AjBool gFormatGenbank(AjPSeq seq, AjPStr *inseq){
AjPSeqout seqout = NULL;
AjPFeattabOut featout = NULL;
AjPFeattable feat = NULL;
AjPStr seqline = NULL;
AjPStr featline = NULL;
AjPFile seqfile = NULL;
AjPFile featfile = NULL;
AjPStr filename = NULL;
gAssignUniqueName(&filename);
feat = ajSeqGetFeatCopy(seq);
if(!feat)
return ajFalse;
seqout = ajSeqoutNew();
if(!ajSeqoutOpenFilename(seqout,filename))
embExitBad();
ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));
ajSeqoutWriteSeq(seqout,seq);
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
seqfile = ajFileNewInNameS(filename);
ajSysFileUnlinkS(filename);
featout = ajFeattabOutNew();
if(!ajFeattabOutOpen(featout,filename))
return ajFalse;
ajFeattableWriteGenbank(featout,feat);
ajFeattableDel(&feat);
//ajFeattabOutDel(&featout);
ajFileClose(&(featout->Handle));
featfile = ajFileNewInNameS(filename);
ajSysFileUnlinkS(filename);
while(ajReadline(seqfile,&seqline)){
if(ajStrMatchC(seqline,"ORIGIN\n")){
while(ajReadline(featfile,&featline)){
ajStrAppendS(inseq, featline);
}
}
ajStrAppendS(inseq, seqline);
}
ajStrDel(&seqline);
ajStrDel(&featline);
ajStrDel(&filename);
ajFileClose(&seqfile);
ajFileClose(&featfile);
return ajTrue;
}
static void splitter_AddSubSeqFeat(AjPFeattable ftable, ajuint start,
ajuint end, const AjPSeq oldseq)
{
AjPFeattable old_feattable = NULL;
AjIList iter = NULL;
old_feattable = ajSeqGetFeatCopy(oldseq);
if(!old_feattable)
return;
iter = ajListIterNewread(old_feattable->Features);
while(!ajListIterDone(iter))
{
AjPFeature gf = ajListIterGet(iter);
AjPFeature copy = NULL;
if (((ajFeatGetEnd(gf) < start + 1) &&
(gf->End2 == 0 || gf->End2 < start + 1)) ||
((ajFeatGetStart(gf) > end + 1) &&
(gf->Start2 == 0 || gf->Start2 > end + 1)))
{
continue;
}
copy = ajFeatNewFeat(gf);
copy->Start = copy->Start - start;
copy->End = copy->End - start;
if (copy->Start2 > 0)
copy->Start2 = copy->Start2 - start;
if (copy->End2 > 0)
copy->End2 = copy->End2 - start;
ajFeatTrimOffRange (copy, 0, 1, end - start + 1, AJTRUE, AJTRUE);
ajFeattableAdd(ftable, copy);
}
ajFeattableDel(&old_feattable);
ajListIterDel(&iter);
return;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeqout seqout;
AjPSeq seq;
ajint before;
ajint after;
AjBool join;
AjPFeattable featab;
AjBool featinname;
AjPStr describe;
/* feature filter criteria */
AjPStr source = NULL;
AjPStr feattype = NULL;
ajint sense;
float minscore;
float maxscore;
AjPStr tag = NULL;
AjPStr value = NULL;
AjBool testscore = AJFALSE;
embInit("extractfeat", argc, argv);
seqall = ajAcdGetSeqall("sequence");
seqout = ajAcdGetSeqout("outseq");
before = ajAcdGetInt("before");
after = ajAcdGetInt("after");
join = ajAcdGetBoolean("join");
featinname = ajAcdGetBoolean("featinname");
describe = ajAcdGetString("describe");
/* feature filter criteria */
source = ajAcdGetString("source");
feattype = ajAcdGetString("type");
sense = ajAcdGetInt("sense");
minscore = ajAcdGetFloat("minscore");
maxscore = ajAcdGetFloat("maxscore");
tag = ajAcdGetString("tag");
value = ajAcdGetString("value");
testscore = (minscore || maxscore);
if(minscore && !maxscore)
if(minscore > maxscore)
maxscore = minscore;
if(!minscore && maxscore)
if(minscore > maxscore)
minscore = maxscore;
while(ajSeqallNext(seqall, &seq))
{
/* get the feature table of the sequence */
featab = ajSeqGetFeatCopy(seq);
/* delete features in the table that don't match our criteria */
extractfeat_FeatureFilter(featab, source, feattype, sense,
testscore, minscore, maxscore, tag, value);
/* extract the features */
extractfeat_FeatSeqExtract(seq, seqout, featab, before,
after, join, featinname, describe);
ajFeattableDel(&featab);
}
ajSeqoutClose(seqout);
ajSeqoutDel(&seqout);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&describe);
ajStrDel(&source);
ajStrDel(&feattype);
ajStrDel(&tag);
ajStrDel(&value);
embExit();
return 0;
}
