fastacmd(1) [debian man page]

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

NAME

       fastacmd - retrieve FASTA sequences from a BLAST database

SYNOPSIS

       fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t]

DESCRIPTION

       fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option.  An example fastacmd call would be

								fastacmd -d nr -s p38398

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D N   Dump the entire database in some format:
	      1      fasta
	      2      GI list
	      3      Accession.version list

       -I     Print database information only (overrides all other options)

       -L start,stop
	      Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)

       -P N   Retrieve sequences with Protein Identification Group (PIG) N.

       -S N   Strand on subsequence (nucleotide only):
	      1      top (default)
	      2      bottom

       -T     Print taxonomic information for requested sequence(s)

       -a     Retrieve duplicate accessions

       -c     Use ^A (01) as non-redundant defline separator

       -d str Database (default is nr)

       -i str Input file with GIs/accessions/loci for batch retrieval

       -l N   Line length for sequence (default = 80)

       -o filename
	      Output file (default = stdout)

       -p type
	      Type of file:
	      G      guess (default): look for protein, then nucleotide
	      T      protein
	      F      nucleotide

       -s str Comma-delimited search string(s).  GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'

       -t     Definition line should contain target GI only

EXIT STATUS

	      0      Completed successfully.
	      1      An error (other than those below) occurred.
	      2      The BLAST database was not found.
	      3      A search (accession, GI, or taxonomy info) failed.
	      4      No taxonomy database was found.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blast(1), /usr/share/doc/blast2/fastacmd.html.

NCBI
								    2005-11-04							       FASTACMD(1)

ASN2GB(1)						     NCBI Tools User's Manual							 ASN2GB(1)

NAME

       asn2gb - convert ASN.1 biological data to a GenBank-style flat format

SYNOPSIS

       asn2gb  [-]  [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode]
       [-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N] [-u N] [-y N]

DESCRIPTION

       asn2gb converts descriptions of biological sequences from NCBI's ASN.1 format to one of several flat-file formats, and is the successor	to
       asn2ff(1).

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A accession
	      Accession  to  fetch;  may  take	the  form accession,complexity,flags where complexity should normally be 0 and a flags value of -1
	      enables fetching of external features (as with the legacy -F option)

       -F     Fetch remote annotations (equivalent to specifying -A accession,0,-1)

       -a asn-type
	      ASN.1 Type:
	      [Single record]
	      a      Any (autodetected; default)
	      e      seq-Entry
	      b      Bioseq
	      s      bioseq-Set
	      m      seq-subMit
	      q      Catenated
	      [Release file; components individually processed and freed]
	      t      baTch bioseq-set
	      u      batch seq-sUbmit

       -b     Input file is binary

       -c     Batch file is compressed

       -d     Seq-loc minus strand

       -f format
	      Format:
	      b      GenBank (default)
	      bp or pb
		     GenBank and GenPept
	      e      EMBL
	      p      GenPept
	      q      nucleotide GBSet (XML)
	      r      protein GBSet (XML)
	      t      Feature table only
	      x      nucleotide INSDSet (XML)
	      y      tiny seq (XML)
	      Y      FASTA
	      z      protein INSDSet (XML)

       -g N   Bit flags (all default to off):
	      1      HTML
	      2      XML
	      4      ContigFeats
	      8      ContigSrcs
	      16     FarTransl

       -h N   Lock/Lookup Flags (all default to off):
	      8      LockProd
	      16     LookupComp
	      64     LookupProd

       -i filename
	      Input file name (default = stdin)

       -j N   Start location (default is 0, beginning of sequence)

       -k N   End location (default is 0, end of sequence)

       -l filename
	      Log file

       -m mode
	      Mode:
	      r      Release
	      e      Entrez
	      s      Sequin (default)
	      d      Dump

       -n filename
	      Asn2Flat Executable (default = asn2flat)

       -o filename
	      Output file name (default = stdout)

       -p     Propagate top descriptors

       -q filename
	      Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff)

       -r     Enable remote fetching

       -s style
	      Style:
	      n      Normal (default)
	      s      Segment
	      m      Master
	      c      Contig

       -t N   Batch:
	      1      Report
	      2      Sequin/Release
	      3      asn2gb SSEC/nocleanup
	      4      asn2flat BSEC/nocleanup
	      5      asn2gb/asn2flat
	      6      asn2gb NEW dbxref/OLD dbxref
	      7      oldasn2gb/newasn2gb
       -u N Custom flags (all default to off):
	      4      Hide features
	      1792   Hide references
	      8192   Hide sources
	      262144 Hide translations

       -y N   Feature itemID

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1), insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz.

NCBI
								    2011-09-02								 ASN2GB(1)