Hello Patrice,
You can get the output you want (without the repeating lines) using the
Table
Browser ('Tables' from the top blue navigation bar). Configure it like so:
group: All Tables
database: uniProt
table: uniProt.description
identifiers (if you have a list, paste it here)
filter: [I pasted in your example into the acc field: O95751]
output format: selected fields from primary and related tables
Then press the "get output" button.
On the following page, check both fields in uniProt.description table
(acc &
val). Then, from the list below, choose hg18.kgXref table and press the "Allow
Selection from Checked Table" button. Then, in the hg18.kgXref table, check
the
following fields:
kgID
geneSymbol
Then press the "get output" button.
You will see output similar to this (for the protein you had in your
original
email):
#uniProt.description.acc uniProt.description.val hg18.kgXref.kgID
hg18.kgXref.geneSymbol
O95751 Protein LDOC1 (Leucine zipper protein down-regulated in cancer cells).
uc004fbj.1 LDOC1
If you want more (or less) information in your output, simply
(de)select the
appropriate fields.
For more details on using the Table Browser in this way, please see:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FilterSingle
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields
I hope this information is helpful to you. Please don't hesitate to
contact
the mail list again if you require further assistance.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Eydoux, Patrice wrote:
> Hello,
> Made some progress since my last email today.
> I can download some information, but only the first line, repeated a
> number of times, e.g.:
> uc004fbj.1 LDOC1 Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,Protein LDOC1 (Leucine zipper protein
> down-regulated in cancer cells).,
>
> I just go into the browser, get the tables (kgXref and
> uniProt.description fields). This output is generated in the same way
> for all genes, first line repeated - I suppose as many times as there
> are lines in the uniprot comment.
> Is this a bug?
>
> Thanks.
> Patrice.
>
> Patrice Eydoux.
> Clinical Professor, University of British Columbia
> Director, Cytogenetics
> Cytogenetics Laboratory, Laboratory Genetics
> Department of Pathology and Laboratory Medicine
> Children's and Women's Health Center of British Columbia
> 4480 Oak Street
> Vancouver, BC V6H 3N1
> Canada
>
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