Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-07-15

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All times shown according to UTC.

Time Nick Message
04:33 ende joined #bioperl
10:34 faceface hi
10:35 faceface does SearchIO work on the html dump of a blast report?
10:37 * faceface wonders
10:40 faceface I just wnat to pass it a string
10:44 faceface : File name too long
11:09 faceface http://osdir.com/ml/lang.perl.bi​o.general/2003-08/msg00124.html ??
11:14 faceface some modules should not be oo
11:15 faceface my $string = HTML::Strip->new->parse( $blast->as_string );
11:15 faceface seems to work!
12:52 kyanardag_ joined #bioperl
15:11 asjo joined #bioperl
15:13 asjo Hi! When I read the pod for Bio::SeqIO::abi it looks like I can write abi-files with BioPerl, but when I try I get a "Error while Writing format 'abi'; either bad input or writing not supported by Staden read lib". Is writing not supported, or am I doing it wrong(tm)?
15:13 asjo (The reason I want to is to create input for automated tests.)
15:14 perl_splut depends on your staden version if I'm reading the error correctly
15:20 asjo Hm, my Bio::SeqIO::staden::read seems to be version 1.51.
15:21 asjo I
15:22 asjo 'm using staden 1.7.0.
15:23 perl_splut and how are you setting up the call create the object that will do the writing?
15:24 asjo I've tried just creating a Bio::Seq with a simple sequence, and I've tried reading in an EMBL-file. Same error in both settings.
15:25 asjo Oh, the SeqIO-object? Like this: my $out=Bio::SeqIO->new(-file=>'>test.ab1', -format=>'abi');
15:26 perl_splut hmm...
15:26 perl_splut and how are you calling the write method?
15:27 asjo $out->write_seq($seq);
15:27 asjo Pretty much straight from the Bio::SeqIO::abi pod.
15:28 asjo So basically I'm wondering whether stadens libread can write abi-files :-)
15:29 asjo I might be able to get away with .scf files instead, though. But the write_seq documentation in Bio::SeqIO::scf is a little ambiguous to me.
15:31 asjo (::scf says I can just pass in a SequenceWithQuality object, but when I pass in a Bio::Seq::SeqWithQuality I get an exception)
15:34 perl_splut Well, tracing down how bioperl sets up the object tree, sounds like it is a problem with your staden library
15:34 asjo (Ah, reading the code is seems that " SequenceWithQuality object" should be interpreted as Bio::Seq::Quality).
15:35 perl_splut oh, and the module version and the library version aren't going to be the same
15:35 asjo Yes, but I don't know if it fails because staden doesn't implement writing abi files or if I'm not calling it correctly. So I was hoping someone would say: "Yeah, you're doing it wrong" or "No, staden can't write abi".
15:35 asjo versions: I know, but you asked :-)
15:36 perl_splut the module matches whatever version of BioPerl you are using (in this case 1.5.1)
15:36 asjo Yup, I thought we upgraded to 1.6, but apparantly I've still got an older 1.5.2 dev-release.
15:38 asjo (Ok, passing in a Bio::Seq::Quality object allows me to write an .scf file; I hope phredphrap will eat it).
15:38 asjo Thanks for the help!
15:38 perl_splut might want to upgrade bioperl to 1.6 at some point
15:38 asjo Yes.
15:39 perl_splut could be an incompatibility between staden and 1.5...
15:39 perl_splut or could be that staden 1.7 has writing disabled by default
15:39 asjo Last release of staden was before the version of 1.5 I've got.
15:39 asjo So you know that staden can write abi-files?
15:42 perl_splut don't see why a dev would have created a specific write function in the abi module if it couldn't
15:43 perl_splut if you don't create a write_seq method in a SeqIO format module then you are left with the root version which will print out that the write_seq method was not implemented
15:43 asjo Yup.
16:00 faceface asjo: can you read in an abi?
16:01 asjo faceface: Let me try...
16:03 asjo faceface: Yes.
16:03 faceface cool
16:03 faceface I want to make an ABI database, so I was curious
16:03 asjo I get a Bio::Seq::Quality object back, with sequence, desc and stuff in it.
16:04 asjo I should try to write that...
16:04 asjo Nope, same error.
16:08 faceface ty
16:34 asjo As far as I can see t/SeqIO/abi.t tests reading only.
16:36 perl_splut needs bioperl-ext to do writing
16:42 asjo Ah.
16:42 asjo Thanks.
16:44 asjo bioperl-ext doesn't seem to test writing either :-)
16:46 perl_splut not sure how much loving it and the other packages were given
17:10 conte joined #bioperl
17:14 conte Hi - I'm trying to write a script based on the first example in the EUtilities HOWTO, but I'm getting a strange error: "------------- EXCEPTION: Bio::Root::Exception -------------
17:14 conte MSG: Response Error
17:14 conte Can't "redo" outside a loop block
17:14 conte STACK: Error::throw
17:14 conte STACK: Bio::Root::Root::throw /Library/Perl/5.8.6/Bio/Root/Root.pm:357
17:14 conte STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.6/Bio/DB/GenericWebAgent.pm:184
17:14 conte STACK: fetch_fasta_from_genbank.pl:32
17:14 conte "
17:14 conte Has anyone seen this before?
17:47 perl_splut nope, but sounds like the script is slightly broken
17:49 perl_splut either in the .pl script or in one of the modules a "redo" is called, but isn't in/near a loop block that is valid to redo
18:25 conte here is my script:
18:25 conte my @accs;
18:25 conte while (<>) {
18:25 conte chomp;
18:25 conte push (@accs, $_);
18:25 conte }
18:25 conte my $factory = Bio::DB::EUtilities->new(
18:25 conte -eutil => 'efetch',
18:25 conte -db => 'nucest',
18:25 conte -rettype => 'fasta',
18:25 conte -id => \@accs);
18:25 conte
18:25 conte my $file = "myseqs.gb";
18:25 conte $factory->get_Response(-file => $file);
18:25 conte the input file is just a list off accession numbers, one per line
18:39 deafferret conte: don't paste in channel. use pastebin.com or another.
18:41 conte http://pastebin.com/d64750588
18:41 conte thanks
18:43 deafferret conte++   :)
18:44 deafferret what version of BioPerl?
18:53 conte good question
18:54 conte is there an easy way to find that out?
18:54 deafferret -ponder-
18:55 deafferret perl -MBio::Perl\ 100
18:55 deafferret that's not the official number, but it might help me
18:59 deafferret hmm... I guess this is the official number:   perl -MBio::Root::Version\ 100
19:02 conte hmm, that gives me an error, but if I run perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
19:02 conte I get 1.005002103
19:05 deafferret k. you're a couple years behind. let me see what I get
19:07 deafferret what's an acc throwing that error?
19:09 conte hmm, no one in particular, perhaps the number of acc's is causing the problem?
19:10 deafferret dunno. just trying to reproduce your report. what's the first acc you feed in?
19:10 conte if I do a file of 530 acc's it works, but it doesn't like 13,000
19:10 deafferret oh. then it's probably a specific acc, yes?
19:10 conte perhaps, let me see if I can narrow it down
19:11 conte bbiab
19:11 conte thanks
19:11 deafferret natch
20:48 conte thanks again deafferret, that was the problem
20:52 deafferret :)

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