Commit 3f9737cb by Eric Coissac

fusion des branches 1.0 ets 1.0-beta

parent 55895410
Sequence record editing options
-------------------------------
.. cmdoption:: --rank
.. cmdoption:: --seq-rank
Adds a new attribute named ``seq_rank`` to the sequence record indicating
its entry number in the sequence file.
......
......@@ -127,7 +127,7 @@ on a set of reference sequence records, and according to specified parameters.
No multi match of a primer on the same sequence record.
.. cmdoption:: -U <TEXT>
.. cmdoption:: -R <TEXT>
Defines the reference sequence identifier of the sequence records in the database.
......@@ -227,7 +227,7 @@ Examples
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 -r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (in the ``ecoPCR format``,
Launches a search for barcodes and corresponding primers on mydatabase (in the ``ecoPCR format``,
see :py:mod:`obiconvert`), with a maximum of two mismatches for each primer. The minimum and
maximum barcode lengths (excluding primers) are 30 bp and 120 bp, respectively. The search is
restricted to the Vertebrates, excluding Bacteria and Hominidae (7742, 2, and 9604 corresponds to
......
......@@ -7,32 +7,60 @@
The taxonomic rank at which frequencies have to be computed.
Possible values are:
- class
- class
- family
- forma
- genus
- infraclass
- infraorder
- kingdom
- order
- parvorder
- phylum
- species (default)
- species group
- species subgroup
- subclass
- subfamily
- subgenus
- subkingdom
- suborder
- subphylum
- subspecies
- subtribe
- superclass
- superfamily
- superkingdom
- superorder
- superphylum
- tribe
- varietas
\ No newline at end of file
.. automodule:: ecotag
:py:mod:`ecotag` specific options
------------------------------------
---------------------------------
.. cmdoption:: -R <FILENAME>, --ref-database=<FILENAME>
......
.. automodule:: ngsfilter
:py:mod:`ngsfilter` specific options
--------------------------------------
------------------------------------
.. cmdoption:: -t, --tag-list
......
.. automodule:: obiclean
:py:mod:`obiclean` specific options
--------------------------------------
-----------------------------------
.. cmdoption:: -d <INTEGER>, --distance=<INTEGER>
......
......@@ -2,7 +2,7 @@
:py:mod:`obicount` specific options
------------------------------------
-----------------------------------
.. cmdoption:: -a, --all
......
......@@ -2,7 +2,7 @@
:py:mod:`obidistribute` specific options
------------------------------------
----------------------------------------
.. cmdoption:: -n <INT>, --number=<INT>
......@@ -13,8 +13,8 @@
Prefix added at each file name.
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
.. automodule:: obijoinpairedend
:py:mod:`obijoinpairedend` specific options
--------------------------------------------
-------------------------------------------
.. cmdoption:: -r <FILENAME>, --reverse-reads=<FILENAME>
......
.. automodule:: obisort
:py:mod:`obisort` specific options
------------------------------------
----------------------------------
.. cmdoption:: -k <KEY>, --key=<KEY>
......
......@@ -2,7 +2,7 @@
:py:mod:`obisplit` specific options
----------------------------------
-----------------------------------
.. cmdoption:: -p <PREFIX FILENAME>, --prefix=<PREFIX FILENAME>
......
.. automodule:: obistat
:py:mod:`obistat` specific options
------------------------------------
----------------------------------
.. cmdoption:: -c <KEY>, --category-attribute=<KEY>
......
.. automodule:: obitail
:py:mod:`obitail` specific options
----------------------------------
.. cmdoption:: -n <INTEGER>, --sequence-count <INTEGER>
Number of sequence records to be selected (default value : 10).
Number of sequence records to be selected (default value : 10).
.. include:: ../optionsSet/inputformat.txt
......
......@@ -3,7 +3,7 @@
:py:mod:`obiuniq` specific options
------------------------------------
----------------------------------
.. cmdoption:: -m <KEY>, --merge=<KEY>
......
.. automodule:: oligotag
:py:mod:`oligotag` specific options
------------------------------------
-----------------------------------
.. cmdoption:: -L <filename>, --oligo-list=<filename>
......@@ -127,7 +127,7 @@
Reference
---------
E. Coissac. Oligotag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13Ð31, 2012.
E. Coissac. Oligotag: a program for designing sets of tags for next-generation sequencing of multiplexed samples. Methods Mol Biol, 888:13-31, 2012.
......@@ -6,6 +6,7 @@ Utilities
:maxdepth: 2
scripts/oligotag
scripts/obidistribute
scripts/obisort
scripts/obitaxonomy
\ No newline at end of file
......@@ -5,9 +5,8 @@
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the
``-d``option) and an ecoPCR output (ideally computing on the specified ecoPCR database).
The :py:mod:`ecotaxstat` command requires two parameters : an ecoPCR formatted database (specified with the ``-d``option)
and an ecoPCR output (ideally computing on the specified ecoPCR database).
The command outputs for every ranks the coverage of the ecoPCR output, that is the fraction of taxids that
have a sequence in the database and have also have a sequence in the ecoPCR output file.
......
#!/usr/local/bin/python
'''
:py:mod:`ngsfilter` : Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
========================================================================================================================
===================================================================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
"""
:py:mod:`obicomplement`: Reverse-complements sequences
======================================================
:py:mod:`obicomplement`: Reverses complements sequences
=======================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
:py:mod:`obigrep`: Filters sequence file
=========================================
========================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
:py:mod:`obihead`: Extracts the first sequence records
=======================================================
======================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
:py:mod:`obijoinpairedend`: Joins paired-end reads
:py:mod:`obijoinpairedend`: joins paired end reads
==================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
:py:mod:`obisample`: Randomly resamples sequence records
=========================================================
========================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
#!/usr/local/bin/python
'''
:py:mod:`obisplit`: Splits a sequence file in a set of subfiles
================================================================
===============================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
......@@ -97,6 +97,8 @@ def mean(values,options):
def variance(v):
if len(v)==1:
return 0
s = reduce(lambda x,y:(x[0]+y,x[1]+y**2),v,(0.,0.))
return s[1]/(len(v)-1) - s[0]**2/len(v)/(len(v)-1)
......
#!/usr/local/bin/python
'''
:py:mod:`obitail`: Extracts the last sequence records
======================================================
=====================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
......@@ -6,7 +6,7 @@ def addSequenceEditTagOptions(optionManager):
group = optionManager.add_option_group('Sequences and attributes editing options')
group.add_option('--rank',
group.add_option('--seq-rank',
action="store_true", dest='addrank',
default=False,
help="add a rank attribute to the sequence "
......
......@@ -47,7 +47,7 @@ def weigthedSample(events,size):
cumul[i]=s
i+=1
c = randrange(xrange(s),size)
c = [randrange(0,s) for x in xrange(size)]
c.sort()
i = 0
......
#!/usr/local/bin/python
'''
:py:mod:`oligotag`: Designs a set of oligonucleotides with specified properties
=========================================================
===============================================================================
.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
......
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