[EMBOSS] Indexing the ID field of EMBL-formatted databases.

[Charles Plessy]

Le Wed, May 30, 2007 at 02:33:11PM +0100, Peter Rice a écrit :
> in emboss/dbiflat.c function dbiflat_ParseEmbl, add a conversion to upper case:
> 
> 	if(lineType == FLATTYPE_ID)
> 	{
> 	    ajRegExec(regEmblId, rline);
> 	    ajRegSubI(regEmblId, 1, myid);
> 	    ajStrFmtUpper(&myid);
> 	    ajDebug("++id '%S'\n", *myid);
> 	    ajRegSubI(regEmblId, 3, &tmpfd);


Dear Peter,

I tried to apply the following patch:

--- ./emboss/dbiflat.c.old      2007-06-01 15:00:55.000000000 +0900
+++ ./emboss/dbiflat.c  2007-06-01 15:03:59.000000000 +0900
@@ -739,6 +739,7 @@
        {
            ajRegExec(regEmblId, rline);
            ajRegSubI(regEmblId, 1, myid);
+           ajStrFmtUpper(&myid);
            ajDebug("++id '%S'\n", *myid);
            ajRegSubI(regEmblId, 3, &tmpfd);
            if(svnfield >= 0 && ajStrGetLen(tmpfd))

But now dbiflat segfaults... (I am running Debian GNU/Linux 4.0 on a
iMac G5).

regards,

-- 
Charles