max_score is incorrect when --allScores option is used
iljungr opened this issue · comments
Run with these arguments:
12flies -f3 --allScores --orf=ATGStop --minCodons=1 Bug.fa --species=dmel,dsim
Result:
Bug.fa orf_score(decibans) -90.7230 93 215
Bug.fa orf_score(decibans) -9.3641 100 111
Bug.fa orf_score(decibans) -15.4172 160 237
Bug.fa orf_score(decibans) -29.8306 65 154
Bug.fa orf_score(decibans) -40.1296 20 154
Bug.fa max_score(decibans) -90.7230 93 215
max_score is obviously not the maximum score, though without the --allScores option it correctly reports the max_score to be -9.364. In other cases, it is not the maximum absolute value, not the first, and sometimes not even one of the scores listed. (Those scores should be listed, reported separately.) Similar problems with minCodons=25 and with 12 flies.
Here's Bug.fa:
dmel
GATAGACATCAATTTGAAAAATGGGCCAAGAGAGCAGGAGCAACGAAAAACAAACACGGCGAACAATGGG
CTACCCAAAAGCAGGCGTAGAACATGAGGAATGGATTTGTTTTAGGATTTCGATTTGGAAACACCCAGTA
TTTGCAACTTGTATATAGATATGACTTTCAGTCGGTCCCCGTTAAATGTGTTGTTATACGGAACAGTCCT
TTCACGTAAACAGCTATCCCAGGACTCTTGAAGCCAGACGGCGACCTATGTGTACTCAACGTTACT
dsim
GATAGACATCAATTTGAAAAATGGGCCAAAAGAGCAGGAGCAACGAAAAACAAACACGGCGAACAATGGG
CTACCGAAAAGCAGGCGTGGAACATGAGGAATGGGTTTGTTTTAGGATTTCGATTTGGAAACATCCTATT
TTTGCACCTAGTATATAGTTATGACTTTCAGTCGGTCCCCATAAAATGTGTTGTTATATAGAACTGTCCT
CTCACGTAAACAGCCATCCCAGGACTCTTGAAGCCAGACGGCGACCTATGTATACTCAACGTTAGT