Re: [base] array design GTF import - not 9 columns
Thanks for the quick reply Nicklas, We'll strip out the comments for now and keep on testing. cheers, Bob On Mon, May 26, 2014 at 7:37 AM, Nicklas Nordborg nicklas.nordb...@med.lu.se wrote: Thanks for testing this. It feels like it was a long time ago this was implemented and we have not really started to use it yet. Anyway, you are correct that the problem is something deeper than the usual importer. To make GTF files parsable by the regular importers, there is a pre-parsing step that add headers and rewrites the attributes column (column 9) so that each attribute value is tab-separated instead of semicolon-separated. It is the pre-parser that complains if a line doesn't have at least 9 columns. I checked the code and found a TODO comment about implementing support for comments, but for some reason it has been overlooked. It should be easy enough to implement this, and I can probably fix this for the next (BASE 3.3) release. But for now, the importer will choke on anything that is not a Field line as described by http://www.ensembl.org/info/website/upload/gff.html /Nicklas On 2014-05-23 18:17, Bob MacCallum wrote: Hi all, [mods please delete the mail I sent from my gmail account, or add me with that account but with no delivery, thank] Just upgraded from 2-3 and now trying out the NGS feaures. Quick question about GTF import for array designs... When doing array design-import the importer is complaining: Error: A line must have at least 9 columns, at line: 1 stack trace below (using GTF reporter map importer (version 3.2.5-dev)) The same error came up when we first created the array design (because I checked the validate files box. I know the first line has fewer columns because it has some # commented lines so in the importer configuration I configured the Ignore field like this: ^#.* But still the same error... Even if I set Default error handling = skip it's the same. Seems to be something deeper than the usual tab delimited importer parser settings. I guess we should make a new GTF file with no comments but I just wanted to check if this was the intended behaviour? cheers, Bob -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] array design GTF import - not 9 columns
Thanks for testing this. It feels like it was a long time ago this was implemented and we have not really started to use it yet. Anyway, you are correct that the problem is something deeper than the usual importer. To make GTF files parsable by the regular importers, there is a pre-parsing step that add headers and rewrites the attributes column (column 9) so that each attribute value is tab-separated instead of semicolon-separated. It is the pre-parser that complains if a line doesn't have at least 9 columns. I checked the code and found a TODO comment about implementing support for comments, but for some reason it has been overlooked. It should be easy enough to implement this, and I can probably fix this for the next (BASE 3.3) release. But for now, the importer will choke on anything that is not a Field line as described by http://www.ensembl.org/info/website/upload/gff.html /Nicklas On 2014-05-23 18:17, Bob MacCallum wrote: Hi all, [mods please delete the mail I sent from my gmail account, or add me with that account but with no delivery, thank] Just upgraded from 2-3 and now trying out the NGS feaures. Quick question about GTF import for array designs... When doing array design-import the importer is complaining: Error: A line must have at least 9 columns, at line: 1 stack trace below (using GTF reporter map importer (version 3.2.5-dev)) The same error came up when we first created the array design (because I checked the validate files box. I know the first line has fewer columns because it has some # commented lines so in the importer configuration I configured the Ignore field like this: ^#.* But still the same error... Even if I set Default error handling = skip it's the same. Seems to be something deeper than the usual tab delimited importer parser settings. I guess we should make a new GTF file with no comments but I just wanted to check if this was the intended behaviour? cheers, Bob -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] array design GTF import - not 9 columns
Hi all, [mods please delete the mail I sent from my gmail account, or add me with that account but with no delivery, thank] Just upgraded from 2-3 and now trying out the NGS feaures. Quick question about GTF import for array designs... When doing array design-import the importer is complaining: Error: A line must have at least 9 columns, at line: 1 stack trace below (using GTF reporter map importer (version 3.2.5-dev)) The same error came up when we first created the array design (because I checked the validate files box. I know the first line has fewer columns because it has some # commented lines so in the importer configuration I configured the Ignore field like this: ^#.* But still the same error... Even if I set Default error handling = skip it's the same. Seems to be something deeper than the usual tab delimited importer parser settings. I guess we should make a new GTF file with no comments but I just wanted to check if this was the intended behaviour? cheers, Bob -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
