Hi Jayson, I am glad that it all worked out for you. I can only apologize that our release candidate 0.8 rc6 is not yet as usable as we would like it to be. We'll try to improve on that in the coming months. Your feedback has been very useful
a On Mon, Feb 6, 2012 at 9:56 PM, HARSHBARGER Jayson <[email protected]>wrote: > Hello Arek,**** > > ** ** > > Thank you for your response. In recent days I’ve actually had much better > luck using the 0.7 mart-j tools (martbuilder and marteditor) to create the > mart then adding the registry to the 0.8 martconfigurator. The field names > are much easier to manage in the 0.7 mart-j gui and surprisingly wild cards > work in 0.8 when the mart is created in 0.7 mart-j tools. How is that > possible? Is this how others are using 0.8 RC as well?**** > > ** ** > > I’m still missing TSV and XLS output (in 0.8) and the ability to search > for strings that contain a comma (both 0.7 and 0.8). I’ll keep a lookout > for new 0.8 releases.**** > > ** ** > > Thanks again for taking the time to answer questions.**** > > ** ** > > Jayson**** > > ** ** > > *From:* Arek Kasprzyk [mailto:[email protected]] > *Sent:* Tuesday, February 07, 2012 1:20 AM > > *To:* HARSHBARGER Jayson > *Cc:* [email protected] > *Subject:* Re: [BioMart Users] New User Questions**** > > ** ** > > Hi Jayson,**** > > ** ** > > Re: column names**** > > I don't think these defaults can be changed right now but we can look if > we can change this behaviour in the future releases**** > > ** ** > > Re: wildcard search**** > > I don't think such option is available yet**** > > ** ** > > Re: TSV**** > > There is no timeline yet but we can prioritize them**** > > ** ** > > I am sorry i could not be more helpful but we can definitely look into > prioritizing all your requests because they all sound sensible**** > > (If anybody can give Jayson better suggestions please jump in and correct > me)**** > > ** ** > > a**** > > ** ** > > On Wed, Feb 1, 2012 at 7:49 PM, HARSHBARGER Jayson <[email protected]> > wrote:**** > > 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**** > > **** > > > > **** > > ** ** > > -- **** > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead**** > > ** ** > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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