[galaxy-dev] Is there a way to turn of the pretty display for VCF files
Hi,Is there a way to turn of the special pretty print version for VCF files since it is not working correctly?I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is...Where is this pretty printer and how do I turn it off?ThanksThon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look. Do you see any javascript errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the Show All option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
What Galaxy revision are you running? Given the new information I'd guess it's an erroneous console.log that was removed in bb7f51fb545d. On May 29, 2012, at 6:49 PM, Anthonius deBoer wrote: Interestingly when I open the Developer Tools in Chrome, my VCF file is actually loading...As soon as I close the developer tool, it stops loading the the page again (and it resumes loading when I re-open the Developer tools...) Really funky... Here's theVCF file...On my computer it only shows up to line 5 112175639 rs121913332 C T 3206.18 PASS AC=3;AF=0.0174;AN=172;COSMIC;DB;DP=15405;Dels=0.00;EFF=DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0502371|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0504915|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0507379|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0512211|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0514164|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0257430|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0457016|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0508376|exon_5_112173250_112181753),TRANSCRIPT(MODIFIERCTC-554D6.1|processed_transcript|NON_CODING|ENST0520401|),UTR_3_PRIME(MODIFIERAPC|protein_coding|CODING|ENST0508624|);GC=45.64;HRun=0;MQ0=0;OND=0.01;set=variant5-variant49-variant10 On May 29, 2012, at 03:39 PM, Dannon Baker dannonba...@me.com wrote: Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look. Do you see any javascript errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the Show All option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ CalledVariants-Select.zip ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Is there a way to turn of the pretty display for VCF files
I'm running the latest galaxy central verson that I pulled down today...On May 29, 2012, at 03:59 PM, Dannon Baker dannonba...@me.com wrote:What Galaxy revision are you running? Given the new information I'd guess it's an erroneous console.log that was removed in bb7f51fb545d. On May 29, 2012, at 6:49 PM, Anthonius deBoer wrote: Interestingly when I open the Developer Tools in Chrome, my VCF file is actually loading...As soon as I close the developer tool, it stops loading the the page again (and it resumes loading when I re-open the Developer tools...)Really funky...Here's theVCF file...On my computer it only shows up to line5 112175639 rs121913332 C T 3206.18 PASS AC=3;AF=0.0174;AN=172;COSMIC;DB;DP=15405;Dels=0.00;EFF=DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0502371|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0504915|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0507379|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0512211|),DOWNSTREAM(MODIFIERAPC|protein_coding|CODING|ENST0514164|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0257430|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0457016|exon_5_112173250_112181936),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R1450*|APC|protein_coding|CODING|ENST0508376|exon_5_112173250_112181753),TRANSCRIPT(MODIFIERCTC-554D6.1|processed_transcript|NON_CODING|ENST0520401|),UTR_3_PRIME(MODIFIERAPC|protein_coding|CODING|ENST0508624|);GC=45.64;HRun=0;MQ0=0;_OND_=0.01;set=variant5-variant49-variant10 On May 29, 2012, at 03:39 PM, Dannon Baker dannonba...@me.com wrote:Hmm. Chrome on OSX looks good to me, please do send over the VCF file and I can take a look.Do you see any _javascript_ errors in the browser console? On May 29, 2012, at 6:31 PM, Anthonius deBoer wrote: Hi Dannon, I could share the VCF file, but I think it is dependent on the browser you use... I used the same file on FireFox on Linux and there it loaded the complete VCF file (Still don't see the "Show All" option) but on my chrome on Windows 7 it only shows the first 5 lines or so of the genotypes and then nothing...The stuff that IS shown looks correctly formatted etc. it just does not show the rest of the file which it normally does Thon On May 29, 2012, at 03:01 PM, Dannon Baker dannonba...@me.com wrote: There isn't a universe toggle for the tabular display. The VCF datatype inherits the pretty printing from the base tabular datatype, and if you'd like to disable it one way would be to override the display_data method in VCF using the raw Data display_data method. That said, I'd rather just fix your problem. Looking at a few VCF files I have, they look fine. Can you share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: Hi,Is there a way to turn of the special pretty print version for VCF files since it is not working correctly?I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is...Where is this pretty printer and how do I turn it off?ThanksThon___Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at:http://lists.bx.psu.edu/ CalledVariants-Select.zip ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
