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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