man fastacmd (Commandes) - retrieve FASTA sequences from a BLAST database
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 (\001) 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.