Dear all
I'm using emboss 5.0 version, and come out of some problem.
I've got a alignment of 15 dna sequence, generated by clustalw (emma).
Thsi file is in fatsa format.
I want to calculate the distance between all of this using fdnadist:
$fdnadist -sequence globin-align.fasta -method f -outfile globin.fnadist
All run without problem, and my output file is like this:
15
CHIHBA1 0.000000 0.010022 0.264744 0.167372 0.315764 0.319542
0.394008 0.397425 0.500520 0.498700 0.696916 1.352558 1.223696
1.327388 1.223196
CHIHBB1 0.010022 0.000000 0.226115 0.171012 0.318000 0.321806
0.403662 0.403176 0.510729 0.508896 0.696097 1.333125 1.241254
../..
This file format seems to generate a issu with fneighbor, as it
complains about 0 rows found in place of 15:
$ fneighbor -datafile globin.fnadist -outfile globin.fneighbor
Phylogenies from distance matrix by N-J or UPGMA method
Error: Distances file found 0 rows, expected 15
Error: Unable to read distances file 'globin.fnadist'
Died: fneighbor terminated: Bad value for '-datafile' and no prompt
This problem disapeared if i format the distance file in one line for
each sequence. As i do all of this command as default, maybe i forgot a
option in the fdnadist ? This command is inside a flow of cemboss
commands, so it's complicated for me to edit by hand each distance file
to be "correct" for fneighbor..
Someone can explain me where i'm wrong?
Regards
--
-- Jérôme
Moi j'aime bien quand M. Blédurt raconte ses histoires de guerre,
une fois il m'a expliqué comment il a capturé, tout seul,
un sous-marin pleins d'ennemis.
(Histoires inédites du Petit Nicolas, Goscinny & Sempé)
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