write_psl

Biopiece: write_psl

Description

write_psl outputs PSL records from the stream. The PSL format consists of up to 21 columns:

1. MATCHES - Number of non-repeat matches.
2. MISMATCHES - Number of mismatches.
3. REPMATCHES - Number of repeat matches.
4. NCOUNT - Number of Ns.
5. QNUMINSERT - Number of inserts in query.
6. QBASEINSERT - Number of bases inserted in query.
7. SNUMINSERT - Number of inserts in subject.
8. SBASEINSERT - Number of bases inserted in subject.
9. STRAND - Strand.
10. Q_ID - Query ID.
11. Q_LEN - Query length.
12. Q_BEG - Query begin.
13. Q_END - Query end.
14. S_ID - Subject ID.
15. S_LEN - Subject length.
16. S_BEG - Subject begin.
17. S_END - Subject end.
18. BLOCKCOUNT - Block count.
19. BLOCKSIZES - Block sizes.
20. Q_BEGS - Query sequence blocks begins.
21. S_BEGS - Subject sequence blocks begins.

Records can be written to BED format if the REC_TYPE equals PSL. read_psl results in Biopiece records of the PSL type.

For more about the PSL format:

http://genome.ucsc.edu/FAQ/FAQformat#format2

Usage

... | write_psl [options]

Options

[-?         | --help]               #  Print full usage description.
[-x         | --no_stream]          #  Do not emit records.
[-o <file>  | --data_out=<file>]    #  Write result to file.
[-I <file!> | --stream_in=<file!>]  #  Read input from stream file  -  Default=STDIN
[-O <file>  | --stream_out=<file>]  #  Write output to stream file  -  Default=STDOUT
[-Z         | --compress]           #  Compress output using gzip.
[-v         | --verbose]            #  Verbose output.

Examples

... | write_psl -x -o table.psl     #  Output data to file 'table.psl'.
... | write_psl -Z -o table.psl.gz  #  Output zipped data to file 'table.psl.gz'.

See also

read_psl

blat_seq

Author

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

[email protected]

August 2007

License

GNU General Public License version 2

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

Help

write_psl is part of the Biopieces framework.

http://www.biopieces.org