Commit a5ba8e6f by Eric Coissac

Fixes #6, by clarifying the help of the --seeds option

parent 750a6bd4
......@@ -9,7 +9,17 @@
- ``protChloroArabidopsis``
- ``protMitoCapra``
- ``protMitoMachaon``
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis seqindex
A set of seed sequences must be or nucleic or proteic. For initiating
assembling with both nucleic and proteic sequences you must use at least two
``--seeds`` options one for each class of sequences.
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis --seeds rDNAChloro.fasta seqindex
\ No newline at end of file
......@@ -130,8 +130,8 @@ def addOptions(parser):
action='append',
default=[],
type=str,
help='protein seeds; either a fasta file containing '
'seeds proteic sequences or internal set of seeds '
help='protein or nucleic seeds; either a fasta file containing '
'seed sequences or the name of one of the internal set of seeds '
'among %s' % str(list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples)))))
......
......@@ -38,14 +38,6 @@ def addOptions(parser):
help='the number of bases taken at the end of '
'contigs to jump with pared-ends [default: <estimated>]')
parser.add_argument('--seeds', dest ='compact:seeds',
metavar='seeds',
default=None,
type=str,
help='protein seeds; either a file containing '
'seeds proteic sequences or internal set of seeds '
'among %s' % str(list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples))) ))
def run(config):
......
......@@ -113,10 +113,10 @@ def addOptions(parser):
metavar='seeds',
default=None,
type=str,
help='protein seeds; either a file containing '
'seeds proteic sequences or internal set of seeds '
'among %s' % list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples))) )
help='protein or nucleic seeds; either a fasta file containing '
'seed sequences or the name of one of the internal set of seeds '
'among %s' % str(list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples))) ))
def estimateMinRead(index,minoverlap,coverage):
......
......@@ -36,8 +36,8 @@ def addOptions(parser):
action='append',
default=[],
type=str,
help='protein seeds; either a fasta file containing '
'seeds proteic sequences or internal set of seeds '
help='protein or nucleic seeds; either a fasta file containing '
'seed sequences or the name of one of the internal set of seeds '
'among %s' % str(list(filter(lambda s: s.startswith('prot') or
s.startswith('nuc'),dir(orgasm.samples)))))
......
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