static void jaspextract_getjaspdirs(AjPList jdirlist) { const AjPStr datadir = NULL; AjPStr line = NULL; ajuint n = 0; ajuint i = 0; datadir = ajDatafileValuePath(); if(!datadir) ajFatal("jaspextract: Cannot determine the EMBOSS data directory"); n = ajFilelistAddPathDir(jdirlist, datadir); for(i=0; i < n; ++i) { ajListPop(jdirlist,(void **)&line); if(ajStrFindC(line,"JASPAR_") != -1) ajListPushAppend(jdirlist,(void *)line); else ajStrDel(&line); } return; }
static void remap_read_file_of_enzyme_names(AjPStr *enzymes) { AjPFile file = NULL; AjPStr line; const char *p = NULL; if(ajStrFindC(*enzymes, "@") == 0) { ajStrTrimC(enzymes, "@"); /* remove the @ */ file = ajFileNewInNameS(*enzymes); if(file == NULL) ajFatal("Cannot open the file of enzyme names: '%S'", enzymes); /* blank off the enzyme file name and replace with the enzyme names */ ajStrSetClear(enzymes); line = ajStrNew(); while(ajReadlineTrim(file, &line)) { p = ajStrGetPtr(line); if(!*p || *p == '#' || *p == '!') continue; ajStrAppendS(enzymes, line); ajStrAppendC(enzymes, ","); } ajStrDel(&line); ajFileClose(&file); } return; }
static void makeprotseq_parse_pepstats(AjPList* list,AjPFile data) { AjPStr line = ajStrNew(); AjPStr ch; AjPStr chcopy = NULL; const AjPStr tok; double value = 0.0; ajint count = 0; ajint i = 0; ajDebug("Parsing pepstats file.\n"); /* skip the lines before residues */ while(ajReadline(data,&line)) { if(ajStrFindC(line,"Residue") == 0) break; } /* parse residue part */ while(ajReadlineTrim(data,&line)) { if(ajStrParseCountC(line," \t") == 0) break; ch = ajStrNew(); tok = ajStrParseWhite(line); ajStrAppendS(&ch,tok); ajStrFmtLower(&ch); for(count = 1; count < 5; count++) tok = ajStrParseWhite(NULL); ajStrToDouble(tok,&value); count = (ajint) (value * 100) + ((value - (int) value ) >= 0.5 ? 1 : 0); for(i=0; i<count; i++) { chcopy = ajStrNewS(ch); ajListstrPush(*list,chcopy); } ajStrDel(&ch); } ajStrDel(&line); return; }
static void notseq_readfile(const AjPStr exclude, AjPStr *pattern) { AjPFile file = NULL; AjPStr line; AjPStr filename = NULL; const char *p = NULL; if(ajStrFindC(exclude, "@") != 0) { ajStrAssignS(pattern, exclude); } else { ajStrAssignS(&filename, exclude); ajStrTrimC(&filename, "@"); /* remove the @ */ file = ajFileNewInNameS(filename); if(file == NULL) ajFatal("Cannot open the file of sequence names: '%S'", filename); /* blank off the file name and replace with the sequence names */ ajStrSetClear(pattern); line = ajStrNew(); while(ajReadlineTrim(file, &line)) { p = ajStrGetPtr(line); if(!*p || *p == '#' || *p == '!') continue; ajStrAppendS(pattern, line); ajStrAppendC(pattern, ","); } ajStrDel(&line); ajStrDel(&filename); ajFileClose(&file); } return; }
static void eprimer3_write_primer(AjPFile outfile, const char *tag, const AjPStr pos, const AjPStr tm, const AjPStr gc, const AjPStr seq, AjBool rev, ajint begin) { ajint startint; ajint lenint; float tmfloat; float gcfloat; AjPStr start = NULL; AjPStr lenstr = NULL; ajlong comma; if(ajStrGetLen(pos)) { ajStrToFloat(tm, &tmfloat); ajStrToFloat(gc, &gcfloat); comma = ajStrFindC(pos, ","); ajStrAssignS(&start, pos); ajStrCutRange(&start, comma, ajStrGetLen(start)-1); ajStrToInt(start, &startint); startint += begin; ajStrAssignS(&lenstr, pos); ajStrCutRange(&lenstr, 0, comma); ajStrToInt(lenstr, &lenint); if(rev) startint = startint - lenint + 1; ajFmtPrintF(outfile, " %s %6d %4d %2.2f %2.2f %S\n\n", tag, startint, lenint, tmfloat, gcfloat, seq); } ajStrDel(&start); ajStrDel(&lenstr); return; }
AjPPatlistRegex ajPatlistRegexRead (const AjPStr patspec, const AjPStr patname, const AjPStr fmt, ajuint type, AjBool upper, AjBool lower) { AjPPatlistRegex patlist = NULL; AjPStr line = NULL; AjPStr pat = NULL; AjPStr name = NULL; AjPFilebuff infile = NULL; AjPStr patstr = NULL; ajuint ifmt; ajuint npat = 0; AjPStr namestr = NULL; ajStrAssignS(&namestr, patname); ajStrAssignEmptyC(&namestr, "regex"); ajStrAssignS(&patstr, patspec); patlist = ajPatlistRegexNewType(type); ifmt = patternRegexFormat(fmt); if(ajStrGetCharFirst(patspec) == '@') { ajStrCutStart(&patstr, 1); infile = ajFilebuffNewNameS(patstr); if(!infile) { ajErr("Unable to open regular expression file '%S'", patstr); return NULL; } line = ajStrNew(); pat = ajStrNew(); name = ajStrNew(); if(!ifmt) { ajBuffreadLineTrim(infile,&line); if(ajStrPrefixC(line, ">")) ifmt = 2; else ifmt = 1; ajFilebuffReset(infile); } switch(ifmt) { case 1: while (ajBuffreadLineTrim(infile,&line)) { npat++; ajStrAppendS (&pat,line); if(lower) ajStrFmtLower(&pat); if(upper) ajStrFmtUpper(&pat); ajFmtPrintS(&name, "%S%u", namestr, npat); ajPatternRegexNewList(patlist,name,pat); ajStrSetClear(&pat); } break; default: while (ajBuffreadLineTrim(infile,&line)) { if (ajStrFindC(line,">")>-1) { npat++; if (ajStrGetLen(name)) { if(lower) ajStrFmtLower(&pat); if(upper) ajStrFmtUpper(&pat); ajPatternRegexNewList(patlist,name,pat); ajStrSetClear(&name); ajStrSetClear(&pat); } ajStrCutStart(&line,1); ajStrAssignS (&name,line); if(!ajStrGetLen(name)) ajFmtPrintS(&name, "%S%u", namestr, npat); } else ajStrAppendS (&pat,line); } ajStrAssignEmptyS(&name, patname); ajPatternRegexNewList(patlist,name,pat); ajStrSetClear(&pat); break; } ajFilebuffDel(&infile); } else { ajStrAssignS(&pat, patspec); if(lower) ajStrFmtLower(&pat); if(upper) ajStrFmtUpper(&pat); ajStrAssignS(&name, namestr); ajPatternRegexNewList(patlist,name,pat); } ajStrDel(&name); ajStrDel(&namestr); ajStrDel(&patstr); ajStrDel(&line); ajStrDel(&pat); return patlist; }
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; }