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Shell Programming and Scripting
Extract regular expression and line below
Post 302691793 by pathunkathunk on Saturday 25th of August 2012 06:56:16 PM
08-25-2012
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LEARN ABOUT DEBIAN
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)