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)

Check Out this Related Man Page

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)

Linux and UNIX Man Pages

fastacmd(1) [debian man page]

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