This is the command sindex that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
sindex - index a sequence database for sfetch
SYNOPSIS
sindex [options] seqfile1 [seqfile2...]
DESCRIPTION
sindex indexes one or more seqfiles for future sequence retrievals by sfetch. An SSI
("squid sequence index") file is created in the same directory with the sequence files. By
default, this file is called <seqfile>.ssi.
If there is more than one sequence file on the command line, the SSI filename will be
constructed from the last sequence file name. This may not be what you want; see the -o
option to specify your own name for the SSI file.
sindex is capable of indexing large files (>2 GB) if optional LFS support has been enabled
at compile-time. See INSTALL instructions that came with @PACKAGE@.
OPTIONS
-h Print brief help; includes version number and summary of all options, including
expert options.
-o <ssi outfile>
Direct the SSI index to a file named <outfile>. By default, the SSI file would go
to <seqfile>.ssi.
EXPERT OPTIONS
--64 Force the SSI file into 64-bit (large seqfile) mode, even if the seqfile is small.
You don't want to do this unless you're debugging.
--external
Force sindex to do its record sorting by external (on-disk) sorting. This is only
useful for debugging, too.
--informat <s>
Specify that the sequence file is definitely in format <s>; blocks sequence file
format autodetection. This is useful in automated pipelines, because it improves
robustness (autodetection can occasionally go wrong on a perversely malformed
file). Common examples include genbank, embl, gcg, pir, stockholm, clustal, msf, or
phylip; see the printed documentation for a complete list of accepted format names.
--pfamseq
A hack for Pfam; indexes a FASTA file that is known to have identifier lines in
format ">[name] [accession] [optional description]". Normally only the sequence
name would be indexed as a primary key in a FASTA SSI file, but this allows
indexing both the name (as a primary key) and accession (as a secondary key).
Use sindex online using onworks.net services
