read_blast_tab

Biopiece: read_blast_tab

Description

read_blast_tab and written to file with write_blast - or with blastall and the -m 8 or -m 9 switch. Each column in the table corresponds to the following keys:

1. Q_ID - Query ID.
2. S_ID - Subject ID.
3. IDENT - Identity (%).
4. ALIGN_LEN - Alignment length.
5. MISMATCHES - Number of mismatches.
6. GAPS - Number of gaps.
7. Q_BEG - Query begin.
8. Q_END - Query end.
9. S_BEG - Subject begin.
10. S_END - Subject end.
11. E_VAL - Expect value.
12. BIT_SCORE - Bit score.

Furthermore, two extra keys are added to the record:

• STRAND - Strand.
• REC_TYPE - Record type.

Usage

read_blast_tab [options] -i <BLAST tabular file(s)>

Options

[-?          | --help]               #  Print full usage description.
[-i <files!> | --data_in=<files!>]   #  Comma separated list of files or glob expression to read.
[-n <uint>   | --num=<uint>]         #  Limit number of records to read.
[-I <file!>  | --stream_in=<file!>]  #  Read input stream from file  -  Default=STDIN
[-O <file>   | --stream_out=<file>]  #  Write output stream to file  -  Default=STDOUT
[-v          | --verbose]            #  Verbose output.

Examples

To read all BLAST entries from a file:

read_blast_tab -i test.blast

To read in only 10 records from a BLAST file:

read_blast_tab -n 10 -i test.blast

To read all BLAST entries from multiple files:

read_blast_tab -i test1.blast,test2.blast

To read BLAST entries from multiple files using a glob expression:

read_blast_tab -i '*.blast'

See also

create_blast_index

blast_seq

write_blast

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

mail@maasha.dk

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

read_blast_tab is part of the Biopieces framework.

http://www.biopieces.org