Commit 667b2b36 authored by Vidjil Team's avatar Vidjil Team
Browse files

Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil into rbx.vidjil.org

parents 37b5b723 653828b6
......@@ -20,9 +20,9 @@ present in the =.vidjil= file.
** =.vidjil= file -- one sample
This is a kind a minimal =.vidjil= file, describing clones in one sample.
This is a minimal =.vidjil= file, describing clones in one sample.
The segmentation is here =TRGV5*01 5/CC/0 TRGJ1*02=.
Note that other elments could be added by some program (such as =tag= or =clusters=).
Note that other elements could be added by some program (such as =tag= or =clusters=).
#+BEGIN_SRC js
{
......@@ -63,8 +63,11 @@ Note that other elments could be added by some program (such as =tag= or =cluste
** =.vidjil= file -- several samples
This a =.vidjil= file obtaining by mergin with =fuse.py= two =.vidjil= files corresponding to two samples.
This a =.vidjil= file obtained by merging with =fuse.py= two =.vidjil= files corresponding to two samples.
Clones that have a same =id= are gathered.
It is the responsability of the program generating the initial =.vidjil= files to choose these =id= to
do a correct gathering ('windows' is used by Vidjil, 'clone sequence' is used by EC-NGS/Brno pipeline,
and 'IMGT clonotype (AA) or (nt)' could also be used by some programs).
#+BEGIN_SRC js
{
......
......@@ -94,6 +94,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
## execute la commande vidjil
print "===Vidjil output==="
print cmd
db.commit()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
p.wait()
print p.stdout.read()
......@@ -129,6 +130,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
print "===fuse output==="
print cmd
db.commit()
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
p.wait()
print p.stdout.read()
......
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