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Use 'badly' formated coordinates in search field?

asked 2013-05-18 04:21:41 -0700

Hi there,

I am often copy and paste genomic positions from spreadsheets or directly from BED files. In both cases I don't have the nice format like

chr1:1-100

instead it is tab separated

chr1   1   100

To look up many region it would be extremely helpful if the browser would automatically recognise such format. Or did I miss some way to do this?

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answered 2013-05-30 10:57:00 -0700

Hi Pascal,

I wanted to let you know that we have released version 1.1.2 of GenomeBrowse. With the new version Sam was able to make the changes to the allowable input for the location bar.

In particular, it has been improved to be able to take whitespace delimited region descriptions like "chr7 123,456 444,555" as well as many other types. As you type, the normalized range that was detected is shown in the results drop down so you know exactly what range will be used when you hit Enter.

You can update to the newest version of GenomeBrowse by downloading the installer from our website.

Please let us know if you have any further requests.

Thanks, Jami...

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answered 2013-05-20 17:25:19 -0700

Sam Gardner gravatar image

I think I can make this work. I'm currently developing a solution, while addressing some other location bar parsing concerns.

The change should make it into the next GenomeBrowse release which is planned for later this week.

My tentative solution would allow the chromosome, start, and stop sections of the coordinate entry to be separated by any white space (such as the tabs in your example).

As long as all goes well, it should handle text formatted like any of the examples below:

1 10 20
1:10-20
1:10:20
1-10-20
1 10 - 20
1 : 10 - 20
chr1 10 20
chr1:10-20
chr1:10:20
chr1-10-20
chr1 - 10 20
chr1 - 10 : 20

This might mean that it can't handle something like:

chr 1 : 10 - 20

but, we will see.

Thanks for the suggested improvement.

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Asked: 2013-05-18 04:21:41 -0700

Seen: 95 times

Last updated: May 30 '13