asn2idx(1) [debian man page]

ASN2IDX(1)						     NCBI Tools User's Manual							ASN2IDX(1)

NAME

       asn2idx - index ASN.1 Bioseq-sets for fast access to individual sequences

SYNOPSIS

       asn2idx [-] [-b] [-d dir] [-f filter] -p path [-r path] [-t] [-x str]

DESCRIPTION

       asn2idx	indexes  ASN.1	Bioseq-sets (such as GenBank release files) to speed retrieval of the individual sequences they contain.  For each
       file that it processes, it yields an output file in the same directory with the extension .idx.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -b     Bioseq-sets are Binary

       -d dir Required Subdirectory

       -f filter
	      Filter (default = gbcon,gbest,gbgss,gbhtg,gbsts)

       -p path
	      Path to Files

       -p path
	      Path for Results

       -t     Recurse

       -x str File Selection Substring (default = .aso)

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2asn(1), asndhuff(1).

NCBI
								    2008-12-13								ASN2IDX(1)

ASN2FSA(1)						     NCBI Tools User's Manual							ASN2FSA(1)

NAME

       asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS

       asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k]
       [-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z]

DESCRIPTION

       asn2fsa converts biological sequence data from ASN.1 to FASTA.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A acc Accession to fetch

       -D     Use Dash for Gap

       -E     Extended Seq-ids

       -H     HTML spans

       -L filename
	      Log file

       -T     Use Threads

       -a type
	      Input ASN.1 type:
	      a      Automatic (default)
	      z      Any
	      e      Seq-entry
	      b      Bioseq
	      s      Bioseq-set
	      m      Seq-submit
	      t      batch processing (suitable for official releases; autodetects specific type)

       -b     Bioseq-set is Binary

       -c     Bioseq-set is Compressed

       -d path
	      Path to ReadDB Database

       -e N   Line length (70 by default; may range from 10 to 120)

       -f path
	      Path to indexed FASTA data

       -g     Expand delta gaps into Ns

       -h filename
	      Far component cache output file name

       -i filename
	      Single input file (standard input by default)

       -k     Local fetching

       -l     Lock components in advance

       -m     Master style for near segmented sequences

       -o filename
	      Nucleotide Output file name

       -p path
	      Path to ASN.1 Files

       -q filename
	      Quality score output file name

       -r     Remote fetching from NCBI

       -s     Far genomic contig for quality scores

       -u     Recurse

       -v filename
	      Protein output file name

       -x str File selection substring (.ent by default) [String]

       -z     Print quality score gap as -1

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).

NCBI
								    2011-09-02								ASN2FSA(1)