Cannot download/find BPbl2seq module

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Cannot download/find BPbl2seq module

Turnsek, Jernej

Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu

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oaf.pl (12K) Download Attachment
mysequence.fasta (1K) Download Attachment
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Re: Cannot download/find BPbl2seq module

Mark A. Jensen

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:

Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Mark A. Jensen

Oops, I am wrong about this.
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:

Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu

_______________________________________________
Bioperl-l mailing list
[hidden email]
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Re: Cannot download/find BPbl2seq module

Brian Osborne-2
In reply to this post by Mark A. Jensen
Jernej,

Can you show us this error message?

There is a module called Bio::Tools::BPbl2seq, but from very old versions of BioPerl, it’s not found in recent versions.

Brian O.


On May 25, 2016, at 2:26 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark
On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:

Dear BioPerl community,

I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq

I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Brian Osborne-2
In reply to this post by Mark A. Jensen
Mark,

Bio::Tools::BPbl2seq was a part of the BLAST parsing BPLite package, written by Ian Korf way back when. BPLite was removed from Bioperl some years ago.

Brian O.


On May 25, 2016, at 3:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,



I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.




I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Fields, Christopher J
In reply to this post by Mark A. Jensen
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,



I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.




I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Turnsek, Jernej

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:


"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."


The error message I see is here:




Jernej

From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,



I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.




I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Turnsek, Jernej

LINK to the website mentioned.



From: Turnsek, Jernej
Sent: Wednesday, May 25, 2016 5:06 PM
To: Fields, Christopher J; Mark Jensen; Brian Osborne
Cc: [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:


"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."


The error message I see is here:




Jernej

From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark

On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,



I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.




I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Fields, Christopher J
In reply to this post by Turnsek, Jernej
Yep, those tools used Ian’s old BPLite, see here:


These would last be in the 1.5.2 release series and were removed prior to v1.6 as their functionality was largely subsumed by Bio::SearchIO.

chris

On May 25, 2016, at 4:06 PM, Turnsek, Jernej <[hidden email]> wrote:

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:

"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."

The error message I see is here:

<OAF_error.png>

Jernej

From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.
On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark
On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq

I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.



I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
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Re: Cannot download/find BPbl2seq module

Turnsek, Jernej

Wonderful. I'll give it a shot with v1.5.2 or lower then.


Thank you all again!


Jernej



From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 5:10:35 PM
To: Turnsek, Jernej
Cc: Mark Jensen; Brian Osborne; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
Yep, those tools used Ian’s old BPLite, see here:


These would last be in the 1.5.2 release series and were removed prior to v1.6 as their functionality was largely subsumed by Bio::SearchIO.

chris

On May 25, 2016, at 4:06 PM, Turnsek, Jernej <[hidden email]> wrote:

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:

"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."

The error message I see is here:

<OAF_error.png>

Jernej

From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.
On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark
On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:


Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq

I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.



I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
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Re: Cannot download/find BPbl2seq module

Mark A. Jensen

Ok -- because I am so embarrassed about my lack of historical BioPerl knowledge, and also about the state of the BioPerl distribution, I decided to have a look at oaf and see if it could at least use the latest modules.

I think it can. In fact, oaf was shipping an instance of  Bio/Tools/Run/StandAloneBlast.pm frozen in time. That was where the ancient BPbl2seq was used. If you installed it with perl Makefile.PL, Jernej, you would have written over the version that comes with BP-1.6.9. 

I pulled the frozen modules out of the original distribution and MANIFEST, and created https://github.com/majensen/oaf-repackage. I added hints about where to get the latest versions of the external tools. I have tried the perl Makefile.PL,... mantra, and I seem to get something on his test data.

Do I have time for this? No, but good Lord, I can't stand the idea of any self-respecting bioinformatician installing 1.5.2.

MAJ

 

On 2016-05-25 20:09, Turnsek, Jernej wrote:

Wonderful. I'll give it a shot with v1.5.2 or lower then.

 

Thank you all again!

 

Jernej

 
 

From: Fields, Christopher J
Sent: Wednesday, May 25, 2016 5:10:35 PM
To: Turnsek, Jernej
Cc: Mark Jensen; Brian Osborne; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
Yep, those tools used Ian’s old BPLite, see here:
 
 
These would last be in the 1.5.2 release series and were removed prior to v1.6 as their functionality was largely subsumed by Bio::SearchIO.
 
chris

On May 25, 2016, at 4:06 PM, Turnsek, Jernej <[hidden email]> wrote:

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:
 
"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."
 
The error message I see is here:
 
 
 
 
Jernej

From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; [hidden email]
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:
 
 
chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <[hidden email]> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.
On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <[hidden email]> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark
On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <[hidden email]> wrote:

 
Dear BioPerl community,
 
 
I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq

I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.
 
 
 
I look forward to hearing from you.
 
Thank you and kind regards,
 
Jernej Turnsek
 
 

 
 
 
Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l

 

 

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