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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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The misc_feature location off by 1 #48

Closed deprekate closed 3 years ago

deprekate commented 3 years ago

The misc_features added to the input genbank file that represent the PhiSpy prophage calls is off by 1

$ grep pp3 prophage_coordinates.tsv 
pp3 NC_002737   1191309 1222549 1193572 1193583 1220349 1220360 TCAGATTTTTT AAAAAATCTGA Longest Repeat flanking phage and within 2000 bp

$ head -n 25734 Streptococcus_pyogenes_M1_GAS.gb | tail -n 2
     misc_feature    1191310..1222549
                     /note="prophage region pp3 identified with PhiSpy v4.2.6"

It should be:

     misc_feature    1191309..1222549