Options to specify input format
-------------------------------

.. program:: obitools


Restrict the analysis to a sub-part of the input file
.....................................................

.. cmdoption::  --skip <N>

      The N first sequence records of the file are discarded from the analysis and 
      not reported to the output file
      

.. cmdoption::  --only <N>

      Only the N next sequence records of the file are analyzed. The following sequences
      in the file are neither analyzed, neither reported to the output file.
      This option can be used conjointly with the `--skip` option.
      


Sequence annotated format
.........................

.. cmdoption::  --genbank 

      Input file is in :doc:`genbank <../genbank>` format.
      
.. cmdoption::    --embl     
 
      Input file is in :doc:`embl <../embl>` format.
      
:doc:`fasta <../fasta>` related format
.......................................
      
      
.. cmdoption::    --fasta               
 
      Input file is in :doc:`fasta  <../fasta>` format (including
      OBITools :doc:`fasta  <../fasta>` extensions).

:doc:`fastq <../fastq>` related format
.......................................

.. cmdoption::      --sanger              

       Input file is in Sanger :doc:`fastq <../fastq>` format (standard
       :doc:`fastq <../fastq>` used by HiSeq/MiSeq sequencers).

.. cmdoption::      --solexa              

       Input file is in :doc:`fastq <../fastq>` format produced by
       Solexa (Ga IIx) sequencers.

ecoPCR related format
.....................

.. cmdoption::      --ecopcr              

       Input file is in :doc:`ecoPCR <../formats>` format.

.. cmdoption::      --ecopcrdb              

       Input is an :doc:`ecoPCR <../formats>` database.

Specifying the sequence type
............................

.. cmdoption::    --nuc       

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

      Input file contains protein sequences.
      
 