Provided by: squizz_0.99a-2_i386
squizz - Sequence format checker
squizz [-AShlns] [-c format] [-f format] file
Following command line options are allowed:
-A Restrict detection/verification to alignment formats (conflict with
-S Restrict detection/verification to sequence formats (conflict with
Convert detected sequence/alignment into format. This option
implies strict alignment checking.
Assume input format is format. Do not try to detect the format,
just verify that the given one is correct.
-h Usage display.
-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).
squizz is a sequence format file checker, but it has some conversion
squizz can detect the most common sequence and alignment formats :
* EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and
* CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and
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 (firstname.lastname@example.org), Institut Pasteur.