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Plotting tool for HMMER3 hmm files based on TikZ

License: MIT License

Python 100.00%

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hmmer2pdf's Issues

`Dimension too large` error

I'm getting the following error with all the HMMs that I try:

! Dimension too large.
<recently read> \pgf@x 
       
l.22952 ...7695473305250398\lwidth] (d214) -- (d215)
                                                   node [prob] {$0.385$};
I can't work with sizes bigger than about 19 feet.
Continue and I'll use the largest value I can.

Here's a full log as well: hmm.log.

Required latex packages

Hi, thanks for making this utility.
It seems that, in addition to the stated dependencies, you also need the following packages within your latex distribution:

tikz
standalone

On Ubuntu/Debian , you therefore need the following packages: texlive texlive-latex-extra texlive-luatex. It might be helpful to mention this somewhere in the readme.

ERROR - Invalid insertion state emission probablity string

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!

Cannot reproduce the example

Hello,

I'm sorry to disturb you again.

After I solve the issue #1, I encounter another difficulty:

Reading HMM file... Done.
LaTeX Conversion... Done.
Compiling...
ERROR - LaTeX compiler failed. You may want to inspect the .log and .tex files in
/tmp/tmpi7j_dlks

Environment

Python: 3.7.7
LaTeX (latex --version)
- pdfTeX 3.14159265-2.6-1.40.17 (TeX Live 2016)
- kpathsea version 6.2.2
LuaTeX: Version 0.95.0 (TeX Live 2016)

The log file is 500 lines.
How could I provide clues that will help you?

Thank you.

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