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The script blast2gff.py will convert BLAST results to a GFF GFF3 file, with track decoration options. You can check the options for the script by running
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blast2gff.py --help |
blast2gff.py parses a file of BLAST results and writes out the relevant parts of the BLAST records in GFF3 format. The script provides options for decorating the data when loaded into a genome browser (specifically IGV or the UCSC Genome Browser) as a track. Most of the options provided will work with either IGV or the UCSC Genome Browser, but a few of them are specific to IGV.
Parsing BLAST results is most reliable when the BLAST results are in XML format. blast2gff.py accepts tabular data, but the script expects a specific table layout when parsing the data. XML is more reliable.
To run blast2gff.py, simply give the script the input BLAST file, and use standard Unix redirection to write the GFF3 results to file. For example:
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blast2gff.py blastresults.xml > track_based_on_blastresults.gff
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To add track options, simply append the name of the option to the command, along with the parameter, as specified by the standard track line designation. A generic example:
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blast2gff.py blastresults.xml --name "Track_Title" --color 167,208,118 --graphType bar > track_based_on_blastresults.gff
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To see the supported options, run blast2gff.py --help