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;
}
int main(int argc, char **argv)
{
AjPSeq seq = NULL;
AjPReport report = NULL;
AjPFeattable feat=NULL;
AjPStr sstr = NULL;
const AjPStr sname = NULL;
AjPStr revcomp = NULL;
ajint RStotal;
AjPStr enzymes = NULL; /* string for RE selection */
AjPList relist = NULL;
ajint begin;
ajint end;
ajint radj;
ajint start;
AjBool sshow;
AjBool tshow;
AjBool allmut;
AjPList results1 = NULL; /* for forward strand */
AjPList results2 = NULL; /* for reverse strand */
AjPList shits;
AjPList nshits;
AjPStr tailstr = NULL;
embInit("silent", argc, argv);
seq = ajAcdGetSeq("sequence");
enzymes = ajAcdGetString("enzymes");
sshow = ajAcdGetBoolean("sshow");
tshow = ajAcdGetBoolean("tshow");
allmut = ajAcdGetBoolean("allmut");
report = ajAcdGetReport ("outfile");
shits = ajListNew();
nshits = ajListNew();
/*calling function to read in RE info*/
RStotal = silent_restr_read(&relist,enzymes);
begin = ajSeqGetBegin(seq); /* returns the seq start posn, or 1
if no start has been set */
end = ajSeqGetEnd(seq); /* returns the seq end posn, or seq
length if no end has been set */
radj=begin+end+1; /* posn adjustment for complementary
strand */
ajStrAssignSubC(&sstr,ajSeqGetSeqC(seq),--begin,--end);
ajStrFmtUpper(&sstr);
sname = ajSeqGetNameS(seq);
ajStrAssignC(&revcomp,ajStrGetPtr(sstr));
ajSeqstrReverse(&revcomp);
start = begin+1;
feat = ajFeattableNewDna(ajSeqGetNameS(seq));
if(sshow)
{
silent_fmt_sequence("SEQUENCE", sstr,&tailstr,start,ajTrue);
}
results1 = silent_mismatch(sstr,relist,&tailstr,sname,RStotal,begin,radj,
ajFalse,end,tshow);
silent_split_hits(&results1,&shits,&nshits,allmut);
ajReportSetHeaderC(report,
"KEY:\n"
"EnzymeName: Enzyme name\n"
"RS-Pattern: Restriction enzyme recognition site "
"pattern\n"
"Base-Posn: Position of base to be mutated\n"
"AAs: Amino acid. Original sequence(.)After mutation\n"
"Silent: Yes for unchanged amino acid\n"
"Mutation: The base mutation to perform\n\n"
"Creating silent and non-silent mutations\n");
silent_fmt_hits(shits,feat, ajTrue, ajFalse);
if(allmut)
{
silent_fmt_hits(nshits,feat, ajFalse, ajFalse);
}
if(sshow)
{
silent_fmt_sequence("REVERSE SEQUENCE", revcomp,&tailstr,start,ajTrue);
}
results2 = silent_mismatch(revcomp,relist,&tailstr,
sname,RStotal,begin,radj,
ajTrue,end,tshow);
silent_split_hits(&results2,&shits,&nshits,allmut);
silent_fmt_hits(shits,feat, ajTrue, ajTrue);
if(allmut)
{
silent_fmt_hits(nshits,feat, ajFalse, ajTrue);
}
ajReportSetStatistics(report, 1, ajSeqGetLenTrimmed(seq));
ajReportSetTailS(report, tailstr);
(void) ajReportWrite (report,feat,seq);
ajFeattableDel(&feat);
ajStrDel(&revcomp);
ajStrDel(&enzymes);
ajListFree(&results1);
ajListFree(&results2);
ajListFree(&shits);
ajListFree(&nshits);
ajReportClose(report);
ajReportDel(&report);
ajSeqDel(&seq);
ajStrDel(&sstr);
silent_relistdel(&relist);
ajStrDel(&tailstr);
embExit();
return 0;
}
