squizz - Sequence format checker" 4
-
squizz [-AShlnsv] [-c format]
[-f format] file
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.
-
seqfmt(5), alifmt(5)
Nicolas Joly (
[email protected]), Institut Pasteur.