/***************************************************************************** * * testval.c * check translations * check for stop codons * Check for and fix non 3.0 asn spec things * * $Id: rtestval.c,v 1.3 2001/11/21 21:58:01 kans Exp $ * *****************************************************************************/ #include #include #include #define NUMARG 15 Args myargs[NUMARG] = { {"Filename for asn.1 input","stdin",NULL,NULL,TRUE,'i',ARG_FILE_IN,0.0,0,NULL}, {"Input is a Seq-entry","F", NULL ,NULL ,TRUE,'e',ARG_BOOLEAN,0.0,0,NULL}, {"Input is a Seq-submit","F", NULL ,NULL ,TRUE,'s',ARG_BOOLEAN,0.0,0,NULL}, {"Input asnfile in binary mode","F",NULL,NULL,TRUE,'b',ARG_BOOLEAN,0.0,0,NULL}, {"Filename for error messages","stderr",NULL,NULL,TRUE,'x',ARG_FILE_OUT,0.0,0,NULL} , {"Filename for asn.1 output",NULL,NULL,NULL,TRUE,'o',ARG_FILE_OUT,0.0,0,NULL}, {"Output asnfile in binary mode","F",NULL,NULL,TRUE,'t',ARG_BOOLEAN,0.0,0,NULL}, {"Severity of error for count in return code","4","0","4",FALSE,'r',ARG_INT,0.0,0,NULL}, {"Continue on ASN.1 error?","F",NULL,NULL,TRUE,'c',ARG_BOOLEAN,0.0,0,NULL}, {"Patch invalid sequence residues?","F",NULL,NULL,TRUE,'p',ARG_BOOLEAN,0.0,0,NULL}, {"Lowest severity of error to show","3","0","4",FALSE,'q',ARG_INT,0.0,0,NULL}, {"ASN.1 spec level to filter","0","0","3",FALSE,'l',ARG_INT,0.0,0,NULL}, {"Use SeqMgr indexing?","T",NULL,NULL,TRUE,'d',ARG_BOOLEAN,0.0,0,NULL}, {"Validate alignments?","F",NULL,NULL,TRUE,'a',ARG_BOOLEAN,0.0,0,NULL}, {"Use remote Fetch?","F",NULL,NULL,TRUE,'f',ARG_BOOLEAN,0.0,0,NULL}}; CharPtr AsnIoGets PROTO((AsnIoPtr aip)); /* from asnio.h */ void LIBCALLBACK error_ret PROTO((Int2 value, CharPtr msg)); Int2 Main(void) { AsnIoPtr aip, aipout=NULL; SeqEntryPtr sep; AsnTypePtr atp, atp2; AsnModulePtr amp; ValidStructPtr vsp; Int2 numerrors, fatal_error = 0, error_level, i, spec_version; CharPtr tmp; Boolean found; DataVal av; /* check command line arguments */ if ( ! GetArgs("testval",NUMARG, myargs)) return 1; /* load the sequence alphabets */ /* (and sequence parse trees) */ if (! SeqEntryLoad()) ErrShow(); /* Don't let the program die, no matter what */ ErrSetFatalLevel(SEV_MAX); ErrSetMessageLevel(SEV_MAX); /* don't report errors via Message()*/ ErrSetOptFlags (EO_MSG_CODES); ErrSetLogfile(myargs[4].strvalue, 0); /* report errors by printing to stderr */ ErrSetOpts (ERR_IGNORE, ERR_LOG_ON); /* get pointer to all loaded ASN.1 modules */ amp = AsnAllModPtr(); if (amp == NULL) ErrShow(); if (myargs[2].intvalue) /* Seq-submit */ { if (! SubmitAsnLoad()) ErrPostEx(SEV_FATAL,0,0, "Unable to SeqSubmitLoad."); atp = AsnFind("Seq-submit"); /* get the initial type pointers */ if (atp == NULL) ErrShow(); atp2 = AsnFind("Seq-submit.data.entrys.E"); if (atp2 == NULL) ErrShow(); } else if (! myargs[1].intvalue) /* not Seq-entry */ { atp = AsnFind("Bioseq-set"); /* get the initial type pointers */ if (atp == NULL) ErrShow(); atp2 = AsnFind("Bioseq-set.seq-set.E"); if (atp2 == NULL) ErrShow(); } error_level = (Int2)myargs[7].intvalue; spec_version = (Int2)myargs[11].intvalue; /* open the ASN.1 input file in the right mode */ if ((aip = AsnIoOpen (myargs[0].strvalue, myargs[3].intvalue?"rb":"r")) == NULL) { ErrShow(); return 1; } aip->spec_version = spec_version; /* open the ASN.1 output file in the right mode */ if (myargs[5].strvalue != NULL) { if ((aipout = AsnIoOpen (myargs[5].strvalue, myargs[6].intvalue?"wb":"w")) == NULL) { ErrShow(); return 1; } } if ((! myargs[3].intvalue) && (myargs[2].intvalue)) { /* scan past any headers */ found = FALSE; while (! found) { tmp = AsnIoGets(aip); *(aip->buf + aip->offset -1) = '\0'; if (strstr(tmp, "Seq-submit") != NULL) { found = TRUE; } *(aip->buf + aip->offset - 1) = '\n'; } } if (myargs[14].intvalue) /* enable remote fetch */ { if ( !ID1BioseqFetchEnable("rtestval", TRUE) ) { ErrPostEx(SEV_FATAL,0,0, "Can't initialize ID1"); return 1; } } vsp = ValidStructNew(); vsp->cutoff = (Int2)(myargs[10].intvalue); vsp->useSeqMgrIndexes = (Boolean)(myargs[12].intvalue); /* indexed validate */ vsp->validateAlignments = (Boolean)(myargs[13].intvalue); vsp->farIDsInAlignments = (Boolean)(myargs[13].intvalue); if (myargs[8].intvalue) /* continue on ASN.1 error */ AsnIoSetErrorMsg(aip, error_ret); if (myargs[9].intvalue) /* patch bad sequence residues */ vsp->patch_seq = TRUE; numerrors = 0; if ( myargs[1].intvalue) /* read one Seq-entry */ { sep = SeqEntryAsnRead(aip, NULL); if (sep == NULL) { fatal_error++; numerrors++; ErrPostEx(SEV_ERROR,0,0, "Couldn't load [%s]\n", myargs[0].strvalue); } else { if (aip->io_failure) { vsp->non_ascii_chars = TRUE; aip->io_failure = FALSE; } ValidateSeqEntry(sep, vsp); for (i = 0; i <= 4 ; i++) { numerrors += vsp->errors[i]; if (i >= error_level) fatal_error += vsp->errors[i]; } if (aipout != NULL) SeqEntryAsnWrite(sep, aipout, NULL); SeqEntryFree(sep); } } else /* read Seq-entry's from a Bioseq-set */ { while ((atp = AsnReadId(aip, amp, atp)) != NULL) { if (atp == atp2) /* top level Seq-entry */ { sep = SeqEntryAsnRead(aip, atp); if (sep == NULL) { numerrors++; fatal_error++; } if (aip->io_failure) { vsp->non_ascii_chars = TRUE; aip->io_failure = FALSE; } ValidateSeqEntry(sep, vsp); if (aipout != NULL) SeqEntryAsnWrite(sep, aipout, atp); SeqEntryFree(sep); for (i = 0; i <=4; i++) { numerrors += vsp->errors[i]; if (i >= error_level) fatal_error += vsp->errors[i]; } ValidStructClear(vsp); } else { AsnReadVal(aip, atp, &av); if (aipout != NULL) AsnWrite(aipout, atp, &av); AsnKillValue(atp, &av); } } } AsnIoClose(aip); AsnIoClose(aipout); ValidStructFree(vsp); if (myargs[5].strvalue == NULL) /* no output file */ { if (! numerrors) { printf("All entries are OK!\n"); } else printf("%d messges reported\n", (int)numerrors); } return( fatal_error ); } void LIBCALLBACK error_ret (Int2 level, CharPtr msg) { fprintf(stderr, "%s\n\n", msg); return; }