Hello Arek,
Re: column names Yes, I am adding an existing mysql table to BioMart (virtual mart). I understand that the BioMart names are different from the physical column names in mysql. My question is why is that and can the default be changed. If I have named my mysql columns as I wish them to be displayed (chrom, chromStart, chromEnd, Name, etc) BioMart will create different attribute names (chrom_101, chromStart_101, ect). I will then need to change the attribute names back to the names I wish to have displayed on the website and in the output files. This will prove cumbersome when I have many columns across many tables. Re: wildcard search Am I missing an option to escape plus or comma? Some of my data contains these characters and I have yet to find a work around that enables searching in these fields. Re: TSV Do we have a timeline for these features for BioMart 0.8? Thank you for your reply. Jayson From: Arek Kasprzyk [mailto:[email protected]] Sent: Tuesday, January 31, 2012 12:45 AM To: HARSHBARGER Jayson Cc: [email protected] Subject: Re: [BioMart Users] New User Questions Hi Jayson, Re: column names could you elaborate more on how do you 'connect to this table' and do subsequent search? If you are using a virtual mart (which is what i am assuming that you are doing) than the names of the columns that you quote there are not physical names, your table remains unchanged. Re: wildcard search the wildcard search is not implemented yet but is definitely planned Re: TSV All download formats that are supported in 07 are planned for 08 as well a On Thu, Jan 26, 2012 at 9:12 PM, HARSHBARGER Jayson <[email protected]> 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 _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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