmpstr);
ajFeattableDel(&tab);
ajFileClose(&inf);
embExit();
return 0;
}
void embPatternRegexSearch (AjPFeattable ftable, const AjPSeq seq,
const AjPPatternRegex pat, AjBool reverse)
{
ajint pos=0;
ajint off;
ajint len;
AjPFeature sf = NULL;
AjPStr substr = NULL;
AjPStr seqstr = NULL;
AjPStr tmpstr = NULL;
AjPStr tmp = ajStrNew();
AjPRegexp patexp = ajPatternRegexGetCompiled(pat);
ajint adj;
AjBool isreversed;
AjPSeq revseq;
ajint seqlen;
seqlen = ajSeqGetLen(seq);
if(!seqlen)
return;
isreversed = ajSeqIsReversedTrue(seq);
if(isreversed)
seqlen += ajSeqGetOffset(seq);
pos = ajSeqGetBeginTrue(seq);
adj = ajSeqGetEndTrue(seq);
if(!ajStrGetLen(featMotifProt))
ajStrAssignC(&featMotifProt, "SO:0001067");
if(!ajStrGetLen(featMotifNuc))
ajStrAssignC(&featMotifNuc, "SO:0000714");
/*ajDebug("embPatternRegexSearch pos: %d adj: %d reverse: %B\n",
pos, adj, reverse, isreversed);*/
/*ajDebug("seqlen:%d len: %d offset: %d offend: %d begin: %d end: %d\n",
seqlen , ajSeqGetLen(seq), ajSeqGetOffset(seq),
ajSeqGetOffend(seq), ajSeqGetBegin(seq), ajSeqGetEnd(seq));*/
if (reverse)
{
revseq = ajSeqNewSeq(seq);
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq), pos-1, adj-1);
ajSeqstrReverse(&seqstr);
}
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq), pos-1, adj-1);
ajStrFmtUpper(&seqstr);
while(ajStrGetLen(seqstr) && ajRegExec(patexp, seqstr))
{
off = ajRegOffset(patexp);
len = ajRegLenI(patexp, 0);
if(off || len)
{
ajRegSubI(patexp, 0, &substr);
ajRegPost(patexp, &tmp);
ajStrAssignS(&seqstr, substr);
ajStrAppendS(&seqstr, tmp);
pos += off;
/*ajDebug("match pos: %d adj: %d len: %d off:%d\n",
pos, adj, len, off);*/
if (reverse)
sf = ajFeatNew(ftable, NULL, featMotifNuc,
adj - pos - len + 2,
adj - pos + 1,
0.0, '-', 0);
else
{
if(ajSeqIsProt(seq) || ajFeattableIsProt(ftable))
sf = ajFeatNewProt(ftable, NULL, featMotifProt,
pos, pos + len - 1,
0.0);
else
sf = ajFeatNew(ftable, NULL, featMotifNuc,
pos, pos + len - 1,
0.0, '.', 0);
}
if(isreversed)
ajFeatReverse(sf, seqlen);
ajFmtPrintS (&tmpstr,"*pat %S: %S",
ajPatternRegexGetName(pat),
ajPatternRegexGetPattern(pat));
ajFeatTagAdd (sf,NULL,tmpstr);
pos += 1;
ajStrCutStart(&seqstr, 1);
}
else
{
pos++;
ajStrCutStart(&seqstr, 1);
}
}
ajStrDel(&tmpstr);
ajStrDel(&tmp);
ajStrDel(&substr);
ajStrDel(&seqstr);
if(reverse)
ajSeqDel(&revseq);
return;
}
void embPatternSeqSearch (AjPFeattable ftable, const AjPSeq seq,
const AjPPatternSeq pat, AjBool reverse)
{
const void *tidy;
ajuint hits;
ajuint i;
AjPPatComp pattern;
EmbPMatMatch m = NULL;
AjPFeature sf = NULL;
AjPSeq revseq = NULL;
AjPList list = ajListNew();
AjPStr seqstr = ajStrNew();
AjPStr seqname = ajStrNew();
AjPStr tmp = ajStrNew();
ajint adj;
ajint begin;
AjBool isreversed;
ajint seqlen;
seqlen = ajSeqGetLen(seq);
if(!seqlen)
return;
isreversed = ajSeqIsReversedTrue(seq);
if(isreversed)
seqlen += ajSeqGetOffset(seq);
begin = ajSeqGetBeginTrue(seq);
adj = ajSeqGetEndTrue(seq);
if(!ajStrGetLen(featMotifProt))
ajStrAssignC(&featMotifProt, "SO:0001067");
if(!ajStrGetLen(featMotifNuc))
ajStrAssignC(&featMotifNuc, "SO:0000714");
ajStrAssignS(&seqname,ajSeqGetNameS(seq));
pattern = ajPatternSeqGetCompiled(pat);
if (reverse)
{
revseq = ajSeqNewSeq(seq);
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq),
begin-1,adj-1);
ajSeqstrReverse(&seqstr);
}
else
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq),
begin-1,adj-1);
ajStrFmtUpper(&seqstr);
/*ajDebug("seqlen:%d len: %d offset: %d offend: %d begin: %d end: %d\n"
"'%S'\n",
seqlen , ajSeqGetLen(seq), ajSeqGetOffset(seq),
ajSeqGetOffend(seq), ajSeqGetBegin(seq), ajSeqGetEnd(seq),
seqstr);*/
ajDebug("embPatternSeqSearch '%S' protein: %B reverse: %B\n",
pattern->pattern, pat->Protein, reverse);
embPatFuzzSearchII(pattern,begin,seqname,seqstr,list,
ajPatternSeqGetMismatch(pat),&hits,&tidy);
ajDebug ("embPatternSeqSearch: found %d hits\n",hits);
if(!reverse)
ajListReverse(list);
for(i=0;i<hits;++i)
{
ajListPop(list,(void **)&m);
if (reverse)
sf = ajFeatNew(ftable, NULL, featMotifNuc,
adj - m->start - m->len + begin + 1,
adj - m->start + begin,
0.0, '-', 0);
else
{
if(ajSeqIsProt(seq) || ajFeattableIsProt(ftable))
sf = ajFeatNewProt(ftable, NULL, featMotifProt,
m->start,
m->start + m->len - 1,
0.0);
else
sf = ajFeatNew(ftable, NULL, featMotifNuc,
m->start,
m->start + m->len - 1,
0.0, '.', 0);
}
if(isreversed)
ajFeatReverse(sf, seqlen);
/*
ajUser("isrev: %B reverse: %B begin: %d adj: %d "
"start: %d len: %d seqlen: %d %d..%d '%c'\n",
isreversed, reverse, begin, adj, m->start, m->len, seqlen,
sf->Start, sf->End, sf->Strand);
*/
ajFeatSetScore(sf, (float) (m->len - m->mm));
ajFmtPrintS(&tmp, "*pat %S: %S",
ajPatternSeqGetName(pat),
ajPatternSeqGetPattern(pat));
ajFeatTagAdd(sf,NULL,tmp);
if(m->mm)
{
ajFmtPrintS(&tmp, "*mismatch %d", m->mm);
ajFeatTagAdd(sf, NULL, tmp);
}
embMatMatchDel(&m);
}
ajStrDel(&seqname);
ajStrDel(&seqstr);
ajStrDel(&tmp);
ajListFree(&list);
if (reverse)
ajSeqDel(&revseq);
return;
}
static void cpgreport_cpgsearch(AjPFile outf, ajint from, ajint to,
const char *p,
const char *name, ajint begin, ajint score,
AjPFeattable feattable)
{
ajint i;
ajint c;
ajint z;
ajint sum;
ajint ssum;
ajint lsum;
ajint t;
ajint top;
ajint dcg;
ajint dgc;
ajint gc;
char strand = '+';
ajint frame = 0;
AjPFeature feature;
float score2 = 0.0;
if(!cpgreportSource)
{
ajStrAssignC(&cpgreportSource,"cpgreport");
ajStrAssignC(&cpgreportType,"misc_feature");
}
for(i=from,c=to-1,sum=ssum=t=top=0,lsum=-1,z=begin-1;i<to;++i,ssum=sum)
{
if(p[i]=='C' && p[i+1]=='G' && c-i)
sum += score+1;
--sum;
if(sum<0)
sum = 0;
if(!sum && ssum)
{
cpgreport_calcgc(lsum+1,t+2,p,&dcg,&dgc,&gc);
if(dgc)
{
score2 = (float) top;
feature = ajFeatNew(feattable, cpgreportSource,
cpgreportType,
lsum+2+z,t+2+z,
score2, strand, frame) ;
if(!feature)
ajDebug("Error feature not added to feature table");
ajFmtPrintF(outf,"%-20.20s %6d %6d %5d ",name,lsum+2+z,
t+2+z,top);
ajFmtPrintF(outf," %5d %5.1f %6.2f\n",
dcg,(float)gc*100.0/(float)(t+1-lsum),
(float)(dcg/dgc));
}
else
{
score2 = (float) top;
feature = ajFeatNew(feattable, cpgreportSource,
cpgreportType,
lsum+2+z,t+2+z,
score2, strand, frame) ;
ajFmtPrintF(outf,"%-20s %6d %6d %5d ",name,lsum+2+z,t+2+z,
top);
ajFmtPrintF(outf," %5d %5.1f -\n",
dcg,(float)gc*100.0/(float)(t+1-lsum));
}
cpgreport_cpgsearch(outf,t+2,i,p,name,begin,score,
feattable);
sum = ssum = lsum = t = top = 0;
}
if(sum>top)
{
t = i;
top = sum;
}
if(!sum)
lsum = i;
}
if(sum)
{
cpgreport_calcgc(lsum+1,t+2,p,&dcg,&dgc,&gc);
if(dgc)
{
ajFmtPrintF(outf,"%-20s %6d %6d %5d ",name,lsum+2+z,t+2+z,
top);
ajFmtPrintF(outf," %5d %5.1f %6.2f\n",
dcg,(float)gc*100.0/(float)(t+1-lsum),
((float)dcg/(float)dgc));
score2 = (float) top;
/*score2 = ajFmtPrintS(&score2,"%d.0",top);*/
feature = ajFeatNew(feattable, cpgreportSource,
cpgreportType,
lsum+2+z,t+2+z,
score2, strand, frame);
}
else
{
ajFmtPrintF(outf,"%-20s %6d %6d %5d ",name,lsum+2+z,t+2+z,top);
ajFmtPrintF(outf," %5d %5.1f -\n",dcg,
(float)gc*100.0/(float)(t+1-lsum));
score2 = (float) top;
/*score2 = ajFmtPrintS(&score2,"%d.0",top);*/
feature = ajFeatNew(feattable, cpgreportSource,
cpgreportType,
lsum+2+z,t+2+z,
score2, strand, frame);
}
cpgreport_cpgsearch(outf,t+2,to,p,name,begin,score,feattable);
}
return;
}
