Problem with % characters in maker file names (MWAS)

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Problem with % characters in maker file names (MWAS)

Fourie Joubert
Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
[hidden email]
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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Re: Problem with % characters in maker file names (MWAS)

Carson Hinton Holt
Re: [maker-devel] Problem with % characters in maker file names (MWAS) Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:

Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.


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Re: Problem with % characters in maker file names (MWAS)

Khan, Anar
Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Hi Fourie

 

I removed escape characters from my gff output using:

 

cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape -ne 'print uri_unescape($_)' > new.gff

 

I found the first perl command was needed as often the % characters were themselves escaped (several times), resulting in strings such as %25252E.

 

I’m using GBrowse, and I wasn’t aware it supported escaped chars in gff files. That is useful to know, I need to upgrade!

 

Cheers

Anar

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Carson Holt
Sent: Wednesday, 30 March 2011 4:03 a.m.
To: Fourie Joubert; [hidden email]
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

 

Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:

Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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Re: Problem with % characters in maker file names (MWAS)

Carson Hinton Holt
Re: [maker-devel] Problem with % characters in maker file names (MWAS) Which MAKER version are you using?  This may be important as I may need to debug.

--Carson


On 3/29/11 10:03 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Fourie
 
I removed escape characters from my gff output using:
 
cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape -ne 'print uri_unescape($_)' > new.gff
 
I found the first perl command was needed as often the % characters were themselves escaped (several times), resulting in strings such as %25252E.
 
I’m using GBrowse, and I wasn’t aware it supported escaped chars in gff files. That is useful to know, I need to upgrade!
 
Cheers
Anar
 
 

From: maker-devel-bounces@... [[hidden email]] On Behalf Of Carson Holt
Sent: Wednesday, 30 March 2011 4:03 a.m.
To: Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:
Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.


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Re: Problem with % characters in maker file names (MWAS)

Khan, Anar
Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Hi Carson

 

Version 2.07. Apologies for not letting you know in the first place.

 

Cheers

Anar

 

From: Carson Holt [mailto:[hidden email]]
Sent: Wednesday, 30 March 2011 5:07 p.m.
To: Khan, Anar; Fourie Joubert; [hidden email]
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

 

Which MAKER version are you using?  This may be important as I may need to debug.

--Carson


On 3/29/11 10:03 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Fourie
 
I removed escape characters from my gff output using:
 
cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape -ne 'print uri_unescape($_)' > new.gff
 
I found the first perl command was needed as often the % characters were themselves escaped (several times), resulting in strings such as %25252E.
 
I’m using GBrowse, and I wasn’t aware it supported escaped chars in gff files. That is useful to know, I need to upgrade!
 
Cheers
Anar
 
 

From: maker-devel-bounces@... [[hidden email]] On Behalf Of Carson Holt
Sent: Wednesday, 30 March 2011 4:03 a.m.
To: Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:
Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

-------------------------------------------------------------------------
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to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.


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maker-devel@...
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Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.


 


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Re: Problem with % characters in maker file names (MWAS)

Carson Hinton Holt
Re: [maker-devel] Problem with % characters in maker file names (MWAS) Are you using MWAS or MAKER?  And if it’s MWAS, do you have a local installation?

Thanks,
Carson


On 3/29/11 10:11 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Carson
 
Version 2.07. Apologies for not letting you know in the first place.
 
Cheers
Anar
 

From: Carson Holt [[hidden email]]
Sent: Wednesday, 30 March 2011 5:07 p.m.
To: Khan, Anar; Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Which MAKER version are you using?  This may be important as I may need to debug.

--Carson


On 3/29/11 10:03 PM, "Khan, Anar" <Anar.Khan@...> wrote:
Hi Fourie
 
I removed escape characters from my gff output using:
 
cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape -ne 'print uri_unescape($_)' > new.gff
 
I found the first perl command was needed as often the % characters were themselves escaped (several times), resulting in strings such as %25252E.
 
I’m using GBrowse, and I wasn’t aware it supported escaped chars in gff files. That is useful to know, I need to upgrade!
 
Cheers
Anar
 
 

From: maker-devel-bounces@... [[hidden email]] On Behalf Of Carson Holt
Sent: Wednesday, 30 March 2011 4:03 a.m.
To: Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:
Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

-------------------------------------------------------------------------
This message and attachments are subject to a disclaimer. Please refer
to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.


_______________________________________________
maker-devel mailing list
maker-devel@...
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


 



Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.






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Re: Problem with % characters in maker file names (MWAS)

Fourie Joubert
Hi Carson

Thanks for the reply.

I think we met briefly at PAG in January.

I am running Maker 2-10 locally using MWAS.

An example of an error from the apache log (this was with JBROWSE):

ERROR: The GFF3 file
'/srv/www/htdocs/maker/data/jobs/44/44.maker.output//44_datastore/74/CD/NODE_6128_length_4333_cov_195.390030/NODE_6128_length_4333_cov_195.390030.gff'
does not exist, referer: http://ix.bi.up.ac.za/cgi-bin/maker/maker.cgi

Listing from the dir:

ix:/usr/local/maker/MWAS # ls
/srv/www/htdocs/maker/data/jobs/44/44.maker.output//44_datastore/74/CD/NODE_6128_length_4333_cov_195.390030/
NODE_6128_length_4333_cov_195%2E390030.gff
NODE_6128_length_4333_cov_195%2E390030.maker.augustus_masked.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.augustus_masked.transcripts.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.non_overlapping_ab_initio.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.non_overlapping_ab_initio.transcripts.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.snap_masked.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.snap_masked.transcripts.fasta
run.log
theVoid.NODE_6128_length_4333_cov_195.390030


So there seems to be a discrepancy between the %2E vs the _

Thanks and kindest regards!

Fourie




Carson Holt wrote:

> Are you using MWAS or MAKER? And if it’s MWAS, do you have a local
> installation?
>
> Thanks,
> Carson
>
>
> On 3/29/11 10:11 PM, "Khan, Anar" <[hidden email]> wrote:
>
>     Hi Carson
>
>     Version 2.07. Apologies for not letting you know in the first place.
>
>     Cheers
>     Anar
>
>
>     *From:* Carson Holt [mailto:[hidden email]]
>     *Sent:* Wednesday, 30 March 2011 5:07 p.m.
>     *To:* Khan, Anar; Fourie Joubert; [hidden email]
>     *Subject:* Re: [maker-devel] Problem with % characters in maker
>     file names (MWAS)
>
>     Which MAKER version are you using? This may be important as I may
>     need to debug.
>
>     --Carson
>
>
>     On 3/29/11 10:03 PM, "Khan, Anar" <[hidden email]> wrote:
>     Hi Fourie
>
>     I removed escape characters from my gff output using:
>
>     cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape
>     -ne 'print uri_unescape($_)' > new.gff
>
>     I found the first perl command was needed as often the %
>     characters were themselves escaped (several times), resulting in
>     strings such as %25252E.
>
>     I’m using GBrowse, and I wasn’t aware it supported escaped chars
>     in gff files. That is useful to know, I need to upgrade!
>
>     Cheers
>     Anar
>
>
>
>     *From:* [hidden email]
>     [mailto:[hidden email]] *On Behalf Of *Carson
>     Holt
>     *Sent:* Wednesday, 30 March 2011 4:03 a.m.
>     *To:* Fourie Joubert; [hidden email]
>     *Subject:* Re: [maker-devel] Problem with % characters in maker
>     file names (MWAS)
>
>     Just a few questions. Are you using MWAS online copy or are you
>     using a local installation, as I do not see any result files for
>     MWAS online matching the name given (
>     NODE_31_length_3346_cov_180%2E462341.gff ). If you are using a
>     local copy, what version of MAKER are you using?
>
>     Also GBrowse (most current version) and Jbrowse support % symbols
>     in congtig IDs and file names because they are the suggested
>     method to escape certain characters in contig IDs (there is also a
>     list of characters that are required to be escaped using the %
>     symbol - also know as URI escape - in the GFF3 specification).
>     SOBA has a known issue with % characters in the file name though.
>     There is a fix for that in the online version of MWAS, so if you
>     are using the online version could you give me the job number debug?
>
>     Thanks,
>     Carson
>
>
>     On 3/29/11 3:14 AM, "Fourie Joubert" <[hidden email]> wrote:
>     Hi
>
>     In my maker output, I am getting % signs instead of . in my maker file
>     names, eg. NODE_31_length_3346_cov_180%2E462341.gff.
>
>     This is then breaking the downstream scripts for MWAS viewing and
>     annotation.
>
>     Does anyone know how to fix this?
>
>     Any help would be sincerely appreciated.
>
>     Kindest regards!
>
>     Fourie
>
>
>
>     --
>     --------------
>     Prof Fourie Joubert
>     Associate Professor
>     Bioinformatics and Computational Biology Unit
>     Department of Biochemistry
>     University of Pretoria
>     [hidden email]
>     http://www.bi.up.ac.za
>     Tel. +27-12-420-5802
>     Fax. +27-12-420-5800
>
>     -------------------------------------------------------------------------
>     This message and attachments are subject to a disclaimer. Please refer
>     to www.it.up.ac.za/documentation/governance/disclaimer/ for full
>     details.
>
>
>     _______________________________________________
>     maker-devel mailing list
>     [hidden email]
>     http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>     ------------------------------------------------------------------------
>
>
>     *Attention: *The information contained in this message and/or
>     attachments from AgResearch Limited is intended only for the
>     persons or entities to which it is addressed and may contain
>     confidential and/or privileged material. Any review,
>     retransmission, dissemination or other use of, or taking of any
>     action in reliance upon, this information by persons or entities
>     other than the intended recipients is prohibited by AgResearch
>     Limited. If you have received this message in error, please notify
>     the sender immediately.
>
>     ------------------------------------------------------------------------
>
>
>
>


--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
[hidden email]
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.


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Re: Problem with % characters in maker file names (MWAS)

Khan, Anar
In reply to this post by Carson Hinton Holt
Re: [maker-devel] Problem with % characters in maker file names (MWAS)

MAKER

 

Cheers

Anar

 

From: Carson Holt [mailto:[hidden email]]
Sent: Wednesday, 30 March 2011 5:13 p.m.
To: Khan, Anar; Fourie Joubert; [hidden email]
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

 

Are you using MWAS or MAKER?  And if it’s MWAS, do you have a local installation?

Thanks,
Carson


On 3/29/11 10:11 PM, "Khan, Anar" <Anar.Khan@...> wrote:

Hi Carson
 
Version 2.07. Apologies for not letting you know in the first place.
 
Cheers
Anar
 

From: Carson Holt [[hidden email]]
Sent: Wednesday, 30 March 2011 5:07 p.m.
To: Khan, Anar; Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Which MAKER version are you using?  This may be important as I may need to debug.

--Carson


On 3/29/11 10:03 PM, "Khan, Anar" <Anar.Khan@...> wrote:
Hi Fourie
 
I removed escape characters from my gff output using:
 
cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape -ne 'print uri_unescape($_)' > new.gff
 
I found the first perl command was needed as often the % characters were themselves escaped (several times), resulting in strings such as %25252E.
 
I’m using GBrowse, and I wasn’t aware it supported escaped chars in gff files. That is useful to know, I need to upgrade!
 
Cheers
Anar
 
 

From: maker-devel-bounces@... [[hidden email]] On Behalf Of Carson Holt
Sent: Wednesday, 30 March 2011 4:03 a.m.
To: Fourie Joubert; maker-devel@...
Subject: Re: [maker-devel] Problem with % characters in maker file names (MWAS)

Just a few questions.  Are you using MWAS online copy or are you using a local installation, as I do not see any result files for MWAS online matching the name given ( NODE_31_length_3346_cov_180%2E462341.gff ).  If you are using a local copy, what version of MAKER are you using?

Also GBrowse (most current version) and Jbrowse support % symbols in congtig IDs and file names because they are the suggested method to escape certain characters in contig IDs (there is also a list of characters that are required to be escaped using the % symbol - also know as URI escape - in the GFF3 specification).  SOBA has a known issue with % characters in the file name though.  There is a fix for that in the online version of MWAS, so if you are using the online version could you give me the job number debug?

Thanks,
Carson


On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:
Hi

In my maker output, I am getting % signs instead of . in my maker file
names, eg. NODE_31_length_3346_cov_180%2E462341.gff.

This is then breaking the downstream scripts for MWAS viewing and
annotation.

Does anyone know how to fix this?

Any help would be sincerely appreciated.

Kindest regards!

Fourie



--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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Re: Problem with % characters in maker file names (MWAS)

Carson Hinton Holt
In reply to this post by Fourie Joubert
Re: [maker-devel] Problem with % characters in maker file names (MWAS) FYI.  A new update of MAKER (version 2.11) with a newer version of MWAS is available at http://www.yandell-lab.org
Problems you were experiencing before should be fixed in this version.

--Carson


On 3/30/11 4:10 AM, "Fourie Joubert" <fourie.joubert@...> wrote:

Hi Carson

Thanks for the reply.

I think we met briefly at PAG in January.

I am running Maker 2-10 locally using MWAS.

An example of an error from the apache log (this was with JBROWSE):

ERROR: The GFF3 file
'/srv/www/htdocs/maker/data/jobs/44/44.maker.output//44_datastore/74/CD/NODE_6128_length_4333_cov_195.390030/NODE_6128_length_4333_cov_195.390030.gff'
does not exist, referer: http://ix.bi.up.ac.za/cgi-bin/maker/maker.cgi

Listing from the dir:

ix:/usr/local/maker/MWAS # ls
/srv/www/htdocs/maker/data/jobs/44/44.maker.output//44_datastore/74/CD/NODE_6128_length_4333_cov_195.390030/
NODE_6128_length_4333_cov_195%2E390030.gff
NODE_6128_length_4333_cov_195%2E390030.maker.augustus_masked.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.augustus_masked.transcripts.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.non_overlapping_ab_initio.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.non_overlapping_ab_initio.transcripts.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.snap_masked.proteins.fasta
NODE_6128_length_4333_cov_195%2E390030.maker.snap_masked.transcripts.fasta
run.log
theVoid.NODE_6128_length_4333_cov_195.390030


So there seems to be a discrepancy between the %2E vs the _

Thanks and kindest regards!

Fourie




Carson Holt wrote:
> Are you using MWAS or MAKER? And if it’s MWAS, do you have a local
> installation?
>
> Thanks,
> Carson
>
>
> On 3/29/11 10:11 PM, "Khan, Anar" <Anar.Khan@...> wrote:
>
>     Hi Carson
>
>     Version 2.07. Apologies for not letting you know in the first place.
>
>     Cheers
>     Anar
>
>
>     *From:* Carson Holt [[hidden email]]
>     *Sent:* Wednesday, 30 March 2011 5:07 p.m.
>     *To:* Khan, Anar; Fourie Joubert; maker-devel@...
>     *Subject:* Re: [maker-devel] Problem with % characters in maker
>     file names (MWAS)
>
>     Which MAKER version are you using? This may be important as I may
>     need to debug.
>
>     --Carson
>
>
>     On 3/29/11 10:03 PM, "Khan, Anar" <Anar.Khan@...> wrote:
>     Hi Fourie
>
>     I removed escape characters from my gff output using:
>
>     cat original.gff | perl -pe 's/%(25)+/%/g' | perl -MURI::Escape
>     -ne 'print uri_unescape($_)' > new.gff
>
>     I found the first perl command was needed as often the %
>     characters were themselves escaped (several times), resulting in
>     strings such as %25252E.
>
>     I’m using GBrowse, and I wasn’t aware it supported escaped chars
>     in gff files. That is useful to know, I need to upgrade!
>
>     Cheers
>     Anar
>
>
>
>     *From:* maker-devel-bounces@...
>     [[hidden email]] *On Behalf Of *Carson
>     Holt
>     *Sent:* Wednesday, 30 March 2011 4:03 a.m.
>     *To:* Fourie Joubert; maker-devel@...
>     *Subject:* Re: [maker-devel] Problem with % characters in maker
>     file names (MWAS)
>
>     Just a few questions. Are you using MWAS online copy or are you
>     using a local installation, as I do not see any result files for
>     MWAS online matching the name given (
>     NODE_31_length_3346_cov_180%2E462341.gff ). If you are using a
>     local copy, what version of MAKER are you using?
>
>     Also GBrowse (most current version) and Jbrowse support % symbols
>     in congtig IDs and file names because they are the suggested
>     method to escape certain characters in contig IDs (there is also a
>     list of characters that are required to be escaped using the %
>     symbol - also know as URI escape - in the GFF3 specification).
>     SOBA has a known issue with % characters in the file name though.
>     There is a fix for that in the online version of MWAS, so if you
>     are using the online version could you give me the job number debug?
>
>     Thanks,
>     Carson
>
>
>     On 3/29/11 3:14 AM, "Fourie Joubert" <fourie.joubert@...> wrote:
>     Hi
>
>     In my maker output, I am getting % signs instead of . in my maker file
>     names, eg. NODE_31_length_3346_cov_180%2E462341.gff.
>
>     This is then breaking the downstream scripts for MWAS viewing and
>     annotation.
>
>     Does anyone know how to fix this?
>
>     Any help would be sincerely appreciated.
>
>     Kindest regards!
>
>     Fourie
>
>
>
>     --
>     --------------
>     Prof Fourie Joubert
>     Associate Professor
>     Bioinformatics and Computational Biology Unit
>     Department of Biochemistry
>     University of Pretoria
>     fourie.joubert@...
>     http://www.bi.up.ac.za
>     Tel. +27-12-420-5802
>     Fax. +27-12-420-5800
>
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--
--------------
Prof Fourie Joubert
Associate Professor
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert@...
http://www.bi.up.ac.za
Tel. +27-12-420-5802
Fax. +27-12-420-5800

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