[Bioperl-l] Patching lucy

Andrew Walsh walsh at cenix-bioscience.com
Mon Aug 1 09:03:09 EDT 2005

Hi Phillip,

The patch pasted at the bottom of this e-mail should do the trick.  When 
you say that lucy seg faults, I assume you mean that you get the 
segfault when running lucy on its own.  The module itself does not call 
lucy.  It is only parsing the output from the files that lucy creates. 
lucy itself should be taking phred files as its input.  The patch is 
required if you want to use the stderr from the lucy to get more 
information from the module about the sequences.  If you apply this 
patch, you can try running the test that comes with the lucy tarball 
(see the README.FIRST file in the distribution).  It works for me (Suse 
9.0 on a Pentium 3 box).  Let me know if there are any problems.  I will 
update the Appendix for Bio::Tools::Lucy in CVS.



 >       /* AGW added next line */
 >       fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name);
<     if ((seqs[i].len=bases)<=0)
 >     if ((seqs[i].len=bases)<=0) {
 >       /* AGW added next line */
 >       fprintf(stderr, "Empty: %s\n", seqs[i].name);
 >     }
<       if (left) seqs[i].left+=left;
 >       if (left) {
 >         seqs[i].left+=left;
 >         /*  AGW added next line */
 >         fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name);
 >       }
<       if (right) seqs[i].right-=right;
 >       if (right) {
 >         seqs[i].right-=right;
 >         /*  AGW added next line */
 >         fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name);
 >         }
 >         /* AGW added next line */
 >         fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name);
 >         /* AGW added next line */
 >           fprintf(stderr, "Vector: %s\n", seqs[i].name);

Phillip SanMiguel wrote:
> The patch to lucy source code from (the appendix):
> http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Lucy.html
> seems not to work for lucy-1.19p or lucy-1.19s. Actually patch runs 
> fine, but the resulting executable (after make) seg faults when run on 
> the lucy test data.
> Any advice?
> I've sent email directly to the module creator, Andrew G. Walsh, as 
> requested in the module. But I'm not sure if the module creator 
> regularly monitors the hotmail account listed therein. So I thought I'd 
> post here, in case someone had a patch that would work on lucy-1.19.

Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Tatzberg 47
01307 Dresden
Tel. +49-351-4173 137
Fax  +49-351-4173 109

public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg

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