Shell script for changing the accession number of DNA sequences in a FASTA file Post: 302881551

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fastacmd

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)