[Gmod-ajax] ucsc-to-json.pl -- some types not working

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[Gmod-ajax] ucsc-to-json.pl -- some types not working

pparsons
Hi, I'm using the ucsc-to-json.pl script to convert some dumps from the UCSC database. I am noticing that many of the file types that I need to convert (e.g., rmsk, psl, chain) are giving errors. For example:

"Cannot convert chainSelf track; this script is not capable of handling chain tracks at bin/ucsc-to-json.pl line 200."

"Cannot convert rmsk track; this script is not capable of handling rmsk tracks at bin/uscs-to-json.pl line 200."

It seems that this is not so much a "bug" as it is simply a lack of a feature? Is this correct? The only information I could find is from this thread: http://gmod.827538.n3.nabble.com/Gmod-ajax-UCSC-to-Jbrowse-adaptor-td1679401.html#a1724418 which is from 2010. It suggests that these types are not supported.

If this is the case, is there another way to do this? I'm currently downloading these tracks to my server from this location: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

Thanks.

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Re: ucsc-to-json.pl -- some types not working

Robert Buels-2
Indeed, this is the lack of features.

The ucsc-to-json coverter is kind of old and creaky, and could use some
attention.  Do you have the Perl chops to make some improvements to it?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/25/2013 04:25 PM, Paul Parsons wrote:

> Hi, I'm using the ucsc-to-json.pl <http://ucsc-to-json.pl> script to
> convert some dumps from the UCSC database. I am noticing that many of
> the file types that I need to convert (e.g., rmsk, psl, chain) are
> giving errors. For example:
>
> "Cannot convert chainSelf track; this script is not capable of handling
> chain tracks at bin/ucsc-to-json.pl <http://ucsc-to-json.pl> line 200."
>
> "Cannot convert rmsk track; this script is not capable of handling rmsk
> tracks at bin/uscs-to-json.pl <http://uscs-to-json.pl> line 200."
>
> It seems that this is not so much a "bug" as it is simply a lack of a
> feature? Is this correct? The only information I could find is from this
> thread:
> http://gmod.827538.n3.nabble.com/Gmod-ajax-UCSC-to-Jbrowse-adaptor-td1679401.html#a1724418
> which is from 2010. It suggests that these types are not supported.
>
> If this is the case, is there another way to do this? I'm currently
> downloading these tracks to my server from this location:
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
>
> Thanks.
>
>
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> Shape the Mobile Experience: Free Subscription
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> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up now.
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Re: ucsc-to-json.pl -- some types not working

pparsons
Unfortunately I don't think I can help with that--I've never even worked with perl before.

In the meantime, there is a way around the problem I was having. Instead of downloading the database dump files, BED tracks can be downloaded from here: http://genome.ucsc.edu/cgi-bin/hgTables?command=start. Just make sure to select "BED" as the output format. Then the bin/flatfile-to-json.pl script can be used to load the tracks into JBrowse.


On Mon, Nov 25, 2013 at 7:06 PM, Robert Buels <[hidden email]> wrote:
Indeed, this is the lack of features.

The ucsc-to-json coverter is kind of old and creaky, and could use some attention.  Do you have the Perl chops to make some improvements to it?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 11/25/2013 04:25 PM, Paul Parsons wrote:
Hi, I'm using the ucsc-to-json.pl <http://ucsc-to-json.pl> script to

convert some dumps from the UCSC database. I am noticing that many of
the file types that I need to convert (e.g., rmsk, psl, chain) are
giving errors. For example:

"Cannot convert chainSelf track; this script is not capable of handling
chain tracks at bin/ucsc-to-json.pl <http://ucsc-to-json.pl> line 200."


"Cannot convert rmsk track; this script is not capable of handling rmsk
tracks at bin/uscs-to-json.pl <http://uscs-to-json.pl> line 200."


It seems that this is not so much a "bug" as it is simply a lack of a
feature? Is this correct? The only information I could find is from this
thread:
http://gmod.827538.n3.nabble.com/Gmod-ajax-UCSC-to-Jbrowse-adaptor-td1679401.html#a1724418
which is from 2010. It suggests that these types are not supported.

If this is the case, is there another way to do this? I'm currently
downloading these tracks to my server from this location:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

Thanks.


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