[Bioperl-l] Patching lucy
Phillip San Miguel
pmiguel at purdue.edu
Tue Aug 2 10:48:48 EDT 2005
Andrew,
Yes you are right. Everything looks good now.
A good test (of lucy) was to take the suggested lucy test from
README.FIRST and add the "-c" parameter to it after patching the source
and compiling. The test would be:
lucy -c -v PUC19 PUC19splice atie.seq atie.qul atie.2nd -debug lucy.info
The the output to STDERR shows all the extra information your patches
have caused lucy to include.
Thanks!
Phillip
Andrew Walsh wrote:
> 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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