hmm.HMM.create() fails for DNA models

[andrewparkermorgan]

Hi,

Reading of models built from DNA sequences appears to fail: below I show an example using a motif from the Dfam database (DF0000029).

cp = hmm.HMM.create(input_format = "hmmer", file = "DF0000029.hmm")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm.py", line 261, in create
    hmmer_probabilities = next(HMM.read(file))
  File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm_io.py", line 187, in read
    for i in string_emissions]
  File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm_io.py", line 187, in <listcomp>
    for i in string_emissions]
ValueError: could not convert string to float: 'c'

It seems that too many columns are read from MATCH lines in the model: currently the number of columns is hard-coded as 20 (ie. amino acids) in hmm_io.py @ line 104.

Is there any support for DNA sequences in tral?

[elkeschaper]

Dear Andrew, DNA sequence support was added in dev, but not the the main pip package. So you could install TRAL from git: git@github.com:elkeschaper/tral.git (see: http://stackoverflow.com/questions/20101834/pip-install-from-github-repo-branch) Please let me know if any problems remain! Thanks, Elke

…

On Dec 12, 2016, at 5:57 PM, andrewparkermorgan ***@***.***> wrote: Hi, Reading of models built from DNA sequences appears to fail: below I show an example using a motif from the Dfam database (DF0000029 <http://dfam.org/entry/DF0000029>). cp = hmm.HMM.create(input_format = "hmmer", file = "DF0000029.hmm") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm.py", line 261, in create hmmer_probabilities = next(HMM.read(file)) File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm_io.py", line 187, in read for i in string_emissions] File "/Users/apm/anaconda3/lib/python3.4/site-packages/tral/hmm/hmm_io.py", line 187, in <listcomp> for i in string_emissions] ValueError: could not convert string to float: 'c' It seems that too many columns are read from MATCH lines in the model: currently the number of columns is hard-coded as 20 (ie. amino acids) in hmm_io.py @ line 104. Is there any support for DNA sequences in tral? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#8>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFs9I1eECU--KsppWoBe5aX8ZyoHeZIqks5rHX0CgaJpZM4LKxoy>.