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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I am glad I was able to make a small contribution </span><span style='font-size:11.0pt;font-family:Wingdings;color:#1F497D'>J</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>BTW... when will be have a git repository to make this process a little bit more effective. I am sure lots of people would love to help and fix bugs </span><span style='font-size:11.0pt;font-family:Wingdings;color:#1F497D'>J</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Cheers<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>Duarte<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 08 November 2012 15:57<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] Bugs in gtf2vep.pl script<o:p></o:p></span></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Hi Duarte,<o:p></o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Thanks for the suggestions.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>The @ARGV thing slipped through the net! I've fixed that on the CVS tree, but using a slightly different change to the one you suggest.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>There is nothing in GetOptions that requires you specify --dir or --cache_region_size; GetOptions will only fail if you provide an invalid option, for example providing a string to --db_version instead of an integer.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>cache_region_size is not mentioned at all because it is not an option you should be changing unless you really really know what you are doing - it is there mainly to assist me in development.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Thanks again<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Will McLaren<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Ensembl Variation<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><o:p> </o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'>On 8 November 2012 15:24, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.co.uk" target="_blank">Duarte.Molha@ogt.co.uk</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Dear Developers<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>I had a play around with the new gtf2vep script and came across a few bugs and incomplete help.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>I have made some improvements on the help usage information and corrected the bugs on line 29 , 30 and 34<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Briefly, the first issue I encountered is that I believe the “cache_region_size” and the “dir” arguments are suppose to be optional since they are assigned default values on lines 46 and 49<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>They are set to be required so the script does not pass the GetOptions step if you do not provide them. <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>Also the “cache_region_size” wasn’t even mentioned in the usage information so I added it.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>In line 34 the if statement:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>if(defined($config->{help}) || !@ARGV) <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>would always fail because on a correctly input command line, after the GetOptions step the @ARGV variable should be empty. So the expression for a valid syntax would always return true and the script would not continue. <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>I corrected it to:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>if(defined($config->{help}) || @ARGV) <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>I also took the liberty to indicate in the help session what arguments a really required and what arguments are optional.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'>I hope you agree with the changes.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Best regards</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#888888'> </span><span style='color:#888888'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#888888'>Duarte Molha</span><span style='color:#888888'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt'><span style='color:#888888'> <o:p></o:p></span></p></div></div><p class=MsoNormal style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt'><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></div></body></html>