Following command line options are allowed:
- -A
- Restrict detection/verification to alignment formats (conflict with
-S option).
- -S
- Restrict detection/verification to sequence formats (conflict with
-A option).
- -c format
- Convert detected sequence/alignment into format. This option
implies strict alignment checking.
- -f format
- Assume input format is format. Do not try to detect the format,
just verify that the given one is correct.
- -h
- Display help message and exit.
- -l
- List all supported formats.
- -n
- Count and report detected entries. This option is only available when the
detection is restricted to a single type (with -A or -S
options) and strict checks (without -s option) are enabled.
- -s
- Disable strict format checks (enabled by default).
- -v
- Display version information and exit.
squizz is a sequence format file checker, but it has some
conversion capabilities too.
squizz can detect the most common sequence and alignment
formats :
* CODATA, EMBL, FASTA, GCG,
GDE, GENBANK, IG, NBRF (pir), RAW, and
SWISSPROT.
* CLUSTAL, FASTA, MSF, NEXUS,
PHYLIP (interleaved and sequential) and STOCKHOLM.
squizz can do some conversions too, if the format the input
format is supported. Only 3 types are available : sequence to sequence,
alignment to alignment, and alignment to sequence (the last one, sequence to
alignment, require multiple alignments algorithms and cannot be handled with
formatting tools).
Strict format checks validate the previously detected objects, by
making some sanity checks:
- - sequence strings
must exists.
- - alignment is made
of more than one sequence.
- - alignment
sequence strings must have the same length.
- - alignment
sequence names must exists, and be unique.
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.