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fastacmd1
Retrieve fasta sequences from a blast database
Usage
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]
Overview
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
-DN-
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)
-Lstart,stop-
Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)
-PN-
Retrieve sequences with Protein Identification Group (PIG) N.
-SN-
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
-dstr-
Database (default is nr)
-istr-
Input file with GIs/accessions/loci for batch retrieval
-lN-
Line length for sequence (default = 80)
-ofilename-
Output file (default = stdout)
-ptype-
Type of file:
- G
-
guess (default): look for protein, then nucleotide
- T
-
protein
- F
-
nucleotide
-sstr-
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
-
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.
Releases
7 releases since Debian 3.0 (Woody); the text changed 3 times.
-I since Debian 3.1 (Sarge);
-T since Debian 3.1 (Sarge).
-D until Debian 3.1 (Sarge);
-L until Debian 3.1 (Sarge);
-P until Debian 3.1 (Sarge);
-S until Debian 3.1 (Sarge);
-d until Debian 3.1 (Sarge);
-i until Debian 3.1 (Sarge);
-l until Debian 3.1 (Sarge);
-o until Debian 3.1 (Sarge);
-p until Debian 3.1 (Sarge);
-s until Debian 3.1 (Sarge).