squizz(1) [debian man page]
SQUIZZ(1) User Manuals SQUIZZ(1) NAME
squizz - Sequence format checker SYNOPSIS
squizz [-AShlns] [-c format] [-f format] file OPTIONS
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 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). DESCRIPTION
squizz is a sequence format file checker, but it has some conversion capabilities too. squizz can detect the most common sequence and alignment formats : * EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), 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, align- ment 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. SEE ALSO
seqfmt(5), alifmt(5) AUTHOR
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur. Unix 2009-05-19 SQUIZZ(1)
Check Out this Related Man Page
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p) NAME
mask_by_search - mask sequence(s) based on its alignment results SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type query flag. This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file you BLASTed with as input to this program). Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string' Options: -f/--format=s Search report format (fasta,blast,axt,hmmer,etc) -sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot) --hardmask (booelean) Hard mask the sequence with the maskchar [default is lowercase mask] --maskchar=c Character to mask with [default is N], change to 'X' for protein sequences -e/--evalue=n Evalue cutoff for HSPs and Hits, only mask sequence if alignment has specified evalue or better -o/--out/ --outfile=file Output file to save the masked sequence to. -t/--type=s Alignment seq type you want to mask, the 'hit' or the 'query' sequence. [default is 'hit'] --minlen=n Minimum length of an HSP for it to be used in masking [default 0] -h/--help See this help information AUTHOR - Jason Stajich Jason Stajich, jason-at-bioperl-dot-org. perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)