obitools options to specify input format
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.. program:: obitools

sequence annotated format
.........................

.. cmdoption::  --genbank 

      input file is in :doc:`genbank format <../genbank>`
      
.. cmdoption::    --embl     
 
      input file is in :doc:`embl format <../embl>`
      
fasta related format
....................
      
.. cmdoption::    --fna      
 
      input file is in fasta nucleic format produced by 454 sequencer
      pipeline

.. cmdoption::     --qual=WITHQUALFILE   
 
      Specify the name of a quality file produced by 454
      sequencer pipeline
      
.. cmdoption::    --fasta               
 
      input file is in fasta nucleic format (including
      obitools fasta extentions)

fastq related format
....................

.. cmdoption::      --sanger              

       input file is in sanger fastq nucleic format (standard
       fastq)

.. cmdoption::      --solexa              

       input file is in fastq nucleic format produced by
       solexa sequencer

.. cmdoption::      --illumina            

       input file is in fastq nucleic format produced by old
       solexa sequencer

specifying the sequence type
............................

.. cmdoption::    --nuc       

      input file contains nucleic sequences
      
.. cmdoption::    --prot      

      input file contains protein sequences
      
 