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Description
TRAL parses Phobos output incorrectly.
Example file:
>sequence_id_not_defined
sequence length: 9719
number of ACGTU characters: 9719
dinucleotide 57 : 64 | 8 bp | 8 BP | 6 pt | 100.000 % | 0 mis | 0 ins | 0 del | 0 N | unit AC
Missense:
CACACACA
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CACACACA
hexanucleotide 96 : 107 | 12 bp | 12 BP | 6 pt | 100.000 % | 0 mis | 0 ins | 0 del | 0 N | unit AGGGCC
Missense:
CCAGGGCCAGGG
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CCAGGGCCAGGG
Running tral.sequence.repeat_detection_io.phobos_get_repeats() fails to produce any repeats. It is possible that the Phobos output format has changed significantly since the code was written.