コード例 #1
0
/* @funcstatic seqwords_keysearch  ********************************************
**
** Search swissprot with terms structure and writes a hitlist structure
**
** @param [r] inf   [AjPFile]     File pointer to swissprot database
** @param [r] terms [AjPTerms]    Terms object pointer
** @param [w] hits  [EmbPHitlist*] Hitlist object pointer
**
** @return [AjBool] True on success
** @@
******************************************************************************/
static AjBool seqwords_keysearch(AjPFile inf, 
				 AjPTerms terms,
				 EmbPHitlist *hits)
{
    AjPStr   line           =NULL;	/* Line of text. */
    AjPStr   id             =NULL;	/* Line of text. */
    AjPStr   temp           =NULL;
    ajint    s              =0;         /* Temp. start of hit value. */
    ajint    e              =0;         /* Temp. end of hit value. */
    AjPInt   start          =NULL;      /* Array of start of hit(s). */
    AjPInt   end            =NULL;      /* Array of end of hit(s). */
    ajint    nhits          =0;         /* Number of hits. */
    ajint    x              =0;         
    AjBool   foundkw        =ajFalse;
    AjBool   foundft        =ajFalse;


    /* Check for valid args. */
    if(!inf)
	return ajFalse;
    

    

    /* Allocate strings and arrays. */
    line       = ajStrNew();
    id         = ajStrNew();
    start      = ajIntNew();
    end        = ajIntNew();



    /* Start of main loop. */
    while((ajReadlineTrim(inf,&line)))
    {
	/* Parse the AC line. */
	if(ajStrPrefixC(line,"AC"))
	{
	    /* Copy accesion number and remove the ';' from the end. */
	    ajFmtScanS(line, "%*s %S", &id);
	    ajStrExchangeCC(&id, ";", "\0");
	    
	    
	    /* Reset flags & no. hits. */
	    foundkw=ajFalse;
	    foundft=ajFalse;
	    nhits=0;
	}
	
	
	/* Search the description and keyword lines with search terms. */
	else if((ajStrPrefixC(line,"DE") || (ajStrPrefixC(line,"KW"))))
	{
	    /* 
	     ** Search terms have a leading and trailing space to prevent 
	     ** them being found as substrings within other words.  To 
	     ** catch cases where a DE or KW line begins with a search 
	     ** term, we must add a leading and trailing space to line.
	     ** We must first remove punctation from the line to be parsed.
	     */
	    ajStrExchangeSetCC(&line, ".,;:", "    ");
	    ajStrAppendK(&line, ' ');
	    ajStrInsertC(&line, 0, " ");


	    for (x = 0; x < terms->N; x++)
		/* Search term is found. */
		if((ajStrFindCaseS(line, terms->Keywords[x])!=-1))
		{	
		    foundkw=ajTrue;
		    break;
		}
	}

	
	/* Search the feature table line with search terms. */
	else if((ajStrPrefixC(line,"FT   DOMAIN")))
	{
	    /*	
	     ** Search terms have a leading and trailing space to prevent 
	     ** them being found as substrings within other words.  To 
	     ** catch cases where a FT line ends with a search 
	     ** term, we must add a  trailing space to line 
	     ** We must first remove punctation from the line to be parsed.
	     */
	    ajStrExchangeSetCC(&line, ".,;:", "    ");
	    ajStrAppendK(&line, ' ');
	    

	    for (x = 0; x < terms->N; x++)
		if((ajStrFindCaseS(line, terms->Keywords[x])!=-1))
		{
		    /* Search term is found. */
		    foundft = ajTrue;
		    nhits++;
		    
		    /* Assign start and end of hit. */
		    ajFmtScanS(line, "%*s %*s %d %d", &s, &e);


		    ajIntPut(&start, nhits-1, s);
		    ajIntPut(&end, nhits-1, e);
		    break;
		}
	}
	

	/* Parse the sequence. */
	else if((ajStrPrefixC(line,"SQ") && ((foundkw == ajTrue) ||
					     (foundft == ajTrue))))
	{
	    /* Allocate memory for temp. sequence. */
	    temp       = ajStrNew();


	    /* Read the sequence into hitlist structure. */
	    while((ajReadlineTrim(inf,&line)) && !ajStrPrefixC(line,"//"))
		/* Read sequence line into temp. */
		ajStrAppendC(&temp,ajStrGetPtr(line)+3);
 

	    /* Clean up temp. sequence. */
	    ajStrRemoveWhite(&temp);


	    /*Priority is given to domain (rather than full length) sequence.*/
	    if(foundft)
	    {
		for(x=0;x<nhits;x++)
		{
		    /* Increment counter of hits for subsequent hits*/
		    (*hits)->N++;

		    
		    /* Reallocate memory for array of hits in hitlist
                       structure. */
		    AJCRESIZE((*hits)->hits, (*hits)->N);
		    (*hits)->hits[(*hits)->N-1]=embHitNew();
		    ajStrAssignC(&(*hits)->hits[(*hits)->N-1]->Model,
				 "KEYWORD");
		    

		    /* Assign start and end of hit. */
		    (*hits)->hits[(*hits)->N-1]->Start = ajIntGet(start, x);
		    (*hits)->hits[(*hits)->N-1]->End = ajIntGet(end, x);
				

		    /* Extract sequence within specified range */
		    ajStrAssignSubS(&(*hits)->hits[(*hits)->N - 1]->Seq, temp, 
				(*hits)->hits[(*hits)->N - 1]->Start - 1, 
				(*hits)->hits[(*hits)->N - 1]->End - 1);
		    

		    /* Put id into structure */
		    ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Acc, id);
		}
	    }
	    else
	    {
		/* Increment counter of hits */
		(*hits)->N++;

		    
		/* Reallocate memory for array of hits in hitlist structure */
		AJCRESIZE((*hits)->hits, (*hits)->N);
		(*hits)->hits[(*hits)->N-1]=embHitNew();
		ajStrAssignC(&(*hits)->hits[(*hits)->N-1]->Model, "KEYWORD");

		/* Extract whole sequence */
		ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Seq, temp); 
		(*hits)->hits[(*hits)->N - 1]->Start = 1; 
		(*hits)->hits[(*hits)->N - 1]->End =
		    ajStrGetLen((*hits)->hits[(*hits)->N - 1]->Seq); 


		/* Put id into structure */
		ajStrAssignRef(&(*hits)->hits[(*hits)->N - 1]->Acc, id);
	    }

	    /* Free temp. sequence */
	    ajStrDel(&temp);
	}
    }


    /* Clean up */
    ajStrDel(&line);
    ajStrDel(&id);
    ajIntDel(&start);
    ajIntDel(&end);

    return ajTrue;
}
コード例 #2
0
static void domainalign_ProcessStampFile(AjPStr in, 
					 AjPStr out,
					 AjPDomain domain, 
					 ajint noden, 
					 AjPFile logf)
{
    AjPFile  outf = NULL;  /* Output file pointer.          */
    AjPFile   inf = NULL;  /* Input file pointer.           */
    AjPStr  temp1 = NULL;  /* Temporary string.             */
    AjPStr  temp2 = NULL;  /* Temporary string.             */
    AjPStr  temp3 = NULL;  /* Temporary string.             */
    AjPStr   line = NULL;  /* Line of text from input file. */
    ajint     blk = 1;     /* Count of the current block in the input file.
			      Block 1 is the numbering and protein sequences, 
			      Block 2 is the secondary structure, 
			      Block 3 is the Very/Less/Post similar records*/
    AjBool     ok = ajFalse;
    
    
    /* Initialise strings. */
    line    = ajStrNew();
    temp1    = ajStrNew();
    temp2    = ajStrNew();
    temp3    = ajStrNew();


    /* Open input and output files. */
    if(!(inf=ajFileNewInNameS(in)))
	ajFatal("Could not open input file in domainalign_ProcessStampFile");
    



    /* Start of code for reading input file. 
       Ignore everything up to first line beginning with 'Number'. */
    while((ajReadlineTrim(inf,&line)))
    {
	/* ajFileReadLine will trim the tailing \n. */
	if((ajStrGetCharPos(line, 1)=='\0'))
	{
	    ok = ajTrue;
	    break;
	}
    }
    
    
    
    /* Read rest of input file. */
    if(ok)
    {
	/* Write DOMAIN classification records to file. */
	if(!(outf=ajFileNewOutNameS(out)))
	 ajFatal("Could not open output file in domainalign_ProcessStampFile");

	
	if((domain->Type == ajSCOP))
	{
	    ajFmtPrintF(outf,"# TY   SCOP\n# XX\n");
	    ajFmtPrintF(outf,"# CL   %S",domain->Scop->Class);
	    ajFmtPrintSplit(outf,domain->Scop->Fold,"\n# XX\n# FO   ",
			    75," \t\n\r");
	    ajFmtPrintSplit(outf,domain->Scop->Superfamily,"# XX\n# SF   ",
			    75," \t\n\r");
	    ajFmtPrintSplit(outf,domain->Scop->Family,"# XX\n# FA   ",
			    75," \t\n\r");
	    ajFmtPrintF(outf,"# XX\n");
	}
	else
	{
	    ajFmtPrintF(outf,"# TY   CATH\n# XX\n");
	    ajFmtPrintF(outf,"# CL   %S",domain->Cath->Class);
	    ajFmtPrintSplit(outf,domain->Cath->Architecture,"\n# XX\n# AR   ",
			    75," \t\n\r");
	    ajFmtPrintSplit(outf,domain->Cath->Topology,"# XX\n# TP   ",75,
			    " \t\n\r");
	    ajFmtPrintSplit(outf,domain->Cath->Superfamily,"# XX\n# SF   ",75,
			    " \t\n\r");
	    ajFmtPrintF(outf,"# XX\n");
	}
	if((domain->Type == ajSCOP))
	{
	    if(noden==1) 
		ajFmtPrintF(outf,"# SI   %d\n# XX",domain->Scop->Sunid_Class);
	    else if(noden==2)
		ajFmtPrintF(outf,"# SI   %d\n# XX",domain->Scop->Sunid_Fold);
	    else if(noden==3)
		ajFmtPrintF(outf,"# SI   %d\n# XX",
			    domain->Scop->Sunid_Superfamily);
	    else if(noden==4) 	
		ajFmtPrintF(outf,"# SI   %d\n# XX",
			    domain->Scop->Sunid_Family);
	    else
		ajFatal("Node number error in domainalign_ProcessStampFile");
	}
	else
	{
	    if(noden==5) 
		ajFmtPrintF(outf,"# SI   %d\n# XX", domain->Cath->Class_Id);
	    else if(noden==6)
		ajFmtPrintF(outf,"# SI   %d\n# XX", domain->Cath->Arch_Id);
	    else if(noden==7)
		ajFmtPrintF(outf,"# SI   %d\n# XX",domain->Cath->Topology_Id);
	    else if(noden==8)
		ajFmtPrintF(outf,"# SI   %d\n# XX",
			    domain->Cath->Superfamily_Id);
	    else if(noden==9)  
		ajFmtPrintF(outf,"# SI   %d\n# XX",domain->Cath->Family_Id);
	    else
		ajFatal("Node number error in domainalign_ProcessStampFile");
	}   



	while((ajReadlineTrim(inf,&line)))
	{
	    /* Increment counter for block of file. */
	    if((ajStrGetCharPos(line, 1)=='\0'))
	    {
		blk++;
		if(blk==4)
		    blk=1;
	    
		continue;
	    }



	    /* Block of numbering line and protein sequences. */
	    if(blk==1)
	    {
		/* Print the number line out as it is. */
		if(ajStrPrefixC(line,"Number"))
		    ajFmtPrintF(outf,"\n# %7s %S\n"," ", line);
		else
		{
		    /* Read only the 7 characters
		       of the domain identifier
		       code in. */
		    ajFmtScanS(line, "%S", &temp1);
		    ajStrAssignSubS(&temp2, temp1, 0, 6);


		    /* Read the sequence. */
		    ajStrAssignSubS(&temp3, line, 13, 69);
		    ajStrExchangeSetCC(&temp3, " ", "X");
		    ajFmtPrintF(logf, "Replaced ' ' in STAMP alignment "
				"with 'X'\n");
		    ajStrFmtUpper(&temp3);
		

		    /* Write domain id code and sequence out. */
		    ajFmtPrintF(outf,"%-15S%7d %S%7d\n",
				temp2, 0, temp3, 0);
		}
	    }
	    /* Secondary structure filled with '????' (unwanted). */
	    else if(blk==2)
	    {
		continue;
	    }
	    /* Similarity lines. */
	    else
	    {
		if(ajStrPrefixC(line,"Post"))
		{
		    /* Read the sequence. */
		    ajStrAssignSubS(&temp3, line, 13, 69);

		    /* Write post similar line out. */
		    ajFmtPrintF(outf,"%-15s%7s %S\n","# Post_similar", " ",
				temp3);
		}
		/* Ignore Very and Less similar lines. */
		else continue;
	    }
	}
    }
    else /* ok == ajFalse. */
    {
	ajWarn("\n***********************************************\n"
	       "* STAMP was called but output file was EMPTY! *\n"
	       "*   NO OUTPUT FILE GENERATED FOR THIS NODE.   *\n"
	       "***********************************************\n");
	ajFmtPrintF(logf, "STAMP called but output file empty.  "
		    "No output file for this node!");
    }
    


    /* Clean up and close input and output files. */
    ajFileClose(&outf);
    ajFileClose(&inf);
    ajStrDel(&line);
    ajStrDel(&temp1);
    ajStrDel(&temp2);
    ajStrDel(&temp3);
    

    /* All done. */
    return;
}