The cdskit from kfuku52

cdskit's People

Contributors

Stargazers

Watchers

Forkers

fsaul

cdskit's Issues

cdskit pad: reporting the number of modified seqs

padding optimization by frame length

Currently, cdskit pad tries to minimize the number of stop codons. Under some circumstances, we might be able to get better results if it's judged by the max frame length, not the number of stop codons.

ValueError: max() arg is an empty sequence in cdskit hammer

This error seems to happen when --prevent_gap_only yes with the input from stdin (-i -).

Number of input sequences: 17
108 out of 468 codon sites will be removed.
A gap-only sequence was generated with --nail 4. Will try --nail 3: Triphyophyllum_peltatum_DN37943-c0-g1
Number of input sequences: 0
Traceback (most recent call last):
  File "/opt/conda/envs/biotools/bin/cdskit", line 170, in <module>
    args.handler(args)
  File "/opt/conda/envs/biotools/bin/cdskit", line 93, in command_hammer
    hammer_main(args)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/cdskit/hammer.py", line 11, in hammer_main
    max_len = max([ len(r.seq) for r in records ])//3
ValueError: max() arg is an empty sequence

Recommend Projects