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.. _process_sff:
.. index:: process_sff.py
*process_sff.py* -- Convert sff to FASTA and QUAL files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script converts a directory of sff files into FASTA, QUAL and flowgram files.
**Usage:** :file:`process_sff.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_dir
Input directory of sff files
**[OPTIONAL]**
-f, `-`-make_flowgram
Generate a flowgram file. [default: False]
-t, `-`-convert_to_FLX
Convert Titanium reads to FLX length. [default: False]
`-`-use_sfftools
Use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation
-o, `-`-output_dir
Input directory of sff files [default: same as input dir]
**Output:**
This script results in FASTA and QUAL formatted files.
**Simple example:**
Convert all the sffs in directory "sffs/" to fasta and qual.
::
process_sff.py -i sffs/
**Flowgram example:**
Convert all the sffs in directory "sffs/" to fasta and qual, along with a flowgram file.
::
process_sff.py -i sffs/ -f
**Output example:**
Convert all the sffs in directory "sffs/" to fasta and qual, along with a flowgram file and write them to another directory.
::
process_sff.py -i sffs/ -f -o output_dir
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