ERROR - Invalid insertion state emission probablity string

Shen-Jing commented 4 years ago

Hello,

Thanks for developing and maintain the great tool.

Sorry to bother you, I have a runtime error:

Environment

Python: 3.7.7
LaTeX suite
LuaTeX: Version 0.95.0 (TeX Live 2016)

My HMMER3 file

HMMER3/f [3.3 | Nov 2019]
NAME  customized_case
LENG  10
MAXL  63
ALPH  DNA
RF    no
MM    no
CONS  yes
CS    no
MAP   yes
DATE  Thu Oct 22 13:37:46 2020
NSEQ  14
EFFN  14.000000
CKSUM 2504079262
STATS LOCAL MSV       -5.6552  0.81448
STATS LOCAL VITERBI   -6.3731  0.81448
STATS LOCAL FORWARD   -1.8362  0.81448
HMM          A        C        G        T   
            m->m     m->i     m->d     i->m     i->i     d->m     d->d
  COMPO   0.99446  2.92279  1.55686  1.00650
          2.00588  2.00588  0.51689  2.00588
          0.62538  1.44840  1.46969  0.10669  2.29068  0.00000        *
      1   4.30205  3.83360  4.44552  0.04804      2 T - - -
          1.36180  1.89303  1.89303  0.81516
          0.27859  1.44994  4.76028  0.13537  2.06669  2.27382  0.10861
      2   1.50000  2.49005  1.75638  0.65144      4 t - - -
          1.38629  1.38629  1.38629  1.38629
          0.01727  4.76028  4.76028  1.46634  0.26236  0.73354  0.65432
      3   3.29620  3.78079  0.26877  1.73812      5 g - - -
          1.38629  1.38629  1.38629  1.38629
          0.01432  4.94643  4.94643  1.46634  0.26236  1.80015  0.18065
      4   4.58552  4.11782  4.72593  0.03598      6 T - - -
          1.38629  1.38629  1.38629  1.38629
          0.01432  4.94643  4.94643  1.46634  0.26236  0.40129  1.10701
      5   0.19300  3.95573  4.25947  1.95024      7 a - - -
          1.38629  1.38629  1.38629  1.38629
          0.01242  5.08760  5.08760  1.46634  0.26236  1.09861  0.40547
      6   1.89421  3.48309  0.36699  2.07122      8 g - - -
          1.38629  1.38629  1.38629  1.38629
          0.01242  5.08760  5.08760  1.46634  0.26236  1.09861  0.40547
      7   0.41282  1.80968  2.19298  2.76577      9 a - - -
          0.93103  1.68080  1.17070  2.21203
          0.71404  1.09485  1.73870  0.07337  2.64869  1.09861  0.40547
      8   0.19925  4.31041  1.89188  4.10814     11 a - - -
          1.38629  1.38629  1.38629  1.38629
          0.01551  4.86709  4.86709  1.46634  0.26236  0.27576  1.42295
      9   0.01510  5.56759  4.98805  5.43758     12 A - - -
          1.38629  1.38629  1.38629  1.38629
          0.01287  5.05265  5.05265  1.46634  0.26236  1.09861  0.40547
     10   4.73423  4.27435  4.87202  0.03084     13 T - - -
          1.38629  1.38629  1.38629  1.38629
          0.00645  5.04623        *  1.46634  0.26236  0.00000        *
//

Error message

Reading HMM file...                                                                                                                        
ERROR - Failed to parse hmm file format: Invalid insertion state emission probablity string: '          2.00588  2.00588  0.51689  2.00588'

Thanks for your time!

lkuchenb commented 4 years ago

hmmer2pdf was a quick hack back when I wrote it, it works only on protein alignments as it is now. But allowing DNA alignments should be a no-brainer. I'll take a look.

lkuchenb commented 4 years ago

Fixed in f05b6e3a04f5b10dd904046b3d9c9a19bc411357 - I'll add a setup.py file and make a release

lkuchenb commented 4 years ago

@Shen-Jing The fix is now available in a new release and hmmer2pdf is now installable:

pip install git+https://github.com/lkuchenb/hmmer2pdf@latest

Hope it helps!

Shen-Jing commented 4 years ago

You are so efficient! Thank you very much!

The latest commit works successfully, but I encountered new difficulties (mentioned in issue #5).

lkuchenb / hmmer2pdf