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License: BSD 2-Clause "Simplified" License
Some simple but handy scripts
License: BSD 2-Clause "Simplified" License
Count coverage separate in query and hit coordinate space (wt array) so that bases from overlapping HSPs are not counted twice and all % will be < 100%
For proteins having hits in correct order and orientation.
Create match data structure, add as HSPs are parsed, write data structure to GFF at the end (match,match_part). Move to next match as soon as query region overlaps with previous hit. Should sort HSPs by query start location as they are sorted by Evalue in blast output
https://github.com/suryasaha/Utils/blob/master/joinORFsMascot.pl
Only takes first line of ORF protein nd skips the rest!!
Move calculation inside cutoff block
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