Hi Jayson,
RE: column names
I guess you are referring to the BED format header names being chrom,
chromStart, chromEnd which clearly does not match the biomart default
attribute names. However, to access the biomart data through API, you
use the internalName property of attributes and filters and NOT the
underlying column names of the table. This way, you can rename the
internalName to match the standard header names of BED format (chrom,
chromStart, chromEnd and so on).
HTH,
Syed
On 27/01/2012 02:12, HARSHBARGER Jayson wrote:
Hello Biomart users,
I’ve been testing BioMart 0.8 for my organization but running into some
difficulty. I hope you can guide me in the right direction. I’m new to
BioMart so please forgive me if my questions are mundane.
I’ve setup a single mysql table with the contents of a BED file (chrom,
chromStart, chromEnd, Name, etc). When I connect BioMart to this mysql table
the column names become chrom_101, chromStart_101, ect. This requires me to do
a lot of manual renaming across potentially hundreds of tables (or perhaps
eventually write a script to automate this). Is that typical and can it be
changed?
It appears that 0.8 does not support wildcard searches (‘ABC%’ in the name
field for example). Is that correct? Also related to searching some of my
names include commas and pluses (the text ‘ABC,+’ for example). Both the comma
and plus appear to prevent searching… in other words if I search for ‘ABC,+’ in
the name column I return no results even though I have a ‘ABC,+’ row in my
table. If there is a way to escape these characters I have not found it. This
is especially frustrating considering that I cannot do a wildcard search.
Last, is it true that at this time 0.8 only supports downloads as TSV? I
believe 0.7 included XLS. Is this still in progress?
Lastly, are these issues I’m having related to 0.8 being a release candidate?
Should I be using 0.7 instead. Thank you so much for your time.
Jayson
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