update July 26, 2020
NAME
blblastout.py - Convert BLAST ASN.1
output into other formats, and open those files using the
appropriate application, or write output to a file.
SYNOPSIS
blblastout.py --archive
infile [--delete] --outfmt format
--destination dest [--outfile outfile]
blblastout.py --rid infile
[--delete] --outfmt format --destination
dest [--outfile outfile]
DESCRIPTION
blblastout.py is
a helper application for BioLegato. When BLAST searches are run
from bldna or blprotein, output is originally sent to an ASN.1
file. BioLegato calls blbblastout.py to either launch a viewer or
save the output to a file. In order to do this, blblastout.py
calls blast_formatter to convert the ASN.1 file into the
appropriate format. blblastout.py then opens the application
specified by --destination to view the output, or saves the output
to outfile.
When running BLAST at NCBI using the -remote option, open the
output using blastout.py --rid infile. When running BLAST on
locally-installed databases, call blastout.py --archive infile.
OPTIONS
infile is output from a BLAST search, in ASN.1
format (eg. blastn -outfmt 11)
--archive infile - Use this option if
infile was generated by a BLAST search of a local database
--rid infile - If the BLAST search was done at NCBI
using the blast -remote option, read the RID number from infile.
This will be used by blast_formatter when converting to the format
specified by --outfmt.
Note: --archive and --rid are
mutually exclusive
--delete - Delete infile when finished. This is
mainly intended for running from BioLegato, where infile
is temporary file.
--outfmt format - format is any output format
supported by blast_formatter.
It must be specified on the blblastout.py command line as a
comma-separated list.
Examples
To generate tabular output: --outfmt
7,sacc,slen,evalue
To generate XML output: --outfmt 5
--destination dest - dest is one of the following:
For BLAST viewable Report:
textedit - open output files in text editor
specified by the $BL_TextEditor environment variable browser
- open in web browser specified by $BL_Browser
textfile - write text output to a text file, using the
basename specified by destination.
htmlfile - write to an HTML file
For BLAST tsv Report:
blnfetch - Open in blnfetch, BioLegato
interface for retrieving DNA/RNA entries using ACCESSION
numbers
blpfetch - Open in blpfetch, BioLegato interface for
retrieving protein entries using ACCESSION numbers
tsvfile - write to a tsvfile.
For XML output:
xmlfile - write to an xmlfile.
blastviewer - open XML output in blastviewer
--outfile outfile - base filename for saving an
output file. Do NOT include a file extension. blblastout.py will
automatically add a file extension based on --destination. For
example, if destination was a textfile, a ".txt" file extension
would be added.
EXAMPLES
1. To write BLAST output to a text file:
blblastout.py --archive
mousecat.blastn.asn1 --outfmt 0 --destination textfile --outfile
mousecat.blastn.txt
2. To view BLAST output in a web browser:
blblastout.py --archive
mousecat.blastn.asn1 --outfmt 0 --destination browser
3. To view BLAST output in blnfetch:
blblastout.py --archive
mousecat.blastn.asn1 --outfmt 7,sacc,slen,evalue --destination blnfetch
4. Given an ASN.1 file produced by blastn -outfmt 11, convert the
output to XML and open the XML output in blastviewer.
blblastout.py --archive
mousecat.blastn.asn1 --outfmt 5 --destination blastviewer
ENVIRONMENT
BL_TextEdit (required) - text editor to launch
for viewing text output.
BL_Browser (required) - web browser to launch for viewing
HTML output.
REFERENCES
AUTHOR
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB Canada R3T 2N2
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist