Hi,
We use GBrowse to open GFF files directly and observe a fuzzy thing:
While the header got the proper name of the requested file, the overview
display the name of another file (apparently the smallest file in the
gff directory) and the size of the feature is limited to the size of the
'overview feature'.
So I'm wondering how GBrowse behave while searching the requested file
in a directory containing multiple files.
How not to be limited to a size which is not the
feature-I-want-to-observe size ??
Anyone observed such a behaviour ?
Isabelle
Here is an exemple of gff and conf file.
The gff files are generated by a pipeline
##gff-version 3
ctg98_seb193822 triAnnotPipeline region 1 45440 . +
. iD=ctg98_seb193822
ctg98_seb193822 BLASTN_TREP_nr match_set 504 532 . +
0 iD=BLASTN_ctg98_seb1
93822_gnl|TREP|TREP238_match_set0001;Note=Db:TREP_nr!Align:8408!Significance:2e-07!Description:gnl|TREP|TREP
238_Retrotransposon%2C non-LTR%2C LINE%2C "Isabelle_AF326781-1"%3B
complete element%2C (6 bp TSD);Name=ctg98
_seb193822_gnl|TREP|TREP238
ctg98_seb193822 BLASTN_TREP_nr match_part 504 532 29 +
0 iD=BLASTN_ctg98_seb1
93822_gnl|TREP|TREP238_match_set0001_match_part0001;Parent=BLASTN_ctg98_seb193822_gnl|TREP|TREP238_match_set
0001;Note=HSP_length:29!Identity:100
ctg98_seb193822 BLASTN_TREP_nr region 504 532 . . .
Note=Merged hits
[GENERAL]
description = TriAnnot
db_adaptor = Bio::DB::GFF
db_args = -adaptor memory
-gff '/var/www/triannot/gbrowse'
plugins = AttributeHiliter
reference class = region
# Web site configuration info
#test
stylesheet = /gbrowse/urgi_gbrowse3.css
buttons = /gbrowse/images/buttons
tmpimages = /gbrowse/tmp
js = /gbrowse/js
link =AUTO
image widths = 450 640 800 1024
default width = 800
default features = region
# max and default segment sizes for detailed view
max segment = 500000
default segment = 10000
zoom levels = 100 200 1000 2000 5000 10000 20000 40000 70000 100000
200000
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = CR626926 CR626934
automatic classes = region
--
Isabelle Blanc-Lenfle
INRA URGI
523 place des terrasses de l'agora
91000 Evry - France
Tel : +33 1 60 87 37 59
Fax : +33 1 60 87 37 00
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