[GMOD-devel] Tracking errors.

[Marco A. V. C. <mav...@bi...>]

Hi All,

Gbrowse is picking on me, when I think that one mapping will be alright, 
well...
So let's go,

First, if the gbrowse knows that my sequence is in one chromosome region 
and not displaying it, probably I have one error on my configuration 
file? if not where is the possible error?

History of the entries:
The entries were put on the database using Mummi's 
process_ncbi_human.pl, so that's is not the problem.
My entries were maded with a megablast output so I got GFFs lines like:

<GFF>
Chr13   ORESTES.MEGABLAST       alignment       71191038        71191231
         5e-58   +       .       Target
"Sequence:PM2-MT0009-180400-001-h01" 6 40
</GFF>

OBS: This time the numbers are outside of the quotes.

The conf file has:
[ORESTES]
feature       = alignment:ORESTES.MEGABLAST
feature_low   = alignment:ORESTES.MEGABLAST
glyph        = segments
bgcolor      = red
fgcolor      = black
height       = 10
max_score     = 100
connector     = solid
description   = 0
label         = 0
key           = ORESTES


Looking at MySQL for this particular entrie I have:

 From fgroup:
+--------+----------+---------------------------+
| gid    | gclass   | gname                     |
+--------+----------+---------------------------+
| 117364 | Sequence | PM2-MT0009-180400-001-h01 |
+--------+----------+---------------------------+

 From fdata:
+--------+-------+----------+----------+-------------+---------+--------+---------+--------+--------+---------------+--------------+
| fid    | fref  | fstart   | fstop    | fbin        | ftypeid | fscore 
| fstrand | fphase | gid    | ftarget_start | ftarget_stop |
+--------+-------+----------+----------+-------------+---------+--------+---------+--------+--------+---------------+--------------+
| 165070 | Chr13 | 71191101 | 71191410 | 1000.071191 |      13 |      0 
| -       |        | 117364 |            61 |          370 |
| 165071 | Chr13 | 71191432 | 71191466 | 1000.071191 |      13 |  3e-11 
| -       |        | 117364 |             6 |           40 |
+--------+-------+----------+----------+-------------+---------+--------+---------+--------+--------+---------------+--------------+

 From ftype:
+---------+-----------+-------------------+
| ftypeid | fmethod   | fsource           |
+---------+-----------+-------------------+
|      13 | alignment | ORESTES.MEGABLAST |
+---------+-----------+-------------------+


So what's is wrong this time? Any ideas?

Just on more thing, is possible to have key places where look for the 
error? Especially debug flags will help? Apache log?


If reach here you were very patient with me, thank you.
Marco.

-- 
Marco Aurélio Valtas Cunha
Laboratório de Bioinformática
Hemocentro de Ribeirão Preto
Tel 55 16 3963-9300 R: 9603
http://bit.fmrp.usp.br

"Prediction is very difficult, especially if it's about the future."
Niels Bohr