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Cleaning of the doc, more stuff...

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This commit is contained in:
Eric Coissac
2013-12-24 14:27:03 +00:00
parent 4fe1c167ef
commit 5537714c08
8 changed files with 37 additions and 20 deletions
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6
doc/sphinx/source/optionsSet/sequenceFilter.txt
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@ -73,7 +73,8 @@ Sequence record selection options
Keeps only the sequence records whose identifier is present in the Keeps only the sequence records whose identifier is present in the
``my_id_list.txt`` file. ``my_id_list.txt`` file.
.. cmdoption:: -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>, --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN> .. cmdoption:: -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>,
.. cmdoption:: --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN>
Regular expression pattern matched against the Regular expression pattern matched against the
:doc:`attributes of the sequence record <../fasta>`. the value of this attribute :doc:`attributes of the sequence record <../fasta>`. the value of this attribute
@ -120,7 +121,8 @@ Sequence record selection options
.. code-block:: bash .. code-block:: bash
> obigrep -p '(forward_error<2) and (reverse_error<2)' seq1.fasta > seq2.fasta > obigrep -p '(forward_error<2) and (reverse_error<2)' \
seq1.fasta > seq2.fasta
Keeps only the sequence records whose ``forward_error`` and ``reverse_error`` Keeps only the sequence records whose ``forward_error`` and ``reverse_error``
attributes have a value smaller than two. attributes have a value smaller than two.

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doc/sphinx/source/scripts/ecoPCR.rst
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@ -146,7 +146,8 @@ Examples
.. code-block:: bash .. code-block:: bash
> ecoPCR -d mydatabase -e 3 -l 50 -L 500 TCACAGACCTGTTATTGC TYTGTCTGSTTRATTSCG > mysequences.ecopcr > ecoPCR -d mydatabase -e 3 -l 50 -L 500 \
TCACAGACCTGTTATTGC TYTGTCTGSTTRATTSCG > mysequences.ecopcr
Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`), Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`),
with a maximum of three mismatches for each primer. The minimum and maximum amplified sequence with a maximum of three mismatches for each primer. The minimum and maximum amplified sequence
@ -161,7 +162,8 @@ Examples
.. code-block:: bash .. code-block:: bash
> ecoPCR -d mydatabase -e 2 -l 80 -L 120 -D 50 -r 7742 TTAGATACCCCACTATG#C# TAGAACAGGCTCCTCTA#G# > mysequences.ecopcr > ecoPCR -d mydatabase -e 2 -l 80 -L 120 -D 50 -r 7742 \
TTAGATACCCCACTATG#C# TAGAACAGGCTCCTCTA#G# > mysequences.ecopcr
Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`), Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`),
with a maximum of two mismatches for each primer, but with a perfect match on the last two nucleotides with a maximum of two mismatches for each primer, but with a perfect match on the last two nucleotides

6
doc/sphinx/source/scripts/ecoPrimers.rst
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@ -210,7 +210,8 @@ Examples
.. code-block:: bash .. code-block:: bash
> ecoPrimers -d mydatabase -e 3 -l 50 -L 800 -r 2759 -3 2 > mybarcodes.ecoprimers > ecoPrimers -d mydatabase -e 3 -l 50 \
-L 800 -r 2759 -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 three mismatches for each primer. The minimum and see :py:mod:`obiconvert`), with a maximum of three mismatches for each primer. The minimum and
@ -225,7 +226,8 @@ Examples
.. code-block:: bash .. code-block:: bash
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 -r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers > 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 see :py:mod:`obiconvert`), with a maximum of two mismatches for each primer. The minimum and

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doc/sphinx/source/scripts/obiconvert.rst
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@ -4,7 +4,8 @@
.. code-block:: bash .. code-block:: bash
> obiconvert --ecopcrdb --fasta-output 'my_ecopcr_database' > sequences.fasta > obiconvert --ecopcrdb --fasta-output \
'my_ecopcr_database' > sequences.fasta
Converts an ecopcr database in a sequence file in *extended OBITools fasta* format. Converts an ecopcr database in a sequence file in *extended OBITools fasta* format.

15
doc/sphinx/source/scripts/obitaxonomy.rst
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@ -15,7 +15,8 @@
.. code-block:: bash .. code-block:: bash
> obitaxonomy -d my_ecopcr_database -a 'Gentiana alpina':'species':21496 > obitaxonomy -d my_ecopcr_database \
-a 'Gentiana alpina':'species':21496
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose taxid is 21496. the taxon whose taxid is 21496.
@ -29,7 +30,8 @@
.. code-block:: bash .. code-block:: bash
> obitaxonomy -d my_ecopcr_database -m 1000000000 -a 'Gentiana alpina':'species':21496 > obitaxonomy -d my_ecopcr_database -m 1000000000 \
-a 'Gentiana alpina':'species':21496
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose taxid is 21496, with a taxid greater than or equal to 1000000000. the taxon whose taxid is 21496, with a taxid greater than or equal to 1000000000.
@ -75,7 +77,8 @@
.. code-block:: bash .. code-block:: bash
> obitaxonomy -d my_ecopcr_database -f 'Gentiana algida':10000832 > obitaxonomy -d my_ecopcr_database \
-f 'Gentiana algida':10000832
Adds the favorite scientific name *Gentiana algida* for the taxid 10000832 in the taxonomic database. Adds the favorite scientific name *Gentiana algida* for the taxid 10000832 in the taxonomic database.
@ -91,7 +94,8 @@
.. code-block:: bash .. code-block:: bash
> obitaxonomy -d my_ecopcr_database -k my_taxon_name_key -F my_sequences.fasta > obitaxonomy -d my_ecopcr_database \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
@ -120,7 +124,8 @@
.. code-block:: bash .. code-block:: bash
> obitaxonomy -d my_ecopcr_database -a 33090 -k my_taxon_name_key -F my_sequences.fasta > obitaxonomy -d my_ecopcr_database -a 33090 \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. If database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. If

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src/ecotag.py
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@ -24,7 +24,8 @@ for each taxid.
.. code-block:: bash .. code-block:: bash
> ecotag -d embl_r113 -R ReferenceDB.fasta --sort=count -m 0.95 -r seq.fasta > seq_tag.fasta > ecotag -d embl_r113 -R ReferenceDB.fasta \\
--sort=count -m 0.95 -r seq.fasta > seq_tag.fasta
The above command specifies that each sequence stored in ``seq.fasta`` The above command specifies that each sequence stored in ``seq.fasta``
is compared to those in the reference database called ``ReferenceDB.fasta`` is compared to those in the reference database called ``ReferenceDB.fasta``

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src/obiannotate.py
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@ -12,7 +12,7 @@ annotation attributes attached to sequence records.
Once such attributes are added, they can be used by the other OBITools commands for Once such attributes are added, they can be used by the other OBITools commands for
filtering purposes or for statistics computing. filtering purposes or for statistics computing.
*Example:* *Example 1:*
.. code-block:: bash .. code-block:: bash
@ -20,31 +20,35 @@ filtering purposes or for statistics computing.
The above command adds an attribute named *short* which has a boolean value indicating whether the sequence length is less than 100bp. The above command adds an attribute named *short* which has a boolean value indicating whether the sequence length is less than 100bp.
*Example:* *Example 2:*
.. code-block:: bash .. code-block:: bash
> obiannotate --rank seq1.fasta | obiannotate -C --set-identifier '"'FungA'_%05d" % seq_rank' > seq2.fasta > obiannotate --rank seq1.fasta | \\
obiannotate -C --set-identifier '"'FungA'_%05d" % seq_rank' \\
> seq2.fasta
The above command adds a new attribute whose value is the sequence record The above command adds a new attribute whose value is the sequence record
entry number in the file. Then it clears all the sequence record attributes entry number in the file. Then it clears all the sequence record attributes
and sets the identifier to a string beginning with *FungA_* followed by a and sets the identifier to a string beginning with *FungA_* followed by a
suffix with 5 digits containing the sequence entry number. suffix with 5 digits containing the sequence entry number.
*Example:* *Example 3:*
.. code-block:: bash .. code-block:: bash
> obiannotate -d my_ecopcr_database --with-taxon-at-rank=genus seq1.fasta > se2.fasta > obiannotate -d my_ecopcr_database \\
--with-taxon-at-rank=genus seq1.fasta > seq2.fasta
The above command adds taxonomic information at the *genus* rank to the The above command adds taxonomic information at the *genus* rank to the
sequence records. sequence records.
*Example:* *Example 4:*
.. code-block:: bash .. code-block:: bash
> obiannotate -S 'new_seq:str(sequence).replace("a","t")' seq1.fasta | obiannotate --set-sequence new_seq > seq2.fasta > obiannotate -S 'new_seq:str(sequence).replace("a","t")' \\
seq1.fasta | obiannotate --set-sequence new_seq > seq2.fasta
The overall aim of the above command is to edit the *sequence* object itself, The overall aim of the above command is to edit the *sequence* object itself,
by replacing all nucleotides *a* by nucleotides *t*. First, a new attribute by replacing all nucleotides *a* by nucleotides *t*. First, a new attribute