int main(int argc, char **argv) { /* Global details */ AjBool explain_flag; AjBool file_flag; AjPStr* task; AjBool do_primer; AjBool do_hybrid; ajint num_return; ajint first_base_index; /* "Sequence" Input Tags */ AjPSeqall sequence; AjPRange included_region; AjPRange target; AjPRange excluded_region; AjPStr left_input; AjPStr right_input; /* Primer details */ AjBool pick_anyway; AjPFile mispriming_library; float max_mispriming; float pair_max_mispriming; ajint gc_clamp; ajint opt_size; ajint min_size; ajint max_size; float opt_tm; float min_tm; float max_tm; float max_diff_tm; float opt_gc_percent; float min_gc; float max_gc; float salt_conc; float dna_conc; ajint num_ns_accepted; float self_any; float self_end; ajint max_poly_x; /* Sequence Quality. These are not (yet) implemented */ /* AjPFile sequence_quality; ajint min_quality; ajint min_end_quality; ajint quality_range_min; ajint quality_range_max; */ /* Product details */ ajint product_opt_size; AjPRange product_size_range; float product_opt_tm; float product_min_tm; float product_max_tm; /* Objective Function Penalty Weights for Primers */ float max_end_stability; /* these are not (yet) implemented */ /* float inside_penalty; float outside_penalty; */ /* Primer penalties */ /* these are not (yet) implemented */ /* Internal Oligo "Sequence" Input Tags */ AjPRange internal_oligo_excluded_region; /* Internal Oligo "Global" Input Tags */ AjPStr internal_oligo_input; ajint internal_oligo_opt_size; ajint internal_oligo_min_size; ajint internal_oligo_max_size; float internal_oligo_opt_tm; float internal_oligo_min_tm; float internal_oligo_max_tm; float internal_oligo_opt_gc_percent; float internal_oligo_min_gc; float internal_oligo_max_gc; float internal_oligo_salt_conc; float internal_oligo_dna_conc; float internal_oligo_self_any; float internal_oligo_self_end; ajint internal_oligo_max_poly_x; AjPFile internal_oligo_mishyb_library; float internal_oligo_max_mishyb; /* ajint internal_oligo_min_quality; */ /* Internal Oligo penalties */ /* these are not (yet) implemented */ /* EMBOSS-wrapper-specific stuff */ AjPFile outfile; /* other variables */ AjPStr result = NULL; AjPStr strand = NULL; AjPStr substr = NULL; AjPSeq seq = NULL; ajint begin = 0; ajint end; FILE* stream; AjPStr taskstr = NULL; const AjPStr program = NULL; /* pipe variables */ int *pipeto; /* pipe to feed the exec'ed program input */ int *pipefrom; /* pipe to get the exec'ed program output */ embInit("eprimer3", argc, argv); /* Global details */ explain_flag = ajAcdGetBoolean("explainflag"); file_flag = ajAcdGetBoolean("fileflag"); task = ajAcdGetList("task"); do_primer = ajAcdGetToggle("primer"); do_hybrid = ajAcdGetToggle("hybridprobe"); num_return = ajAcdGetInt("numreturn"); first_base_index = ajAcdGetInt("firstbaseindex"); /* "Sequence" Input Tags */ sequence = ajAcdGetSeqall("sequence"); included_region = ajAcdGetRange("includedregion"); target = ajAcdGetRange("targetregion"); excluded_region = ajAcdGetRange("excludedregion"); left_input = ajAcdGetString("forwardinput"); right_input = ajAcdGetString("reverseinput"); /* Primer details */ pick_anyway = ajAcdGetBoolean("pickanyway"); mispriming_library = ajAcdGetInfile("mispriminglibraryfile"); max_mispriming = ajAcdGetFloat("maxmispriming"); pair_max_mispriming = ajAcdGetFloat("pairmaxmispriming"); gc_clamp = ajAcdGetInt("gcclamp"); opt_size = ajAcdGetInt("osize"); min_size = ajAcdGetInt("minsize"); max_size = ajAcdGetInt("maxsize"); opt_tm = ajAcdGetFloat("otm"); min_tm = ajAcdGetFloat("mintm"); max_tm = ajAcdGetFloat("maxtm"); max_diff_tm = ajAcdGetFloat("maxdifftm"); opt_gc_percent = ajAcdGetFloat("ogcpercent"); min_gc = ajAcdGetFloat("mingc"); max_gc = ajAcdGetFloat("maxgc"); salt_conc = ajAcdGetFloat("saltconc"); dna_conc = ajAcdGetFloat("dnaconc"); num_ns_accepted = ajAcdGetInt("numnsaccepted"); self_any = ajAcdGetFloat("selfany"); self_end = ajAcdGetFloat("selfend"); max_poly_x = ajAcdGetInt("maxpolyx"); AJCNEW0(pipeto,2); AJCNEW0(pipefrom,2); /* Sequence Quality */ /* these are not (yet) implemented */ /* sequence_quality = ajAcdGetInfile("sequencequality"); min_quality = ajAcdGetInt("minquality"); min_end_quality = ajAcdGetInt("minendquality"); quality_range_min = ajAcdGetInt("qualityrangemin"); quality_range_max = ajAcdGetInt("qualityrangemax"); */ /* Product details */ product_opt_size = ajAcdGetInt("psizeopt"); product_size_range = ajAcdGetRange("prange"); product_opt_tm = ajAcdGetFloat("ptmopt"); product_min_tm = ajAcdGetFloat("ptmmin"); product_max_tm = ajAcdGetFloat("ptmmax"); /* Objective Function Penalty Weights for Primers */ max_end_stability = ajAcdGetFloat("maxendstability"); /* these are not (yet) implemented */ /* inside_penalty = ajAcdGetFloat("insidepenalty"); outside_penalty = ajAcdGetFloat("outsidepenalty"); */ /* Primer penalties */ /* these are not (yet) implemented */ /* Internal Oligo "Sequence" Input Tags */ internal_oligo_excluded_region = ajAcdGetRange("oexcludedregion"); internal_oligo_input = ajAcdGetString("oligoinput"); /* Internal Oligo "Global" Input Tags */ internal_oligo_opt_size = ajAcdGetInt("osizeopt"); internal_oligo_min_size = ajAcdGetInt("ominsize"); internal_oligo_max_size = ajAcdGetInt("omaxsize"); internal_oligo_opt_tm = ajAcdGetFloat("otmopt"); internal_oligo_min_tm = ajAcdGetFloat("otmmin"); internal_oligo_max_tm = ajAcdGetFloat("otmmax"); internal_oligo_opt_gc_percent = ajAcdGetFloat("ogcopt"); internal_oligo_min_gc = ajAcdGetFloat("ogcmin"); internal_oligo_max_gc = ajAcdGetFloat("ogcmax"); internal_oligo_salt_conc = ajAcdGetFloat("osaltconc"); internal_oligo_dna_conc = ajAcdGetFloat("odnaconc"); internal_oligo_self_any = ajAcdGetFloat("oanyself"); internal_oligo_self_end = ajAcdGetFloat("oendself"); internal_oligo_max_poly_x = ajAcdGetInt("opolyxmax"); internal_oligo_mishyb_library = ajAcdGetInfile("mishyblibraryfile"); internal_oligo_max_mishyb = ajAcdGetFloat("omishybmax"); /* internal_oligo_min_quality = ajAcdGetInt("oligominquality"); */ /* Internal Oligo penalties */ /* these are not (yet) implemented */ /* EMBOSS-wrapper-specific stuff */ outfile = ajAcdGetOutfile("outfile"); ajStrRemoveWhite(&left_input); ajStrRemoveWhite(&right_input); /* ** OK - we will now try to do a separate fork-exec for each sequence. */ result = ajStrNew(); while(ajSeqallNext(sequence, &seq)) { program = ajAcdGetpathC("primer3_core"); if(!ajSysExecRedirectC(ajStrGetPtr(program),&pipeto,&pipefrom)) ajFatal("eprimer3: Could not exec primer3_core"); stream = eprimer3_start_write(pipeto[1]); /* send primer3 Primer "Global" parameters */ eprimer3_send_bool(stream, "PRIMER_EXPLAIN_FLAG", explain_flag); eprimer3_send_bool(stream, "PRIMER_FILE_FLAG", file_flag); if(do_hybrid) { if(!ajStrCmpC(task[0], "1")) ajStrAssignC(&taskstr, "pick_pcr_primers_and_hyb_probe"); else if(!ajStrCmpC(task[0], "2")) ajStrAssignC(&taskstr, "pick_left_only"); else if(!ajStrCmpC(task[0], "3")) ajStrAssignC(&taskstr, "pick_right_only"); else if(!ajStrCmpC(task[0], "4")) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); if (!do_primer) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); } else { if(!ajStrCmpC(task[0], "1")) ajStrAssignC(&taskstr, "pick_pcr_primers"); else if(!ajStrCmpC(task[0], "2")) ajStrAssignC(&taskstr, "pick_left_only"); else if(!ajStrCmpC(task[0], "3")) ajStrAssignC(&taskstr, "pick_right_only"); else if(!ajStrCmpC(task[0], "4")) ajStrAssignC(&taskstr, "pick_hyb_probe_only"); } eprimer3_send_string(stream, "PRIMER_TASK", taskstr); eprimer3_send_int(stream, "PRIMER_NUM_RETURN", num_return); eprimer3_send_int(stream, "PRIMER_FIRST_BASE_INDEX", first_base_index); eprimer3_send_bool(stream, "PRIMER_PICK_ANYWAY", pick_anyway); /* mispriming library may not have been specified */ if(mispriming_library) eprimer3_send_stringC(stream, "PRIMER_MISPRIMING_LIBRARY", ajFileGetPrintnameC(mispriming_library)); eprimer3_send_float(stream, "PRIMER_MAX_MISPRIMING", max_mispriming); eprimer3_send_float(stream, "PRIMER_PAIR_MAX_MISPRIMING", pair_max_mispriming); eprimer3_send_int(stream, "PRIMER_GC_CLAMP", gc_clamp); eprimer3_send_int(stream, "PRIMER_OPT_SIZE", opt_size); eprimer3_send_int(stream, "PRIMER_MIN_SIZE", min_size); eprimer3_send_int(stream, "PRIMER_MAX_SIZE", max_size); eprimer3_send_float(stream, "PRIMER_OPT_TM", opt_tm); eprimer3_send_float(stream, "PRIMER_MIN_TM", min_tm); eprimer3_send_float(stream, "PRIMER_MAX_TM", max_tm); eprimer3_send_float(stream, "PRIMER_MAX_DIFF_TM", max_diff_tm); eprimer3_send_float(stream, "PRIMER_OPT_GC_PERCENT", opt_gc_percent); eprimer3_send_float(stream, "PRIMER_MIN_GC", min_gc); eprimer3_send_float(stream, "PRIMER_MAX_GC", max_gc); eprimer3_send_float(stream, "PRIMER_SALT_CONC", salt_conc); eprimer3_send_float(stream, "PRIMER_DNA_CONC", dna_conc); eprimer3_send_int(stream, "PRIMER_NUM_NS_ACCEPTED", num_ns_accepted); eprimer3_send_float(stream, "PRIMER_SELF_ANY", self_any); eprimer3_send_float(stream, "PRIMER_SELF_END", self_end); eprimer3_send_int(stream, "PRIMER_MAX_POLY_X", max_poly_x); eprimer3_send_int(stream, "PRIMER_PRODUCT_OPT_SIZE", product_opt_size); eprimer3_send_range2(stream, "PRIMER_PRODUCT_SIZE_RANGE", product_size_range); eprimer3_send_float(stream, "PRIMER_PRODUCT_OPT_TM", product_opt_tm); eprimer3_send_float(stream, "PRIMER_PRODUCT_MIN_TM", product_min_tm); eprimer3_send_float(stream, "PRIMER_PRODUCT_MAX_TM", product_max_tm); eprimer3_send_float(stream, "PRIMER_MAX_END_STABILITY", max_end_stability); /* send primer3 Internal Oligo "Global" parameters */ eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_OPT_SIZE", internal_oligo_opt_size); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MIN_SIZE", internal_oligo_min_size); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MAX_SIZE", internal_oligo_max_size); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_OPT_TM", internal_oligo_opt_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MIN_TM", internal_oligo_min_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_TM", internal_oligo_max_tm); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT", internal_oligo_opt_gc_percent); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MIN_GC", internal_oligo_min_gc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_GC", internal_oligo_max_gc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SALT_CONC", internal_oligo_salt_conc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_DNA_CONC", internal_oligo_dna_conc); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SELF_ANY", internal_oligo_self_any); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_SELF_END", internal_oligo_self_end); eprimer3_send_int(stream, "PRIMER_INTERNAL_OLIGO_MAX_POLY_X", internal_oligo_max_poly_x); /* ** internal oligo mishybridising library may not have been ** specified */ if(internal_oligo_mishyb_library) eprimer3_send_stringC(stream, "PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY", ajFileGetPrintnameC(internal_oligo_mishyb_library)); eprimer3_send_float(stream, "PRIMER_INTERNAL_OLIGO_MAX_MISHYB", internal_oligo_max_mishyb); /* ** Start sequence-specific stuff */ begin = ajSeqallGetseqBegin(sequence) - 1; end = ajSeqallGetseqEnd(sequence) - 1; strand = ajSeqGetSeqCopyS(seq); ajStrFmtUpper(&strand); ajStrAssignSubC(&substr,ajStrGetPtr(strand), begin, end); /* send flags to turn on using optimal product size */ eprimer3_send_float(stream, "PRIMER_PAIR_WT_PRODUCT_SIZE_GT", (float)0.05); eprimer3_send_float(stream, "PRIMER_PAIR_WT_PRODUCT_SIZE_LT", (float)0.05); /* send primer3 Primer "Sequence" parameters */ eprimer3_send_string(stream, "SEQUENCE", substr); /* if no ID name, use the USA */ if(ajStrMatchC(ajSeqGetNameS(seq),"")) eprimer3_send_string(stream, "PRIMER_SEQUENCE_ID", ajSeqGetUsaS(seq)); else eprimer3_send_string(stream, "PRIMER_SEQUENCE_ID", ajSeqGetNameS(seq)); eprimer3_send_range(stream, "INCLUDED_REGION", included_region, begin); eprimer3_send_range(stream, "TARGET", target, begin); eprimer3_send_range(stream, "EXCLUDED_REGION", excluded_region, begin); eprimer3_send_string(stream, "PRIMER_LEFT_INPUT", left_input); eprimer3_send_string(stream, "PRIMER_RIGHT_INPUT", right_input); /* send primer3 Internal Oligo "Sequence" parameters */ eprimer3_send_range(stream, "PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION", internal_oligo_excluded_region, begin); eprimer3_send_string(stream, "PRIMER_INTERNAL_OLIGO_INPUT", internal_oligo_input); /* end the primer3 input sequence record with a '=' */ eprimer3_send_end(stream); /* and close the ouput pipe stream */ eprimer3_end_write(stream); /* read the primer3 output */ eprimer3_read(pipefrom[0], &result); eprimer3_report(outfile, result, num_return, begin); ajStrSetClear(&result); #ifndef WIN32 close(pipeto[1]); close(pipefrom[0]); #endif } /* end of sequence loop */ ajStrDel(&result); ajSeqDel(&seq); ajStrDel(&strand); ajStrDel(&substr); ajFileClose(&outfile); ajStrDel(&taskstr); ajStrDelarray(&task); ajSeqallDel(&sequence); ajSeqDel(&seq); ajRangeDel(&included_region); ajRangeDel(&target); ajRangeDel(&excluded_region); ajRangeDel(&product_size_range); ajRangeDel(&internal_oligo_excluded_region); ajStrDel(&left_input); ajStrDel(&right_input); ajStrDel(&internal_oligo_input); AJFREE(pipeto); AJFREE(pipefrom); ajFileClose(&mispriming_library); embExit(); return 0; }
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; }