On Fri, 27 Feb 2004 09:31:41 -0500, Phillip San Miguel wrote: > Phillip San Miguel wrote: >> I wrote script to convert cross_match output into gff for use with >> ACT. Seems to work fine for ACT version 2 [beta] but the stable >> release of ACT version 2 does not display the gff information, nor is >> the gff listed under "Entries" after loading using "File:Read and Entry". >> I presume something is non-standard in the gff I'm generating but I >> can't see what it would be. Here are the first 4 lines of a gff file >> that won't load: >> >> 5MCconcat fuzznuc RT5E 59441 59461 21.000 + . >> Sequence "5MCconcat.1" >> >> The fields are all tab delimited, although my mail client converted >> the tabs to spaces. >> >> Any suggestions on what might be wrong? >> [..]
> I have more information. Using ACT version 2 on a Solarix box, I have > the same problem. But I can read the exception being thrown when a file > containing only the line: > 5MCconcat fuzznuc RT5E 59441 59461 21.000 + . > Sequence "5MCconcat.1" > is read using the menu "File:Read an Entry". > The exception is: > java.lang.NumberFormatException: For input string: "RT5E" > at > java.lang.NumberFormatException.forInputString(NumberFormatException.java:48) > at java.lang.Integer.parseInt(Integer.java:426) > at java.lang.Integer.valueOf(Integer.java:532) > at Hi. ACT was getting confused by the "5" at the start of the "5MCconcat". The quick fix is to remove the 5 or to put a letter in front of it. I've fixed the bug in the development version. The development release is here for UNIX, GNU/Linux and Macs: ftp://localftp.sanger.ac.uk/pub/pathogens/software/act/builds/act_compiled_latest.tar.gz And here for Windows: ftp://localftp.sanger.ac.uk/pub/pathogens/software/act/builds/act_compiled_latest.jar Artemis had the same bug and should be fixed too. Kim.
