Commands
########

.. _clean_multi_ssake.sh:

**clean_multi_ssake.sh**
   Run to remove intermediate files generated by multi_ssake.py from the current
   directory. 

   *WARNING*: Removes all files matching \*.fasta and \*paired.fa from the current
   directory!
   

.. _compare_genomes.py:

**compare_genomes.py**
   Finds differences between genomes based on the input multi-aligned fasta file
   
.. program-output:: python compare_genomes_test.py --help
   :returncode: 2
   :cwd: /../bin/   


.. _fastq_to_fasta.py:

**fastq_to_fasta.py**
    Converts fastq files to fasta files

.. program-output:: python fastq_to_fasta.py --help
   :returncode: 2
   :cwd: /../bin/
   

.. _find_contig_deletions.py:

**find_contig_deletions.py**
   Find contigs in an assembly that have sections deleted and provide an option to
   insert the missing pieces
    
.. program-output:: python fastq_to_fasta.py --help
   :returncode: 2
   :cwd: /../bin/


.. gff2gtf_simple.py:

**gff2gtf_simple.py**
    Attempts to convert GFF files to GTF files.

.. program-output:: python gff2gtf_simple.py --help
   :returncode: 2
   :cwd: /../bin/ 


.. _maf_net.py:

**maf_net.py**
   Stitch together alignment block from a MAF file, forming an alignment net.

.. program-output:: python maf_net.py --help
   :returncode: 2
   :cwd: /../bin/


.. _makePairedOutput2EQUALfiles_vamp.pl:

**makePairedOutput2EQUALfiles_vamp.pl**
   See :ref:`makePairedOutput2UNEQUALfiles_vamp.pl <makePairedOutput2UNEQUALfiles_vamp.pl>`::

      Usage: makePairedOutput2EQUALfiles_vamp.pl <fasta file 1> <fasta file 2> <library insert size> 
             --- ** Both files must have the same number of records & arranged in the same order
   
.. index:: makePairedOutput2UNEQUALfiles_vamp.pl

.. _makePairedOutput2UNEQUALfiles_vamp.pl: 

**makePairedOutput2UNEQUALfiles_vamp.pl**
   Modified versions of scripts provided by SSAKE_.  They are used to prepare two
   separate paired end fastq files for use by SSAKE_.  The modifications made were
   to accommodate new
   `Illumina style sequence identifiers <http://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers>`_
   introduced with CASAVA 1.8.::
   
      Usage: makePairedOutput2UNEQUALfiles_vamp.pl <fasta file 1> <fasta file 2> <library insert size> 
             --- files could have different # of records & arranged in different order but template ids must match

.. _multi_ssake.py:

**multi_ssake.py**
   Run TQSFastq preprocessing and SSAKE_ using various combinations of parameters and combine the results.

.. program-output:: python multi_ssake.py --help
   :returncode: 2
   :cwd: /../bin/

**translate_cds.py**
    Takes GFF and Fasta input and translates spliced CDS regions from DNA to Amino Acid sequence, reporting errors.

.. program-output:: python translate_cds.py --help
   :returncode: 2
   :cwd: /../bin/


.. _SSAKE: http://www.bcgsc.ca/platform/bioinfo/software/ssake