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ORG.Asm
Commit bb49bc25 by Eric Coissac
Options

Small fixes

parent 0321904a
Showing with 63 additions and 29 deletions
doc/sphinx/source/commands/buildgraph.rst
......@@ -14,7 +14,6 @@ command prototype
.. code-block:: none
<<<<<<< HEAD
usage: oa buildgraph [-h] [--seeds seeds]
[--adapt5 adapt5] [--adapt3 adapt3]
[--coverage BUILDGRAPH:COVERAGE]
......@@ -28,16 +27,7 @@ command prototype
[--back ORGASM:BACK] [--snp]
index [output]
positional arguments
--------------------
.. option:: index
index root filename (produced by the oa index command)
.. option:: output
output prefix
.. include:: ../options/positional.txt
optional arguments
------------------
......
doc/sphinx/source/commands/fillgaps.rst
......@@ -2,3 +2,60 @@
The :program:`fillgaps` command
===============================
command prototype
-----------------
.. program:: oa fillgaps
usage: oa fillgaps [-h] [--minread BUILDGRAPH:MINREAD]
[--coverage BUILDGRAPH:COVERAGE]
[--minratio BUILDGRAPH:MINRATIO]
[--mincov BUILDGRAPH:MINCOV]
[--minoverlap BUILDGRAPH:MINOVERLAP]
[--smallbranches BUILDGRAPH:SMALLBRANCHES]
[--lowcomplexity] [--back ORGASM:BACK] [--snp]
[--adapt5 adapt5] [--adapt3 adapt3] [--seeds seeds]
index [output]
.. include:: ../options/positional.txt
optional arguments:
-h, --help show this help message and exit
--minread BUILDGRAPH:MINREAD
the minimum count of read to consider [default:
<estimated>]
--coverage BUILDGRAPH:COVERAGE
the expected sequencing coverage [default:
<estimated>]
--minratio BUILDGRAPH:MINRATIO
minimum ratio between occurrences of an extension and
the occurrences of the most frequent extension to keep
it. [default: <estimated>]
--mincov BUILDGRAPH:MINCOV
minimum occurrences of an extension to keep it.
[default: 1]
--minoverlap BUILDGRAPH:MINOVERLAP
minimum length of the overlap between the sequence and
reads to participate in the extension. [default:
<estimated>]
--smallbranches BUILDGRAPH:SMALLBRANCHES
maximum length of the branches to cut during the
cleaning process [default: <estimated>]
--lowcomplexity Use also low complexity probes
--back ORGASM:BACK the number of bases taken at the end of contigs to
jump with pared-ends [default: <estimated>]
--snp desactivate the SNP clearing mode
--adapt5 adapt5 adapter sequences used to filter reads beginning by
such sequences; either a fasta file containing adapter
sequences or internal set of adapter sequences among
['adapt5ILLUMINA'] [default: adapt5ILLUMINA]
--adapt3 adapt3 adapter sequences used to filter reads ending by such
sequences; either a fasta file containing adapter
sequences or internal set of adapter sequences among
['adapt3ILLUMINA'] [default: adapt3ILLUMINA]
--seeds seeds protein seeds; either a file containing seeds proteic
sequences or internal set of seeds among
['nucrRNAAHypogastrura', 'nucrRNAArabidopsis',
'protChloroArabidopsis', 'protMitoCapra',
'protMitoMachaon']
doc/sphinx/source/commands/index.rst
......@@ -59,23 +59,13 @@ 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.
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
their 3' end to fit the good length. After the trimming 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
+++++++++++++++++++++++++
......@@ -222,11 +212,8 @@ 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
......
python/orgasm/command/fillgaps.py
......@@ -97,7 +97,7 @@ def addOptions(parser):
help='adapter sequences used to filter reads beginning by such sequences'
'; either a fasta file containing '
'adapter sequences or internal set of adapter sequences '
'among %s' % (str(filter(lambda s: s.startswith('adapt5'),dir(orgasm.samples))),) +' [default: %(default)s]' )
'among %s' % (list(filter(lambda s: s.startswith('adapt5'),dir(orgasm.samples))),) +' [default: %(default)s]' )
parser.add_argument('--adapt3', dest ='orgasm:adapt3',
metavar='adapt3',
......@@ -107,7 +107,7 @@ def addOptions(parser):
help='adapter sequences used to filter reads ending by such sequences'
'; either a fasta file containing '
'adapter sequences or internal set of adapter sequences '
'among %s' % (str(filter(lambda s: s.startswith('adapt3'),dir(orgasm.samples))),) +' [default: %(default)s]' )
'among %s' % (list(filter(lambda s: s.startswith('adapt3'),dir(orgasm.samples))),) +' [default: %(default)s]' )
parser.add_argument('--seeds', dest ='fillgaps:seeds',
metavar='seeds',
......@@ -115,7 +115,7 @@ def addOptions(parser):
type=str,
help='protein seeds; either a file containing '
'seeds proteic sequences or internal set of seeds '
'among %s' % str(filter(lambda s: s.startswith('prot') or
'among %s' % list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples))) )
......
python/orgasm/version.py
......@@ -2,4 +2,4 @@ major = 0
minor = 0
serial= 'alpha'
version = "%2d.%02d %s" % (major,minor,serial)
version = "%2d.%02d.%s" % (major,minor,serial)
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