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  • Sep 13 14:54
    satta commented #920
  • Sep 07 17:57
    satta commented #919
  • Aug 22 02:23
    Maika0519 opened #920
  • Aug 19 17:58
    APigg0070 closed #914
  • Aug 19 17:58
    APigg0070 commented #914
  • Aug 14 14:37
    aperreault opened #919
  • Aug 11 07:44
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    longzhangnation commented #908
  • Jul 24 14:30
    gordon closed #918
  • Jul 24 14:29
    gordon commented #918
  • Jul 23 14:53
    WTarabidopsis edited #918
  • Jul 23 14:52
    WTarabidopsis opened #918
  • Jul 09 05:21
    satta commented #849
  • Jul 08 21:15
    lassancejm commented #849
  • Jun 26 09:07
    gordon closed #916
  • Jun 26 09:07
    gordon commented #916
  • Jun 26 09:07

    gordon on master

    use safer buffer sizes update macOS build for Travis Merge pull request #917 from sa… (compare)

  • Jun 26 09:07
    gordon closed #917
  • Jun 26 09:07
    gordon closed #915
  • Jun 26 09:07
    gordon commented #917
Sascha Steinbiss
@satta
ok so be it :)
will there be a new PR addressing the assertion? otherwise I will wrap up the release tonight
Dirk Willrodt
@Garonenur
I don't have anything for the release - and for that assertion, it will have to be discussed how to handle such cases.
Sascha Steinbiss
@satta
the point is, do we want to release a version that is shown to trigger a failed assertion?
or is condenseq still 'unofficial'?
Dirk Willrodt
@Garonenur
nope it is in the master, so it is official - it will only get more official if i finish my thesis and maybe spin of a publication of it.
so, I will have a look if I can change that behaviour to a warnig.
Sascha Steinbiss
@satta
but you think the assertion is tolerable?
Dirk Willrodt
@Garonenur
no. because assertions should indicate programming errors - and this is more an: you should choose other parameters or the data is to small to be compressed error - so input.
Sascha Steinbiss
@satta
ok. that means we should delay the release until this is fixed?
Dirk Willrodt
@Garonenur
just changed it to a warning.
pr is on its way
Sascha Steinbiss
@satta
ok :)
Sascha Steinbiss
@satta
thanks!
Sascha Steinbiss
@satta
shouldn't it be if (condenseq->ldb_nelems == 0)?
and 'chosen' ;)
Dirk Willrodt
@Garonenur
and THATS why we use PullRequests :stuck_out_tongue:
changed :)
Sascha Steinbiss
@satta
merci
Dirk Willrodt
@Garonenur
would it help/change anything if I merge the typo PR first and the version bumb 2nd?
Sascha Steinbiss
@satta
I'd merge the version bump first
Sascha Steinbiss
@satta
thanks
Dirk Willrodt
@Garonenur
doi for releases? read: http://dx.doi.org/10.1038/nbt.3240
Sascha Steinbiss
@satta
Well, we could have Zenodo track our releases
good idea, as long as people still cite the GenomeTools paper ;)
Dirk Willrodt
@Garonenur
anyone with a CentOS? I did ask for more information on #732, but I have no Idea what may be the reason and my compiler is a complete version higher.
@satta to the rescue :smile:
Sascha Steinbiss
@satta
I can only recommend to use Vagrant for such requests...
there are nice boxes available for CentOS (funny that this is so popular out there)
Dirk Willrodt
@Garonenur
for virtual boxes? OK - next time I'll have a look
Sascha Steinbiss
@satta
it gives you almost seamless development environments for lots of different distros
Dirk Willrodt
@Garonenur
uh - funny thing: GTDIR/obj/ should have the same tree as src? because make sbgt fails on my machine, it searches for .o-files in obj/src/match and those are located at obj/
Sascha Steinbiss
@satta
hmm?
they should be in obj/src/...
IIRC to generate the destination for the .o the Makefile just prefixes the path to the .c file with obj/
Dirk Willrodt
@Garonenur
that's how I thought it works - bit I did compile with amalgamation before I ran make sbgt - there might be something fishy there.
Sascha Steinbiss
@satta
hmm
could be... I don't compile as amalgamation in regular development
Dirk Willrodt
@Garonenur
jup - without amalgamation=yes the sbgt target works. maybe some of the .o-files don't get build at all with amalgamation?
I use amalagamation regularely to check for error there.
well - I just have to remember it does not work with sbgt
Sascha Steinbiss
@satta
well, the point of the amalgamation is to build less object files ;)
you only get a large .o for most of the .c files and IIRC only the tools get compiled individually
Dirk Willrodt
@Garonenur
there is a PR (#749) where a cmp call failed and returned 1 but as it seems all cmp-calls are called with -s to make them silent. this does not help if we want to try to debug these. anyone got a problem with removing those -s flags? cmp has no output anyway if there is no error.
I am talking about travis here.
Sascha Steinbiss
@satta
OK with me...
Abhijit Sanyal
@abhijit_synl_twitter
Hi I am new to gitter. I am looking to asking a question on the "gt cds" command. Is this the correct place?
Sascha Steinbiss
@satta
yep. we're not here 24/7 but it's quite likely you get an answer ;)
Abhijit Sanyal
@abhijit_synl_twitter
Oh ok. Thanks. Here is the question.

I would like to add the CDS feature to my Gff3 file, that has exons in it. I saw that genometools can do this for you.

"gt cds -startcodon -finalstopcodon -seqfile foo.fasta -o foo.gff3 [GFF3-FILE]"

1) I am looking for the CDS to be the longest ORF with an ATG start codon per mRNA. Do the gff3 coordinates in the output reflect that?

2) It is possible that a single mRNA will give rise to two CDS of equal size but with different start and stops. In case of such conflicts, what does gt cds do?

3) I did not see a flag for specifying the genetic code. Is this by default "standard vertebrate"?