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ababaian / palmid

RNA dependent RNA Polymerase Palmprint Analysis
GNU Affero General Public License v3.0
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Parsing of FEV obtained from nucleotide matches is broken #20

Closed asl closed 1 year ago

asl commented 1 year ago

Here is an example hash: https://serratus.io/palmid?hash=cb8c52eaed12dbb84c8959f40314ee1dbeead975

It seems that read.fev and fev2df does not support FEVs obtained from nucleotide matches as two extra fields xlat and frame are present in FEV:

score=54.3  query=NODE_1_length_7593_cov_35.116356  gene=RdRP   confidence=high comments=high-PSSM-score.reward-DDGGDD.good-segment-length. order=ABC   qlen=7593   xlat=yes    pp_start=5355   pp_end=5639 pp_length=285   frame=+3    pssm_total_score=44.3   pssm_min_score=10.8 order=ABC   v1_length=44    v2_length=17    group=Kitrino   super=DDGGDD    motifs=TANDVTGWDTGVxxxSGDPYTWLANTLVNxxxFSGDDFIA

As a result nucleotide sequences could not be analyzed w/o prior explicit translation

Tagging @ababaian @hannahhanle

ababaian commented 1 year ago

This error is now resolved in v0.0.6