afetch(1) Biosquid Manual afetch(1)NAME
afetch - retrieve an alignment from an alignment database
SYNOPSIS
afetch [options] alignmentdb key
afetch --index alignmentdb
DESCRIPTION
afetch retrieves the alignment named key from an alignment database in file alignmentdb.
alignmentdb is a "multiple multiple alignment" file in Stockholm (e.g. native Pfam) format.
key is either the name (ID) of the alignment, or its accession number (AC).
The alignmentdb file should first be SSI indexed with afetch --index for efficient retrieval. An SSI index is not required, but alignment
retrieval without one may be painfully slow.
OPTIONS -h Print brief help; includes version number and summary of all options, including expert options.
EXPERT OPTIONS --index
Instead of retrieving a key, the special command afetch --index alignmentdb produces an SSI index of the names and accessions of the
alignments in the file alignmentdb. This should be run once on the alignmentdb file to prepare it for all future afetch's.
SEE ALSO alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), strans-
late(1), weight(1).
AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU
General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy@genetics.wustl.edu
Biosquid 1.9g January 2003 afetch(1)
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seqstat(1) Biosquid Manual seqstat(1)NAME
seqstat - show statistics and format for a sequence file
SYNOPSIS
seqstat [options] seqfile
DESCRIPTION
seqstat reads a sequence file seqfile and shows a number of simple statistics about it.
The printed statistics include the name of the format, the residue type of the first sequence (protein, RNA, or DNA), the number of
sequences, the total number of residues, and the average and range of the sequence lengths.
OPTIONS -a Show additional verbose information: a table with one line per sequence showing name, length, and description line. These lines are
prefixed with a * character to enable easily grep'ing them out and sorting them.
-h Print brief help; includes version number and summary of all options, including expert options.
-B (Babelfish). Autodetect and read a sequence file format other than the default (FASTA). Almost any common sequence file format is
recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal align-
ment formats). See the printed documentation for a complete list of supported formats.
EXPERT OPTIONS --informat <s>
Specify that the sequence file is in format <s>, rather than the default FASTA format. Common examples include Genbank, EMBL, GCG,
PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option
overrides the default expected format (FASTA) and the -B Babelfish autodetection option.
--quiet
Suppress the verbose header (program name, release number and date, the parameters and options in effect).
SEE ALSO afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
weight(1).
AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU
General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy@genetics.wustl.edu
Biosquid 1.9g January 2003 seqstat(1)