gmane.comp.lang.perl.bio.general

problem with bp_genbank2gff3.pl

ANJAN PURKAYASTHA — 2008-12-01T22:05:16

hi, i copied and pasted the genbank2gff3.pls script into a file /usr/bin/bp_genbank2gff3.pl and tried running it. error message: Can't locate object method "FT_SO_map" via package "Bio::SeqFeature::Tools::TypeMapper" at /usr/bin/bp_genbank2gff3.pl line 285. any idea how i get to the map FT_SO_map method? thanks, anjan

on FootPrinter

Munirul Islam — 2008-12-01T23:44:24

Hi: We are trying to install FootPrinter on a linux machine. But we are getting errors. We also tried on MAC. Anyone here successfully installed it? I saw bioperl supports FootPrinter. http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm Your installation experience would definitely help us. Thank you. Munir Computer Science Wayne State University

Re: undefined sub-sequence with a single base

Chris Fields — 2008-11-30T21:07:58

Steve, If you can look through it that would be great, if it gets fixed for 1.6 even better, but it's not a blocker by any means and I would rather have it fixed robustly vs. a problematic quickie fix 'for now'. I think a documentation note indicating potential issues would suffice for me for the time being. Sendu also made some changes on this for 1.5.2 if memory serves (made it a bit more robust), so it might be worth looking over the revision history. Somewhat related: I noticed that Bio::Search::BlastUtils and Bio::Search::SearchUtils is redundant (both have the same methods, including tile_hsps, but the latter module seems to be more up-to- date). Should we deprecate one for the other? They are both used (but I'm sure SearchUtils could drop-in replace BlastUtils). chris On Nov 30, 2008, at 11:58 AM, Mark A. Jensen wrote:

Re: undefined sub-sequence with a single base

Mark A. Jensen — 2008-11-30T17:58:08

I think we're (Dave, Chris, and I) are making progress on the subsequence boundary issues. The fix should propagate through everything having this issue...we hope--stay tuned... ----- Original Message ----- From: "Steve Chervitz" bioperl.org> To: "Jason Stajich" bioperl.org> Cc: "Chris Fields" illinois.edu>; lists.open-bio.org>; "Alexie Papanicolaou" ice.mpg.de> Sent: Sunday, November 30, 2008 12:50 PM Subject: Re: [Bioperl-l] undefined sub-sequence with a single base

Re: undefined sub-sequence with a single base

Steve Chervitz — 2008-11-30T17:50:26

Apologies for the trouble my tile_hsps method has caused. My original intent for it was to provide approximate answers at the level of the Hit object, providing a means of summing over all HSPs in a reasonable way. I don't think it has ever gone through extensive testing with different blast flavors and edge cases. What to do with it? Maybe provide warnings to it's limitations with advice on other ways to proceed. Or bite the bullet and make it more robust. As for the specific exception reported in this thread, it looks like there's a bug causing it to not properly handle zero-length ranges: "Undefined sub-sequence (548,548). Valid range = 51 - 548" Patching this might be fairly straightforward and could help in the short term. I'll take a look. Steve On Mon, Nov 17, 2008 at 10:16 AM, Jason Stajich bioperl.org> wrote:

Re: undefined sub-sequence with a single base

Mark A. Jensen — 2008-11-29T14:38:06

## sorry about the multi-post All- Thought I would throw this up to this thread. Patch to http://bugzilla.open-bio.org/show_bug.cgi?id=2476 using mapping-aware subseq() seems to solve the problem. It appears to translate cleanly between aas and nts, and gives single-residue subseqs naturally (even at the boundaries). Comments please... cheers Mark

Re: How to write a Bio::DB:Fasta sequence into a file?

Mark A. Jensen — 2008-11-29T14:34:33

## sorry about the multiple posts What you are doing is a little unclear. If you have obtained a sequence object, from Bio::DB::Fasta or anywhere, you can write it to a FASTA file by using the write_sequence call. Maybe you have done $seq = read_sequence("theirseqs.fas", 'fasta'); or ($seq, < at >more_seqs) = read_all_sequences("theirseqs.fas", 'fasta'); or even $db = new Bio::DB::Fasta("theirseqs.fas"); $seq = $db->get_Seq_by_id('THX1138'); then write it with write_sequence(">myseqs.fas", 'fasta', $seq); or append it to your file with write_sequence(">>myseqs.fas", 'fasta', $seq); If your problem is, you have a sequence string, and you want to write it to a file in FASTA format, then you create a sequence object directly: $seq = new_sequence( 'atcgtgcaat', 'THX1138' ) and write it using write_sequence() as above. Hope this helps- Mark

Re: How to write a Bio::DB:Fasta sequence into a file?

Mark A. Jensen — 2008-11-29T05:57:56

What you are doing is a little unclear. If you have obtained a sequence object, from Bio::DB::Fasta or anywhere, you can write it to a FASTA file by using the write_sequence call. Maybe you have done $seq = read_sequence("theirseqs.fas", 'fasta'); or ($seq, < at >more_seqs) = read_all_sequences("theirseqs.fas", 'fasta'); or even $db = new Bio::DB::Fasta("theirseqs.fas"); $seq = $db->get_Seq_by_id('THX1138'); then write it with write_sequence(">myseqs.fas", 'fasta', $seq); or append it to your file with write_sequence(">>myseqs.fas", 'fasta', $seq); If your problem is, you have a sequence string, and you want to write it to a file in FASTA format, then you create a sequence object directly: $seq = new_sequence( 'atcgtgcaat', 'THX1138' ) and write it using write_sequence() as above. Hope this helps- Mark

Re: undefined sub-sequence with a single base

Mark A. Jensen — 2008-11-29T05:06:09

All- Thought I would throw this up to this thread. Patch to http://bugzilla.open-bio.org/show_bug.cgi?id=2476 using mapping-aware subseq() seems to solve the problem. It appears to translate cleanly between aas and nts, and gives single-residue subseqs naturally (even at the boundaries). Comments please... cheers Mark

Re: general coordinate transformation in LocatableSeq

Dave Messina — 2008-11-28T23:28:13

Mark, you rock! I'll take a look at your patches in detail tomorrow and check them in (unless Chris beats me to it). Thanks so much for taking the time. Dave

Re: general coordinate transformation in LocatableSeq

Mark A. Jensen — 2008-11-28T21:54:56

Dave- this was an excellent trial run. Have uploaded patches to #2476 that seem to eliminate the problem there. Will need to explore other issues (length_aln, particularly) further. MAJ ----- Original Message ----- From: "Dave Messina" sbc.su.se> To: "Mark A. Jensen" fortinbras.us> Cc: "BioPerl List" lists.open-bio.org>; "Chris Fields" illinois.edu> Sent: Friday, November 28, 2008 3:33 AM Subject: Re: [Bioperl-l] general coordinate transformation in LocatableSeq

Re: general coordinate transformation in LocatableSeq

Mark A. Jensen — 2008-11-28T15:34:26

It's likely it could help, since one of Bert's tweaks was to fix a wrong transformation. I will dig into it. ----- Original Message ----- From: Dave Messina To: Mark A. Jensen Cc: BioPerl List ; Chris Fields Sent: Friday, November 28, 2008 3:33 AM Subject: Re: [Bioperl-l] general coordinate transformation in LocatableSeq I wonder if this would be useful for sorting out the subsequence issues that we've seen in Bio::Search::SearchUtils::tile_hsps, Bio::Search::Hit::GenericHit::length_aln, et al. (e.g. Bug 2476 ). Not for release 1.6, but a 1.6.x point release perhaps. Dave

Re: verbose turned on by PrimarySeq->new()

Dave Messina — 2008-11-28T13:24:43

I just hacked it silent in its DESTROY method a few days ago. Maybe I think so; I reverted your changes, reran t/AlignIO/largemultifasta.t and saw no warnings. Thanks, done. Dave

Re: verbose turned on by PrimarySeq->new()

Heikki Lehvaslaiho — 2008-11-28T12:49:46

Dave, Could this be the same reason LargeLocatableSeq was printing out these same warnings? I just hacked it silent in its DESTROY method a few days ago. Maybe that can be revoked now? I can not see any reasons why module code itself should increase verbosity level, so go and fix it. -Heikki bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm 2008/11/28 Dave Messina sbc.su.se>:

verbose turned on by PrimarySeq->new()

Dave Messina — 2008-11-28T12:11:13

Hey everyone, In trying to figure out why the SeqIO::largefasta tests were being verbose about tempfile cleanup, I discovered that the PrimarySeq constructor turns on verbose, which gets inherited by LargePrimarySeq, which in turn cause RootIO to overshare about the temp files. (see PrimarySeq.pm line 164). The verbose flag was put in when Mira Han added -nowarnonempty. Turning verbose off doesn't seem to cause any tests to fail, so it looks like it might have been turned on for initial debugging purposes and never removed. Mira (or anyone else in the know), could you comment on this? Dave

Re: general coordinate transformation in LocatableSeq

Dave Messina — 2008-11-28T08:33:39

I wonder if this would be useful for sorting out the subsequence issues that we've seen in Bio::Search::SearchUtils::tile_hsps, Bio::Search::Hit::GenericHit::length_aln, et al. (e.g. Bug 2476 ). Not for release 1.6, but a 1.6.x point release perhaps. Dave

general coordinate transformation in LocatableSeq

Mark A. Jensen — 2008-11-28T02:20:30

Chris and others interested- Under bug #2689 I've taken a stab add moving in and out of sequence coordinate systems in a general way (aa to/from nt, but also say repeats to/from mnemonics), under the guise of a subseq() method for LocatableSeq. Prob not for this release, but may be helpful for other components as things become (even) more generalized in future. This subseq also handles frameshifts. Would be grateful for comments (after the rush)- cheers MAJ

Re: [ANNOUNCEMENT] BioPerl 1.6 release agenda

Chris Fields — 2008-11-27T22:45:12

On Nov 27, 2008, at 3:53 PM, Dave Messina wrote: No problem at all! As long as we know what everyone is working on (noted on the wiki or here), shouldn't be a problem, so the more involved the better. Turkey day here so I'll be intermittent, but I'll work on updating the wiki over the next day or two. I'm working on a few more bugs (including that stockholm one) and will update the SearchIO/AlignIO tests along the way. Thanks again for the help! chris

Re: [ANNOUNCEMENT] BioPerl 1.6 release agenda

Dave Messina — 2008-11-27T21:53:18

Agreed. Sounds good. I'll add those to the TODO list on the wiki. I've updated the 1.6 release talk page to describe the hierarchical t/ structure I used for SeqIO. Will do. Yes, anyone looking to lend a hand, please speak up! Restructuring these test files does not require much expertise in BioPerl, and it's a good way to get your feet wet. I've gone through the list of outstanding bugs on the release page and tried to do some triage on which release they seemed appropriate for -- see the big TODO table on: http://www.bioperl.org/wiki/Talk:Release_1.6 Chris, I know you've been working hard on going through a lot of bugs in the last few days. Hope I'm not stepping on your toes there; just trying to get something written down on the list for each one of them so we can all discuss and see what's left to be done. Dave

Re: [ANNOUNCEMENT] BioPerl 1.6 release agenda

Chris Fields — 2008-11-27T18:58:30

Possible candidates to be moved out of core into a dev (unless we come up with some tests!). I agree. Still warrants some investigation, but I agree. We can turn off warning if needed, but I would rather try to find what is triggering them (it's almost always something). I like! I'll change AlignIO and SearchIO over to this and work on cleaning up test file names. We'll need to update the wiki accordingly. Thanks Dave! Feel free to do more restructuring along these lines; we have the other IO's (Assembly, Resstriction, Tree, Feature, and a few others I think), and I could see collecting various modules into a collective structure, such as Ontology, Tools, Graphics, etc. If you do just post a note here or on the wiki (I'll do likewise) so we don't work on the same thing. Anyone else wanting to join in please let us know likewise. chris

Re: [ANNOUNCEMENT] BioPerl 1.6 release agenda

Hilmar Lapp — 2008-11-27T17:20:47

Looks like a great structure! (Sorry I can't help much at this time, so I'm resigning myself to cheering from the sidelines :) -hilmar On Nov 27, 2008, at 12:05 PM, Dave Messina wrote: