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; }