Commit 296f7ab6 by Eric Coissac

Merge branch 'orgasm-python3' of

git@git.metabarcoding.org:org-asm/org-asm.git into orgasm-python3

Conflicts:
	doc/sphinx/source/algorithms.rst
	doc/sphinx/source/commands/buildgraph.rst
	doc/sphinx/source/commands/index.rst
	doc/sphinx/source/index.rst
parents a5fc5964 dd4aea99
......@@ -14,6 +14,7 @@ command prototype
.. code-block:: none
<<<<<<< HEAD
usage: oa buildgraph [-h] [--seeds seeds]
[--adapt5 adapt5] [--adapt3 adapt3]
[--coverage BUILDGRAPH:COVERAGE]
......@@ -200,3 +201,4 @@ Gap filling option
jump with pared-ends [default: <estimated>]
.. _`bwa`: http://sourceforge.net/projects/bio-bwa/
.. _`yed`: https://www.yworks.com/en/products/yfiles/yed/
......@@ -59,6 +59,7 @@ the limit are discarded, read longer than the limit are trimmed on their
The user defined read length
++++++++++++++++++++++++++++
<<<<<<< HEAD
Using the option :ref:`--length <index.length>`, users can specify the read
length to index. If the specified read length is even, it is decreased by one.
......@@ -66,6 +67,15 @@ As for the default strategy, read pairs containing a read shorter than the
specified limit are discarded, read longuer than the limit are trimmed on
their 3' end to fit the good length. After read pairs containing a
:ref:`IUPAC <iupac_code>` ambiguity code are also discarded.
=======
Using the option :ref:`--length <opt_idx_length>`, users can specify the read
length to index. If the specified read length is even, it is decreased by one.
As for the default strategy, reads shorter than the specified limit are
discarded, read longuer than the limit are trimmed on their 3' end to fit the
good length. After the trimming reads containing :ref:`IUPAC <iupac_code>`
ambiguity code are also discarded.
>>>>>>> branch 'orgasm-python3' of git@git.metabarcoding.org:org-asm/org-asm.git
The estimated read length
+++++++++++++++++++++++++
......@@ -212,8 +222,11 @@ Limit for the indexation
from the length of the first read of the forward file or through the
:option:`--estimate-length #.##` option.
<<<<<<< HEAD
.. _index.estimate-length:
=======
>>>>>>> branch 'orgasm-python3' of git@git.metabarcoding.org:org-asm/org-asm.git
.. option:: --estimate-length #.##
`#.##` ranging between 0.0 and 1.0, indicates which fraction
......
......@@ -29,6 +29,8 @@ default_config = {
'outputfilename' : None,
'back' : None,
'seeds' : None,
'seedmincov' : 1,
'kup' : None,
'progress' : True
}
......
......@@ -82,6 +82,7 @@ def getSeeds(index,config,extension=".omx"):
# looks if the internal blast was already run
output = config['orgasm']['outputfilename']
logger=config['orgasm']['logger']
kup=-1 if config['orgasm']['kup'] is None else config['orgasm']['kup']
probes = getProbes(config)
filename=output+extension
......@@ -95,7 +96,8 @@ def getSeeds(index,config,extension=".omx"):
logger.info(" -> probe set: %s" % probename)
seeds = index.lookForSeeds(p,
mincov=config['buildgraph']['mincov'],
mincov=config['orgasm']['seedmincov'],
kup=kup,
logger=logger)
probes[probename][1]=seeds
......
......@@ -103,7 +103,7 @@ def addOptions(parser):
parser.add_argument('--snp', dest='buildgraph:snp',
action='store_true',
default=False,
help='desactivate the SNP clearing mode')
help='activate the SNP clearing mode')
parser.add_argument('--adapt5', dest ='orgasm:adapt5',
metavar='adapt5',
......@@ -135,6 +135,13 @@ def addOptions(parser):
'among %s' % str(list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples)))))
parser.add_argument('--kup', dest='orgasm:kup',
type=int,
action='store',
default=None,
help='The word size used to identify the seed reads '
'[default: protein=4, DNA=12]')
def estimateMinRead(index,minoverlap,coverage):
MINREAD=10
......
......@@ -46,15 +46,17 @@ def addOptions(parser):
parser.add_argument(dest='index:forward', metavar='forward',
help='Filename of the forward reads')
parser.add_argument(dest='index:reverse', metavar='reverse',
nargs='?',
default=None,
parser.add_argument(dest='index:reverse',
metavar='reverse',
nargs='?',
default=None,
help='Filename of the reverse reads' )
parser.add_argument('--single', dest='index:single',
action='store_true',
default=None,
parser.add_argument('--single',
dest='index:single',
action='store_true',
default=None,
help='Single read mode')
parser.add_argument('--mate-pairs', dest='index:mate',
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment