3
$\begingroup$

I want to use TRAL to annotate tandem repeats in the reference genome of Caenorhabditis elegans. For this, I need to install some external software, such as Phobos. 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.

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 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.

$\endgroup$
4
  • 2
    $\begingroup$ I can reproduce this, so I think it might be a TRAL bug. See github.com/acg-team/tral/issues/12 $\endgroup$
    – Quantum7
    Jul 17 '18 at 11:25
  • $\begingroup$ 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. $\endgroup$
    – Quantum7
    Jul 27 '18 at 13:35
  • $\begingroup$ 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. $\endgroup$ Jul 28 '18 at 13:31
  • $\begingroup$ 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. $\endgroup$
    – Quantum7
    Jul 30 '18 at 18:28
3
$\begingroup$

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
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.