Hi all, Please correct me if I'm wrong. I believe that all blast tables (blast result files in table format) are read into artemis as read-only, hence uneditable.
If you wish to edit those files, you will have to translate the blast table into a genbank/embl format before reading it into artemis. Cheers, -- yealing -- On Fri, May 14, 2010 at 2:31 PM, Henrik Lantz <henrik.la...@mikrob.slu.se>wrote: > Once again, big thanks goes out to Yealing and Alex. I am learning perl now > and will have those names extracted soon. > > One more question: > I am using Artemis on MacOSX Snow Leopard. When I read the blasthits into > Artemis, they are read only. Pressing "e" opens the edit window, but I can't > do anyhting with them. I can edit the contigs just fine, but not the blast > results. I took the contig file and blast file to a friends computer and > loaded it into his Artemis, and we had the same problem. He had never had > that problem with his own files. I have checked that I have read/write > permission on all files and the application itself. I have refrained from > asking here, as I though it was a MacOSX problem and not an Artemis problem, > but now I am not so sure. The problem is there even when I transfer the > files to another computer and seems associated with the blast result file > itself. Any setting in Artemis I am missing? > > Anyone know what might be causing my problems? > /Henrik > ________________________________________ > Från: artemis-users-boun...@sanger.ac.uk [ > artemis-users-boun...@sanger.ac.uk] för Bossers, Alex [ > alex.boss...@wur.nl] > Skickat: den 11 maj 2010 20:58 > Till: artemis-users@sanger.ac.uk > Ämne: Re: [Artemis-users] Multiple contigs and Blastall-results > > Henrik, > yealing's second option is also how I do it. If you have local blast its > not that bad..... > Alex > > > ________________________________ > > Van: artemis-users-boun...@sanger.ac.uk namens Yealing > Verzonden: di 11-5-2010 9:57 > Aan: Henrik Lantz > CC: artemis-users@sanger.ac.uk > Onderwerp: Re: [Artemis-users] Multiple contigs and Blastall-results > > > Hello Hendrik > > Not very sure about the blastall from blast+ package, but the blastall > package from NCBI blast package only outputs the gi/accession number for all > the blast hits in -m 8 (table) format. > > We have two ways to deal with this: > (1) run blastall and use -m 0, which defaults and output all the long > names, then use a script to parse the file into a table format. The parsing > can be really slow, we're using a bioperl script. this is how most of the > people in my lab does it. > (2) run blastall and use -m 8, which outputs the table format with short > names. Then, using a script, collect all gi/accession the significant blast > hits in a text file, use batch entrez to get the long names, then use > another script to replace the short names in the blast output file with the > long names. this is how i do it, again, my scripting is really bad so I > apologize for not sharing the script. > > All the best, > -- yealing -- > > > > On Tue, May 11, 2010 at 3:16 PM, Henrik Lantz <henrik.la...@mikrob.slu.se> > wrote: > > > Hi > > A big thank you to Tim, Yealing and Alex for all the help! > > Here is what I have done so far: I got help from a friend to write a > perl script that transforms the coordinates in the blast result file to > cumulative coordinates. This file can then be read as a feature in Artemis > just fine and maps perfectly onto the contigs. > > I also made some progress with the alternative discussed with Tim, > i.e., loading the contig file in Artemis and choosing "write all bases in > FASTA format" and then blasting this file. I managed to avoid the memory > related problems I had with blastall by using the blast+ package and the > legacyscript included there. The blast results can then be read as a feature > in Artemis without any problems. > > Of these two approaches I prefer the first one since this allows me > to keep the original contigs. > > The "problem" I am having now is getting the names of the proteins > into Artemis. The blast results only include the systematic name of the > blast hits, not the full names in understandable English. I am sure I am > just missing something very simple here, and will soon have a solution, but > if anyone has a suggestion I would also be very interested in hearing about > it. Still in the learning phase... > > Cheers, > Henrik > ________________________________________ > Från: artemis-users-boun...@sanger.ac.uk [ > artemis-users-boun...@sanger.ac.uk] för Yealing [ > yealingt+arte...@gmail.com <yealingt%2barte...@gmail.com> <mailto: > yealingt%2barte...@gmail.com <yealingt%252barte...@gmail.com>> ] > Skickat: den 29 april 2010 11:59 > Till: Tim Carver > Kopia: artemis-users@sanger.ac.uk; Henrik Lantz > Ämne: Re: [Artemis-users] Multiple contigs and Blastall-results > > > Hi > > I've had the same problem in the past. There sometimes are reasons > why we do not wish to join the contigs before we send for a blast, for > example once we join the contigs, the other contig informations are lost. > > I've been able to map the blast results correctly in Artemis, but > because I'm not a very good scripter, things might work or break using the > bash-awk script that I have. So I usually end up doing it sort of manually > for a lot of different people with different data sets. Here's how I do it: > > 1, we need a file containing <contig name> in the first column and > <contig length> in the second column. The make or break problem is that in > this file, the contig names must be arrange to the exact order as Artemis > puts them. > 2, from there, I use a script to generate a file with <contig name> > in the first column and <cummulative contigs length at start of contig> in > the second column. This can be done with excel too, if you're not familiar > with scripting. > 3, I then process the blastall result file, by modifying the start > and stop coordinates (adding the cummulative contigs length at start of > contig to the start and stop coordinate). > > After that, (usually if nothing bad happens) you will be able to > just load the blastall result file in Artemis. Best thing is we get to keep > all the details that we might or might not need. > > Cheers, > -- yealing -- > > > > On Thu, Apr 29, 2010 at 5:02 PM, Tim Carver <t...@sanger.ac.uk > <mailto:t...@sanger.ac.uk>> wrote: > Hi Henrik > > You have found the correct solution. It is just that the blast > reports > coordinates from the start of the sequence and so they need joining > up > before you do the blast. I am not sure why you get that memory > error. If you > have access to another machine you may want to try the blast there. > Alternatively you could possibly try a smaller number of contigs and > then > use the EMBOSS application 'union' to join them back up. > > Regards > Tim > > > > On 4/29/10 8:09 AM, "Henrik Lantz" <henrik.la...@mikrob.slu.se > <mailto:henrik.la...@mikrob.slu.se>> wrote: > > > I was hoping I could get some help with a newbie Artemis question. > Very new to > > all this. > > > > I have made a denovo assembly of a fungus using MIRA and 454-data > only. The > > resulting fasta file with around 4000 contigs loads into Artemis > fine. I can > > check all the contigs, find ORFs etc. The problem appears when I > want to > > import the results of a blastall search on the contig-datafile. > All > > annotations from the blastall results are lumped into the first > five contigs, > > with the overwhelming majority in the first contig. Obviously not > correct. I > > am using the -m 8 flag for the blastall search. Looking through > the resultfile > > from blastall in a text editor I can see that the blastall search > has worked, > > and there are many interesting hits, but I would like to visualize > the results > > on the contigs. > > > > I read through the mail archive and found a user with a similar > problem > > ( > http://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00463.html) > and > > it seems one solution might be to save the contigs as a long > continuous file > > in Artemis, and then use that in the Blastall search. But when I > try that I > > get an error message from blastall: > > > > blastall(33748) malloc: *** mmap(size=1048576) failed (error > code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > Bus error > > > > I am running on MacOSX Snow Leopard with 20 GBs of memory. > > Any help to get an inexperienced user started would be very much > appreciated! > > /Henrik > > _______________________________________________ > > Artemis-users mailing list > > > Artemis-users@sanger.ac.uk<mailto:Artemis-users@sanger.ac.uk> > > > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > > > _______________________________________________ > Artemis-users mailing list > > Artemis-users@sanger.ac.uk<mailto:Artemis-users@sanger.ac.uk> > > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > > > > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users >
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