[Bioperl-l] Patching lucy

[Andrew Walsh]

Hi Phillip,

I ran the patch on version 1.19p (which I downloaded from the TIGR ftp 
site yesterday).  It seemed to work for me (all 7 patches worked).

 > patch -b -i lucy.patch lucy.c
patching file lucy.c

Here are the contents of the patch file.  Perhaps my mail client did 
something funny in formatting this.  I'll send you a separate file as an 
attachment as well.

 > cat lucy.patch
277a278,279
 >       /* AGW added next line */
 >       fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name);
588c590,592
<     if ((seqs[i].len=bases)<=0)
---
 >     if ((seqs[i].len=bases)<=0) {
 >       /* AGW added next line */
 >       fprintf(stderr, "Empty: %s\n", seqs[i].name);
589a594
 >     }
893c898,902
<       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);
 >       }
896c905,909
<       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);
 >         }
898a912,913
 >         /* AGW added next line */
 >         fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name);
949a965,966
 >         /* AGW added next line */
 >           fprintf(stderr, "Vector: %s\n", seqs[i].name);


Cheers,

Andrew


Phillip San Miguel wrote:
> Hi Andrew,
> 
> Thanks for the effort you went to here. Still looks there is a (more 
> minor) problem though.
> patch gives a few errors (see below) using your new diff. Looks like 2 
> of the 7 patches failed to patch lucy.c from lucy version lucy-1.19p.
> 
> But the resulting source code does compile and run on the lucy test 
> data. But the PolyA patches did not get inserted.
> 
> Do you know if all 7 of your patches were installed into the lucy.c file 
> from lucy-1.19p?
> 
> (By the way, I think we are on the same page.  I do understand that your 
> perl code parses lucy output. I've tried it on lucy 1.19p output and it 
> succeeds--although it, of course, lacks some of the functionality that 
> would be available from the patched version of lucy).
> 
> Phillip
> 
> Here is the output when I run patch:
> 
> (lucy)% cd lucy-1.19p
> (lucy-1.19p)% patch -b -i AndrewsNewPatch.diff lucy.c
>  Looks like a normal diff.
> Hunk #4 failed at line 893.
> Hunk #5 failed at line 896.
> 2 out of 7 hunks failed: saving rejects to lucy.c.rej
>  I can't seem to find a patch in there anywhere.
> 
> Here is the lucy.c.rej file contents:
> 
> ***************
> *** 893,893 ****
> !       if (left) seqs[i].left+=left;
> --- 898,902 ----
> !       if (left) {
> !         seqs[i].left+=left;
> !         /*  AGW added next line */
> !         fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name);
> !       }
> ***************
> *** 896,896 ****
> !       if (right) seqs[i].right-=right;
> --- 905,909 ----
> !       if (right) {
> !         seqs[i].right-=right;
> !         /*  AGW added next line */
> !         fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name);
> !         }
> 
> 
> Andrew Walsh wrote:
> 
>> 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.
>>
>> Cheers,
>>
>> Andrew
>>
>>
>> 277a278,279
>> >       /* AGW added next line */
>> >       fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name);
>> 588c590,592
>> <     if ((seqs[i].len=bases)<=0)
>> ---
>> >     if ((seqs[i].len=bases)<=0) {
>> >       /* AGW added next line */
>> >       fprintf(stderr, "Empty: %s\n", seqs[i].name);
>> 589a594
>> >     }
>> 893c898,902
>> <       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);
>> >       }
>> 896c905,909
>> <       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);
>> >         }
>> 898a912,913
>> >         /* AGW added next line */
>> >         fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name);
>> 949a965,966
>> >         /* 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.
>>>
>>
>>
> 


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

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