Answers.Body: <p>TRAL 0.3.5 has bugs running and parsing Phobos. You can follow progress towards a fix on this issue: <a href="https://github.com/acg-team/tral/issues/16" rel="nofollow noreferrer">https://github.com/acg-team/tral/issues/16</a></p>
  
  <p>Until the issue is fixed, you should remove Phobos from the repeat detector list in your tral config file (~/.tral/config.ini) and use a different repeat detector.</p>
  
  <pre><code>[sequence]
      [[repeat_detection]]
          DNA = TRED, T-REKS, TRF, XSTREAM
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-27T13:07:54.097Z
Answers.LastActivityDate: 2018-07-27T13:07:54.097Z
Answers.UserDisplayName: Quantum7
Body: <p>I want to use <a href="http://www.vital-it.ch/software/tral" rel="nofollow noreferrer">TRAL</a> to annotate tandem repeats in the reference genome of <em>Caenorhabditis elegans</em>. For this, I need to install some external software, such as <a href="http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm" rel="nofollow noreferrer">Phobos</a>. I've downloaded Phobos and I am using it by typing the path to it's executable like this:</p>
  
  <p><code>input/software/phobos-v3.3.12-mac/bin/phobos-mac-intel-64bit-start-from-command-line genome.fa output.txt</code></p>
  
  <p>This works quite well. </p>
  
  <p>In order for TRAL to find Phobos, I changed TRAL's configuration file as explained <a href="http://www.vital-it.ch/software/tral" rel="nofollow noreferrer">here</a>.</p>
  
  <p>I've replaced <code>PHOBOS = phobos</code> with <code>PHOBOS = /Users/user/Documents/.../project/input/software/phobos-v3.3.12-mac/bin/phobos-mac-intel-64bit-start-from-command-line</code></p>
  
  <p>Then, I followed the tutorial <a href="http://www.vital-it.ch/software/tral" rel="nofollow noreferrer">Run and parse de novo repeat detection software</a> and typed the following commands in Python 3 in the Terminal:</p>
  
  <pre><code>import os
  from tral.sequence import sequence
  from tral.paths import PACKAGE_DIRECTORY
  
  proteome_HIV = os.path.join(PACKAGE_DIRECTORY, "examples", "data", "HIV-1_388796.faa")
  sequences_HIV = sequence.Sequence.create(file = proteome_HIV, input_format = 'fasta')
  </code></pre>
  
  <p>So far so good. But the following command creates an error:</p>
  
  <pre><code>tandem_repeats = sequences_HIV[0].detect(denovo = True, detection = {"detectors": ["Phobos"]})
  
  Did not find Phobos result file in /var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/tmpvc20y3i4/001/PHOBOS/phobos.o
  </code></pre>
  
  <p>Note that if I use <code>PHOBOS</code> instead of <code>Phobos</code> in the command, I get the following error:</p>
  
  <pre><code>Traceback (most recent call last):
    File "&lt;stdin&gt;", line 1, in &lt;module&gt;
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/sequence.py", line 162, in detect
      **kwargs['detection'])[0]
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/repeat_detection_run.py", line 962, in run_detector
      Detectors(detectors, sequence_type)
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/repeat_detection_run.py", line 872, in Detectors
      FINDER_LIST.keys()))
  Exception: Unknown TR detector supplied (Supplied: ['PHOBOS']. Known TR detectors: dict_keys(['HHrepID', 'Phobos', 'TRED', 'T-REKS', 'TRF', 'TRUST', 'XSTREAM']))
  </code></pre>
  
  <p>I am working on Mac OS X. I installed TRAL with <code>pip install tral</code>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-17T11:25:06.530Z
Comments.Text: I can reproduce this, so I think it might be a TRAL bug. See https://github.com/acg-team/tral/issues/12
Comments.UserDisplayName: Quantum7
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-27T13:35:54.653Z
Comments.Text: Are you running on DNA or protein? In general, TRAL support for DNA is weaker than we'd like it. If you're searching exons, I might try performing the translation first and running in AA mode.
Comments.UserDisplayName: Quantum7
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-28T13:31:40.830Z
Comments.Text: Running on DNA. I am interested in DNA repeats. Mini-and microsatellites are unlikely to code for anything. If I run it on the translation, then the repeats are not bound to appear at the DNA level because of the genetic code degeneracy.
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-30T18:28:44.110Z
Comments.Text: OK. Just make sure you review the results carefully when using TRAL on DNA, as the parameters were trained for AA. We have a student working on improving DNA repeats now, so this should get easier.
Comments.UserDisplayName: Quantum7
Tags: <sequence-annotation><software-installation><repeat-elements>
Title: TRAL does not find "Phobos result file"
ThreadText: # TRAL does not find "Phobos result file"
  
  (Asked by: username_0 on 2018-07-10)
  
  I want to use [TRAL](http://www.vital-it.ch/software/tral) to annotate tandem repeats in the reference genome of *Caenorhabditis elegans*. For this, I need to install some external software, such as [Phobos](http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm). I've downloaded Phobos and I am using it by typing the path to it's executable like this:
  
  `input/software/phobos-v3.3.12-mac/bin/phobos-mac-intel-64bit-start-from-command-line genome.fa output.txt`
  
  This works quite well.
  
  In order for TRAL to find Phobos, I changed TRAL's configuration file as explained [here](http://www.vital-it.ch/software/tral).
  
  I've replaced `PHOBOS = phobos` with `PHOBOS = /Users/user/Documents/.../project/input/software/phobos-v3.3.12-mac/bin/phobos-mac-intel-64bit-start-from-command-line`
  
  Then, I followed the tutorial [Run and parse de novo repeat detection software](http://www.vital-it.ch/software/tral) and typed the following commands in Python 3 in the Terminal:
  
  ```
  import os
  from tral.sequence import sequence
  from tral.paths import PACKAGE_DIRECTORY
  
  proteome_HIV = os.path.join(PACKAGE_DIRECTORY, "examples", "data", "HIV-1_388796.faa")
  sequences_HIV = sequence.Sequence.create(file = proteome_HIV, input_format = 'fasta')
  
  ```
  
  So far so good. But the following command creates an error:
  
  ```
  tandem_repeats = sequences_HIV[0].detect(denovo = True, detection = {"detectors": ["Phobos"]})
  
  Did not find Phobos result file in /var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/tmpvc20y3i4/001/PHOBOS/phobos.o
  
  ```
  
  Note that if I use `PHOBOS` instead of `Phobos` in the command, I get the following error:
  
  ```
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/sequence.py", line 162, in detect
      **kwargs['detection'])[0]
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/repeat_detection_run.py", line 962, in run_detector
      Detectors(detectors, sequence_type)
    File "/Users/user/anaconda/envs/python3env/lib/python3.6/site-packages/tral/sequence/repeat_detection_run.py", line 872, in Detectors
      FINDER_LIST.keys()))
  Exception: Unknown TR detector supplied (Supplied: ['PHOBOS']. Known TR detectors: dict_keys(['HHrepID', 'Phobos', 'TRED', 'T-REKS', 'TRF', 'TRUST', 'XSTREAM']))
  
  ```
  
  I am working on Mac OS X. I installed TRAL with `pip install tral`.
  
  **Tags:** sequence-annotation, software-installation, repeat-elements
  
  > **Comments:**
  > **username_1**: I can reproduce this, so I think it might be a TRAL bug. See https://github.com/acg-team/tral/issues/12  
  > **username_1**: Are you running on DNA or protein? In general, TRAL support for DNA is weaker than we'd like it. If you're searching exons, I might try performing the translation first and running in AA mode.  
  > **username_0**: Running on DNA. I am interested in DNA repeats. Mini-and microsatellites are unlikely to code for anything. If I run it on the translation, then the repeats are not bound to appear at the DNA level because of the genetic code degeneracy.  
  > **username_1**: OK. Just make sure you review the results carefully when using TRAL on DNA, as the parameters were trained for AA. We have a student working on improving DNA repeats now, so this should get easier.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-07-27. Score: 3 | Accepted answer
  
  TRAL 0.3.5 has bugs running and parsing Phobos. You can follow progress towards a fix on this issue: <https://github.com/acg-team/tral/issues/16>
  
  Until the issue is fixed, you should remove Phobos from the repeat detector list in your tral config file (~/.tral/config.ini) and use a different repeat detector.
  
  ```
  [sequence]
      [[repeat_detection]]
          DNA = TRED, T-REKS, TRF, XSTREAM
  
  ```
  
  
  ---
  
  