find bam index files

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Ulf
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find bam index files

Ulf
Dear all

For each bam file in my history I can download the associated bai (bam
index) file.

I assume these files are stored somewhere under
/mount/galaxy/database/files/_metadata_files. Correct? Is there an easy
way to find the bam index file for a bam file, given only the internal
file name of the bam (e.g.
/mont/galaxy/database/files/089/dataset_89231.dat)?

I am asking because I would like to use the files_to_ftp tool to
automatically download bams together with their associated indices.

Thanks
Ulf

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Re: find bam index files

Nate Coraor (nate@bx.psu.edu)
Hi Ulf,

Unfortunately, metadata files are assigned an id that is unrelated to the dataset id. To link the files you'll need to use the database. The numerical id you see in the filename is the id of the dataset in the `dataset` table. From this you can go backward to the history_dataset_association (hda) table, where hda.dataset_id = dataset.id. Finally, from there, hda.id can be used to find the metadata_file via metadata_file.hda_id.

More succinctly:

dataset.id = history_dataset_association.dataset_id
history_dataset_association.id = metadata_file.hda_id

--nate

On Mon, Sep 15, 2014 at 6:34 AM, Ulf Schaefer <[hidden email]> wrote:
Dear all

For each bam file in my history I can download the associated bai (bam
index) file.

I assume these files are stored somewhere under
/mount/galaxy/database/files/_metadata_files. Correct? Is there an easy
way to find the bam index file for a bam file, given only the internal
file name of the bam (e.g.
/mont/galaxy/database/files/089/dataset_89231.dat)?

I am asking because I would like to use the files_to_ftp tool to
automatically download bams together with their associated indices.

Thanks
Ulf

**************************************************************************
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE
**************************************************************************

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