static void extractfeat_WriteOut(AjPSeqout seqout, AjPStr *featstr, AjBool compall, AjBool sense, ajint firstpos, ajint lastpos, ajint before, ajint after, const AjPSeq seq, AjBool remote, const AjPStr type, AjBool featinname, const AjPStr describestr) { AjPSeq newseq = NULL; AjPStr name = NULL; /* new name of the sequence */ AjPStr value = NULL; /* string value of start or end position */ AjPStr desc = NULL; /* sequence description */ AjBool forward = sense; if(compall) forward = ajFalse; ajDebug("WriteOut %S_%d_%d [%S] %d all:%B fwd:%B remote:%B\n", ajSeqGetNameS(seq), firstpos+1, lastpos+1, type, ajStrGetLen(*featstr), compall, sense, remote); /* see if there is a sequence to be written out */ if(!ajStrGetLen(*featstr)) { ajWarn("feature %S_%d_%d [%S] " "not written out because it has zero length\n", ajSeqGetNameS(seq), firstpos+1, lastpos+1, type); ajDebug("feature not written out because it has length=0 " "(probably first time round)\n"); return; } /* see if must abort because there were Remote IDs in the features */ if(remote) { ajWarn("feature not written out because it has Remote IDs\n"); ajDebug("feature not written out because it has Remote IDs\n"); return; } ajDebug("feature = %d bases\n", ajStrGetLen(*featstr)); /* featstr may be edited, so it is a AjPStr* */ extractfeat_BeforeAfter (seq, featstr, firstpos, lastpos, before, after, forward); ajDebug("feature+before/after = %d bases\n", ajStrGetLen(*featstr)); /* set the extracted sequence */ newseq = ajSeqNew(); ajSeqAssignSeqS(newseq, *featstr); /* create a nice name for the new sequence */ name = ajStrNew(); ajStrAppendS(&name, ajSeqGetNameS(seq)); ajStrAppendC(&name, "_"); value = ajStrNew(); ajStrFromInt(&value, firstpos+1); ajStrAppendS(&name, value); ajStrAppendC(&name, "_"); ajStrFromInt(&value, lastpos+1); ajStrAppendS(&name, value); /* add the type of feature to the name, if required */ if(featinname) { ajStrAppendC(&name, "_"); ajStrAppendS(&name, type); } ajSeqAssignNameS(newseq, name); /* set the sequence description with the 'type' added */ desc = ajStrNew(); ajStrAppendC(&desc, "["); ajStrAppendS(&desc, type); ajStrAppendC(&desc, "] "); if(ajStrGetLen(describestr)) ajStrAppendS(&desc, describestr); ajStrAppendS(&desc, ajSeqGetDescS(seq)); ajSeqAssignDescS(newseq, desc); /* set the type */ if(ajSeqIsNuc(seq)) ajSeqSetNuc(newseq); else ajSeqSetProt(newseq); /* write the new sequence */ ajSeqoutWriteSeq(seqout, newseq); ajSeqDel(&newseq); ajStrDel(&name); ajStrDel(&value); ajStrDel(&desc); return; }
int main(int argc, char **argv) { AjPSeqout outseq = NULL; AjPList list = NULL; AjPSeq seq = NULL; AjPStr insert = NULL; AjPStr seqstr = NULL; AjPStr* seqr = NULL; AjPFile data = NULL; ajint start = 0; ajint length = 0; ajint amount = 0; ajint scmax = 0; ajint extra = 0; embInit("makeprotseq", argc, argv); data = ajAcdGetInfile("pepstatsfile"); insert = ajAcdGetString("insert"); start = ajAcdGetInt("start"); length = ajAcdGetInt("length"); amount = ajAcdGetInt("amount"); outseq = ajAcdGetSeqoutall("outseq"); list = ajListstrNew(); /* this is checked by acd if(amount <=0 || length <= 0) ajFatal("Amount or length is 0 or less. " "Unable to create any sequences"); */ /* if insert, make sure sequence is large enough */ if(ajStrGetLen(insert)) { length -= ajStrGetLen(insert); /* start= start <= 1 ? 0 : --start; */ /* checked in acd */ start--; if(length <= 0) ajFatal("Sequence smaller than inserted part. " "Unable to create sequences."); } /* make the list of AjPStr to be used in sequence creation */ if(data) { ajDebug("Distribution datafile '%s' given checking type\n", ajFileGetPrintnameC(data)); seqstr = ajStrNew(); ajReadlineTrim(data,&seqstr); if(ajStrFindC(seqstr,"PEPSTATS") == 0) { makeprotseq_parse_pepstats(&list,data); } else { ajWarn("Not pepstats file. Making completely random sequences."); makeprotseq_default_chars(&list); } ajStrDel(&seqstr); ajFileClose(&data); } else makeprotseq_default_chars(&list); /* if insert, make sure type is correct */ /* typecheking code is not working, uncomment and test after it is if(ajStrGetLen(insert)) { seqstr = ajStrNew(); if(prot) ajStrAssignC(&seqstr,"pureprotein"); if(!ajSeqTypeCheckS(&insert,seqstr)) ajFatal("Insert not the same sequence type as sequence itself."); ajStrDel(&seqstr); } */ /* array allows fast creation of a sequences */ scmax = (ajuint) ajListstrToarray(list,&seqr); if(!scmax) ajFatal("No strings in list. No characters to make the sequence."); ajDebug("Distribution array done.\nscmax '%d', extra '%d', first '%S'\n", scmax,extra,seqr[0]); ajRandomSeed(); while(amount-- > 0) { seqstr = makeprotseq_random_sequence(seqr,scmax,length); if(ajStrGetLen(insert)) ajStrInsertS(&seqstr,start,insert); ajStrFmtLower(&seqstr); seq = ajSeqNew(); ajSeqAssignSeqS(seq, seqstr); ajSeqSetProt(seq); ajSeqoutWriteSeq(outseq, seq); ajSeqDel(&seq); ajStrDel(&seqstr); } ajSeqoutClose(outseq); ajSeqoutDel(&outseq); ajListstrFreeData(&list); ajStrDel(&insert); AJFREE(seqr); embExit(); return 0; }