Bug #23984 for Bio-Trace-ABIF: Feature request:

Mon Dec 18 15:19:41 2006 MEC [...] Stowers-Institute.org - Ticket created

Subject:	Feature request:
Date:	Mon, 18 Dec 2006 14:18:44 -0600
To:	<bug-Bio-Trace-ABIF [...] rt.cpan.org>
From:	"Cook, Malcolm" <MEC [...] Stowers-Institute.org>

Can you add these methods to it? Thanks!?!? Malcolm Cook Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri sub container_identifier { my $self = shift; unless (defined $self->{'_CTID1'}) { my ($co) = $self->get_data_item('CTID', 1, 'Z*'); $self->{'_CTID1'} = ($co) ? $co : ''; } return $self->{'_CTID1'}; } sub container_name { my $self = shift; unless (defined $self->{'_CTNM1'}) { my ($co) = $self->get_data_item('CTNM', 1, 'Z*'); $self->{'_CTNM1'} = ($co) ? $co : ''; } return $self->{'_CTNM1'}; } sub run_name { my $self = shift; unless (defined $self->{'_RunN1'}) { my ($co) = $self->get_data_item('RunN', 1, 'Z*'); $self->{'_RunN1'} = ($co) ? $co : ''; } return $self->{'_RunN1'}; }

Thu Dec 21 08:58:58 2006 vita [...] cpan.org - Correspondence added

Subject:	Re: [rt.cpan.org #23984] Feature request:
Date:	Thu, 21 Dec 2006 14:58:28 +0100
To:	bug-Bio-Trace-ABIF [...] rt.cpan.org
From:	Nicola Vitacolonna <vitacolonna [...] appliedgenomics.org>

Hi, I'm in the process of adding more methods. Meanwhile, you may use the get_data_item() method, e.g. my ($container_identifier) = $ab->get_data_item('CTID', 1, 'Z*'); Regards Nicola On 18/dic/06, at 21:19, Cook, Malcolm via RT wrote: Show quoted text

> > Mon Dec 18 15:19:41 2006: Request 23984 was acted upon. > Transaction: Ticket created by MEC@Stowers-Institute.org > Queue: Bio-Trace-ABIF > Subject: Feature request: > Broken in: (no value) > Severity: (no value) > Owner: Nobody > Requestors: MEC@Stowers-Institute.org > Status: new > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > > Can you add these methods to it? Thanks!?!? > Malcolm Cook > Database Applications Manager - Bioinformatics > Stowers Institute for Medical Research - Kansas City, Missouri > > > sub container_identifier { > my $self = shift; > unless (defined $self->{'_CTID1'}) { > my ($co) = $self->get_data_item('CTID', 1, 'Z*'); > $self->{'_CTID1'} = ($co) ? $co : ''; > } > return $self->{'_CTID1'}; > } > > sub container_name { > my $self = shift; > unless (defined $self->{'_CTNM1'}) { > my ($co) = $self->get_data_item('CTNM', 1, 'Z*'); > $self->{'_CTNM1'} = ($co) ? $co : ''; > } > return $self->{'_CTNM1'}; > } > > sub run_name { > my $self = shift; > unless (defined $self->{'_RunN1'}) { > my ($co) = $self->get_data_item('RunN', 1, 'Z*'); > $self->{'_RunN1'} = ($co) ? $co : ''; > } > return $self->{'_RunN1'}; > }

Thu Dec 21 08:59:01 2006 The RT System itself - Status changed from 'new' to 'open'

Thu Dec 21 11:26:56 2006 MEC [...] Stowers-Institute.org - Correspondence added

CC:	"Thomasset, Daniel" <DCT [...] Stowers-Institute.org>
Subject:	RE: [rt.cpan.org #23984] Feature request:
Date:	Thu, 21 Dec 2006 10:26:16 -0600
To:	<bug-Bio-Trace-ABIF [...] rt.cpan.org>
From:	"Cook, Malcolm" <MEC [...] Stowers-Institute.org>

Excellent news. Is there any chance of implementing 'setters' and allowing write-back of modified ABIFs. I know this would be unsupported by ABI. I need it mostly for creating test data for testing a dna sequencing LIMS pipeline. Thx, Malcolm Cook Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri Show quoted text

> -----Original Message----- > From: Nicola Vitacolonna via RT > [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] > Sent: Thursday, December 21, 2006 7:59 AM > To: Cook, Malcolm > Subject: Re: [rt.cpan.org #23984] Feature request: > > > <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > Hi, > I'm in the process of adding more methods. Meanwhile, you may > use the > get_data_item() method, e.g. > > my ($container_identifier) = $ab->get_data_item('CTID', 1, 'Z*'); > > Regards > Nicola > > On 18/dic/06, at 21:19, Cook, Malcolm via RT wrote: >

> > > > Mon Dec 18 15:19:41 2006: Request 23984 was acted upon. > > Transaction: Ticket created by MEC@Stowers-Institute.org > > Queue: Bio-Trace-ABIF > > Subject: Feature request: > > Broken in: (no value) > > Severity: (no value) > > Owner: Nobody > > Requestors: MEC@Stowers-Institute.org > > Status: new > > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > > > > > Can you add these methods to it? Thanks!?!? > > Malcolm Cook > > Database Applications Manager - Bioinformatics > > Stowers Institute for Medical Research - Kansas City, Missouri > > > > > > sub container_identifier { > > my $self = shift; > > unless (defined $self->{'_CTID1'}) { > > my ($co) = $self->get_data_item('CTID', 1, 'Z*'); > > $self->{'_CTID1'} = ($co) ? $co : ''; > > } > > return $self->{'_CTID1'}; > > } > > > > sub container_name { > > my $self = shift; > > unless (defined $self->{'_CTNM1'}) { > > my ($co) = $self->get_data_item('CTNM', 1, 'Z*'); > > $self->{'_CTNM1'} = ($co) ? $co : ''; > > } > > return $self->{'_CTNM1'}; > > } > > > > sub run_name { > > my $self = shift; > > unless (defined $self->{'_RunN1'}) { > > my ($co) = $self->get_data_item('RunN', 1, 'Z*'); > > $self->{'_RunN1'} = ($co) ? $co : ''; > > } > > return $self->{'_RunN1'}; > > }

> > >

Thu Dec 21 12:02:53 2006 vita [...] cpan.org - Correspondence added

Subject:	Re: [rt.cpan.org #23984] Feature request:
Date:	Thu, 21 Dec 2006 18:02:24 +0100
To:	bug-Bio-Trace-ABIF [...] rt.cpan.org
From:	Nicola Vitacolonna <vitacolonna [...] appliedgenomics.org>

On 21/dic/06, at 17:26, Cook, Malcolm via RT wrote: Show quoted text

> > Queue: Bio-Trace-ABIF > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > Excellent news. > > Is there any chance of implementing 'setters' and allowing write- > back of > modified ABIFs. I know this would be unsupported by ABI. I need it > mostly for creating test data for testing a dna sequencing LIMS > pipeline.

It was not in my plan since ab1 are usually read only, but it is certainly possible. I will keep a record about it. Nicola

Mon Jan 08 11:18:26 2007 MEC [...] Stowers-Institute.org - Correspondence added

CC:	"Thomasset, Daniel" <DCT [...] Stowers-Institute.org>
Subject:	RE: [rt.cpan.org #23984] Feature request:
Date:	Mon, 8 Jan 2007 10:17:54 -0600
To:	<bug-Bio-Trace-ABIF [...] rt.cpan.org>
From:	"Cook, Malcolm" <MEC [...] Stowers-Institute.org>

Nicola, Excellent. I would appreciate your assistance in allowing write-back if technically possible. Also, a fellow developer (Dan Thomasset, cc:ed) here at the Stowers Institute has discovered that abi sequencing files sometimes can generate an error. He debugged it and reported that: Show quoted text

> The fix for the ABIF error should be sent to the author. In > his code for calculating the 'sample_score', the case where > the '$stop' of the read is before the '$start' of the read > isn't considered. In our broken file, '$start' was 20 and > '$stop' was 19. > > To fix, line 1513 in version 0.02 of Bio::Trace::ABIF was > changed to be: > > return 0 unless ($start >= 0) and ($start <= $stop) and > defined $qv_ref; > > rather than: > > return 0 unless ($start >= 0) and ($stop >= 0) and > defined $qv_ref; > > > Note: the '$start' and '$stop' values are calculated in > Bio::Trace::ABIF functions 'clear_range_start' and > 'clear_range_stop', respectively. The error that the change > fixes may actually lie in those functions.. Intuitively, > 'clear_range_start' should always return a position >= than > 'clear_range_stop', but that didn't happen with this file. > I'll do some more digging to see why the error file causes > the 'clear_range_*' functions to return bad values. >

Thanks again, Malcolm Cook Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri Show quoted text

> -----Original Message----- > From: Nicola Vitacolonna via RT > [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] > Sent: Thursday, December 21, 2006 11:03 AM > To: Cook, Malcolm > Subject: Re: [rt.cpan.org #23984] Feature request: > > > <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > On 21/dic/06, at 17:26, Cook, Malcolm via RT wrote: >

> > > > Queue: Bio-Trace-ABIF > > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > > > Excellent news. > > > > Is there any chance of implementing 'setters' and allowing write- > > back of > > modified ABIFs. I know this would be unsupported by ABI. I need it > > mostly for creating test data for testing a dna sequencing LIMS > > pipeline.

> > It was not in my plan since ab1 are usually read only, but it is > certainly possible. I will keep a record about it. > > Nicola > > > >

Thu Jan 11 05:52:12 2007 vita [...] cpan.org - Correspondence added

Subject:	Re: [rt.cpan.org #23984] Feature request:
Date:	Thu, 11 Jan 2007 11:51:43 +0100
To:	bug-Bio-Trace-ABIF [...] rt.cpan.org
From:	Nicola Vitacolonna <vitacolonna [...] appliedgenomics.org>

Dear Malcolm, sorry for the delayed answer. I need some more time (a couple of weeks?) to produce an update of the module with the requested features, since I am currently called for more urgent tasks; besides, I would like to implement further optimizations that would make it much faster. I can send you a beta version for testing, if you like, before uploading to CTAN. Thanks for reporting a bug in sample_score(): I will investigate the problem. Regards Nicola On 08/gen/07, at 17:18, Cook, Malcolm via RT wrote: Show quoted text

> > Queue: Bio-Trace-ABIF > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > Nicola, > > Excellent. I would appreciate your assistance in allowing write- > back if > technically possible. > > Also, a fellow developer (Dan Thomasset, cc:ed) here at the Stowers > Institute has discovered that abi sequencing files sometimes can > generate an error. He debugged it and reported that: >

>> The fix for the ABIF error should be sent to the author. In >> his code for calculating the 'sample_score', the case where >> the '$stop' of the read is before the '$start' of the read >> isn't considered. In our broken file, '$start' was 20 and >> '$stop' was 19. >> >> To fix, line 1513 in version 0.02 of Bio::Trace::ABIF was >> changed to be: >> >> return 0 unless ($start >= 0) and ($start <= $stop) and >> defined $qv_ref; >> >> rather than: >> >> return 0 unless ($start >= 0) and ($stop >= 0) and >> defined $qv_ref; >> >> >> Note: the '$start' and '$stop' values are calculated in >> Bio::Trace::ABIF functions 'clear_range_start' and >> 'clear_range_stop', respectively. The error that the change >> fixes may actually lie in those functions.. Intuitively, >> 'clear_range_start' should always return a position >= than >> 'clear_range_stop', but that didn't happen with this file. >> I'll do some more digging to see why the error file causes >> the 'clear_range_*' functions to return bad values. >>

> > > Thanks again, > > Malcolm Cook > Database Applications Manager - Bioinformatics > Stowers Institute for Medical Research - Kansas City, Missouri > > >

>> -----Original Message----- >> From: Nicola Vitacolonna via RT >> [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] >> Sent: Thursday, December 21, 2006 11:03 AM >> To: Cook, Malcolm >> Subject: Re: [rt.cpan.org #23984] Feature request: >> >> >> <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >> >> On 21/dic/06, at 17:26, Cook, Malcolm via RT wrote: >>

>>> >>> Queue: Bio-Trace-ABIF >>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >>> >>> Excellent news. >>> >>> Is there any chance of implementing 'setters' and allowing write- >>> back of >>> modified ABIFs. I know this would be unsupported by ABI. I need it >>> mostly for creating test data for testing a dna sequencing LIMS >>> pipeline.

>> >> It was not in my plan since ab1 are usually read only, but it is >> certainly possible. I will keep a record about it. >> >> Nicola >> >> >> >>

Thu Jan 11 11:16:00 2007 MEC [...] Stowers-Institute.org - Correspondence added

CC:	"Thomasset, Daniel" <DCT [...] Stowers-Institute.org>
Subject:	RE: [rt.cpan.org #23984] Feature request:
Date:	Thu, 11 Jan 2007 10:08:31 -0600
To:	<bug-Bio-Trace-ABIF [...] rt.cpan.org>
From:	"Cook, Malcolm" <MEC [...] Stowers-Institute.org>

Thanks Nicola - we would be happy to test your beta and 1) give you timing stats on a large set of ABIFs using old and new Bio::ABIF in our hands 2) confirm sample_score bug is fixed 3) evaluate use your new write back setter to create ABIFs for testing purposes (assuming you plan on implementing this feature). Let us know if this is worth your effort and if there is anything else you're planning on in cluding in forthcoming releases. Thanks! Malcolm Cook Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri Show quoted text

> -----Original Message----- > From: Nicola Vitacolonna via RT > [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] > Sent: Thursday, January 11, 2007 4:52 AM > To: Cook, Malcolm > Subject: Re: [rt.cpan.org #23984] Feature request: > > > <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > Dear Malcolm, > sorry for the delayed answer. I need some more time (a couple of > weeks?) to produce an update of the module with the requested > features, since I am currently called for more urgent tasks; > besides, > I would like to implement further optimizations that would make it > much faster. I can send you a beta version for testing, if you like, > before uploading to CTAN. > > Thanks for reporting a bug in sample_score(): I will investigate the > problem. > > Regards > Nicola > > On 08/gen/07, at 17:18, Cook, Malcolm via RT wrote: >

> > > > Queue: Bio-Trace-ABIF > > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > > > Nicola, > > > > Excellent. I would appreciate your assistance in allowing write- > > back if > > technically possible. > > > > Also, a fellow developer (Dan Thomasset, cc:ed) here at the Stowers > > Institute has discovered that abi sequencing files sometimes can > > generate an error. He debugged it and reported that: > >

> >> The fix for the ABIF error should be sent to the author. In > >> his code for calculating the 'sample_score', the case where > >> the '$stop' of the read is before the '$start' of the read > >> isn't considered. In our broken file, '$start' was 20 and > >> '$stop' was 19. > >> > >> To fix, line 1513 in version 0.02 of Bio::Trace::ABIF was > >> changed to be: > >> > >> return 0 unless ($start >= 0) and ($start <= $stop) and > >> defined $qv_ref; > >> > >> rather than: > >> > >> return 0 unless ($start >= 0) and ($stop >= 0) and > >> defined $qv_ref; > >> > >> > >> Note: the '$start' and '$stop' values are calculated in > >> Bio::Trace::ABIF functions 'clear_range_start' and > >> 'clear_range_stop', respectively. The error that the change > >> fixes may actually lie in those functions.. Intuitively, > >> 'clear_range_start' should always return a position >= than > >> 'clear_range_stop', but that didn't happen with this file. > >> I'll do some more digging to see why the error file causes > >> the 'clear_range_*' functions to return bad values. > >>

> > > > > > Thanks again, > > > > Malcolm Cook > > Database Applications Manager - Bioinformatics > > Stowers Institute for Medical Research - Kansas City, Missouri > > > > > >

> >> -----Original Message----- > >> From: Nicola Vitacolonna via RT > >> [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] > >> Sent: Thursday, December 21, 2006 11:03 AM > >> To: Cook, Malcolm > >> Subject: Re: [rt.cpan.org #23984] Feature request: > >> > >> > >> <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > >> > >> On 21/dic/06, at 17:26, Cook, Malcolm via RT wrote: > >>

> >>> > >>> Queue: Bio-Trace-ABIF > >>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > >>> > >>> Excellent news. > >>> > >>> Is there any chance of implementing 'setters' and allowing write- > >>> back of > >>> modified ABIFs. I know this would be unsupported by ABI.

> I need it

> >>> mostly for creating test data for testing a dna sequencing LIMS > >>> pipeline.

> >> > >> It was not in my plan since ab1 are usually read only, but it is > >> certainly possible. I will keep a record about it. > >> > >> Nicola > >> > >> > >> > >>

> > >

Thu Jan 11 11:50:51 2007 vita [...] cpan.org - Correspondence added

Subject:	Re: [rt.cpan.org #23984] Feature request:
Date:	Thu, 11 Jan 2007 17:50:27 +0100
To:	bug-Bio-Trace-ABIF [...] rt.cpan.org
From:	Nicola Vitacolonna <vitacolonna [...] appliedgenomics.org>

Thanks - I will contact you as soon as the new version is ready for testing. Regards Nicola On 11/gen/07, at 17:16, Cook, Malcolm via RT wrote: Show quoted text

> > Queue: Bio-Trace-ABIF > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > > > Thanks Nicola - we would be happy to test your beta and > > 1) give you timing stats on a large set of ABIFs using old and new > Bio::ABIF in our hands > 2) confirm sample_score bug is fixed > 3) evaluate use your new write back setter to create ABIFs for testing > purposes (assuming you plan on implementing this feature). > > Let us know if this is worth your effort and if there is anything else > you're planning on in cluding in forthcoming releases. > > Thanks! > > Malcolm Cook > Database Applications Manager - Bioinformatics > Stowers Institute for Medical Research - Kansas City, Missouri > >

>> -----Original Message----- >> From: Nicola Vitacolonna via RT >> [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] >> Sent: Thursday, January 11, 2007 4:52 AM >> To: Cook, Malcolm >> Subject: Re: [rt.cpan.org #23984] Feature request: >> >> >> <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >> >> Dear Malcolm, >> sorry for the delayed answer. I need some more time (a couple of >> weeks?) to produce an update of the module with the requested >> features, since I am currently called for more urgent tasks; >> besides, >> I would like to implement further optimizations that would make it >> much faster. I can send you a beta version for testing, if you like, >> before uploading to CTAN. >> >> Thanks for reporting a bug in sample_score(): I will investigate the >> problem. >> >> Regards >> Nicola >> >> On 08/gen/07, at 17:18, Cook, Malcolm via RT wrote: >>

>>> >>> Queue: Bio-Trace-ABIF >>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >>> >>> Nicola, >>> >>> Excellent. I would appreciate your assistance in allowing write- >>> back if >>> technically possible. >>> >>> Also, a fellow developer (Dan Thomasset, cc:ed) here at the Stowers >>> Institute has discovered that abi sequencing files sometimes can >>> generate an error. He debugged it and reported that: >>>

>>>> The fix for the ABIF error should be sent to the author. In >>>> his code for calculating the 'sample_score', the case where >>>> the '$stop' of the read is before the '$start' of the read >>>> isn't considered. In our broken file, '$start' was 20 and >>>> '$stop' was 19. >>>> >>>> To fix, line 1513 in version 0.02 of Bio::Trace::ABIF was >>>> changed to be: >>>> >>>> return 0 unless ($start >= 0) and ($start <= $stop) and >>>> defined $qv_ref; >>>> >>>> rather than: >>>> >>>> return 0 unless ($start >= 0) and ($stop >= 0) and >>>> defined $qv_ref; >>>> >>>> >>>> Note: the '$start' and '$stop' values are calculated in >>>> Bio::Trace::ABIF functions 'clear_range_start' and >>>> 'clear_range_stop', respectively. The error that the change >>>> fixes may actually lie in those functions.. Intuitively, >>>> 'clear_range_start' should always return a position >= than >>>> 'clear_range_stop', but that didn't happen with this file. >>>> I'll do some more digging to see why the error file causes >>>> the 'clear_range_*' functions to return bad values. >>>>

>>> >>> >>> Thanks again, >>> >>> Malcolm Cook >>> Database Applications Manager - Bioinformatics >>> Stowers Institute for Medical Research - Kansas City, Missouri >>> >>> >>>

>>>> -----Original Message----- >>>> From: Nicola Vitacolonna via RT >>>> [mailto:bug-Bio-Trace-ABIF@rt.cpan.org] >>>> Sent: Thursday, December 21, 2006 11:03 AM >>>> To: Cook, Malcolm >>>> Subject: Re: [rt.cpan.org #23984] Feature request: >>>> >>>> >>>> <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >>>> >>>> On 21/dic/06, at 17:26, Cook, Malcolm via RT wrote: >>>>

>>>>> >>>>> Queue: Bio-Trace-ABIF >>>>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=23984 > >>>>> >>>>> Excellent news. >>>>> >>>>> Is there any chance of implementing 'setters' and allowing write- >>>>> back of >>>>> modified ABIFs. I know this would be unsupported by ABI.

>> I need it

>>>>> mostly for creating test data for testing a dna sequencing LIMS >>>>> pipeline.

>>>> >>>> It was not in my plan since ab1 are usually read only, but it is >>>> certainly possible. I will keep a record about it. >>>> >>>> Nicola >>>> >>>> >>>> >>>>

>> >> >>

Fri Jul 20 05:06:46 2007 vita [...] cpan.org - Correspondence added

The latest version of the module (1.01) addresses the features requests and solves the mentioned bugs.

Fri Jul 20 05:07:15 2007 vita [...] cpan.org - Status changed from 'open' to 'resolved'