Configuration¶
Here you see how to configure TRAL after installation. All configuration files are located in your home directory:
~/.tral/
configs.ini - REQUIRED: Supply paths to external software and data.¶
In configs.ini you can set the paths to all external software and data used in TRAL, as well as change default thresholds and behaviours.
De novo repeat detection¶
Enlist all de novo detection algorithms you wish to use. All other algorithms are ignored by default.
[sequence]
[[repeat_detection]]
AA = HHrepID, T-REKS, TRUST, XSTREAM # List of default de novo detectors on amino acid data that you wish to use.
DNA = PHOBOS, XSTREAM #List of default de novo detectors on nucleic data that you wish to use.
If the binaries or executable scripts of any de novo detection algorithm are not in the system path, set the absolute paths in config.ini. Details for each detector (e.g. to create executable scripts) are detailed in Installation of external software.
[sequence]
[[repeat_detector_path]]
PHOBOS = phobos
HHrepID = hhrepid_64
HHrepID_dummyhmm = /path/to/home/.tral/data/hhrepid/dummyHMM.hmm
TRUST = TRUST
TRUST_substitutionmatrix = /path/to/TRUST/Align/BLOSUM50 #Recommended: Use matrices packages shipped with TRUST
XSTREAM = XSTREAM
[...]
Build Hmmer models¶
If hmmbuild is not in your system path, define the absolute path:
[hmm]
hmmbuild = path/to/hmmbuild
Realign tandem repeat units¶
At current, tandem repeat units are realigned with Mafft’s ginsi global aligner. This is required for example if you annotate tandem repeats from profile models. If ginsi is not in your system path, define the absolute path:
[repeat]
ginsi = /path/to/ginsi
Additionally, all detected tandem repeats (either from profile models or denovo can be realigned with the indel-aware proPIP alignment algorithm. To use proPIP you need to have Castor (incl. aligner) which ships with proPIP. If Castor is not in your system path, define the absolute path:
[repeat]
Castor = /path/to/Castor
[[castor_parameter]]
rate_distribution = constant # either constant or gamma
Simulation of evolution in tandem repeats¶
If alfsim is not in your system path, set the absolute path:
[repeat]
alfsim = path/to/alfsim
configs.ini - OPTIONAL: Change TRAL’s default behaviour¶
Define the default filter behaviour.¶
[filter]
[[basic]]
tag = basic_filter
[[[dict]]]
[[[[pvalue]]]]
func_name = pvalue
score = phylo_gap01 # score
threshold = 0.1 # p-Value cut-off
[[[[n_effective]]]]
func_name = attribute
attribute = n_effective # attribute of tandem repeat, e.g. the repeat unit length l_effective
type = min
threshold = 1.9 # p-Value cut-off
Creation of new Repeat instances¶
[repeat]
scoreslist = phylo_gap01, # score
calc_score = False # Is the score calculated?
calc_pvalue = False # Is the pvalue calculated?
precision = 10
ginsi = /path/to/ginsi # Path to the mafft global aligner ginsi.
Castor = Castor
[[castor_parameter]]
rate_distribution = constant # either constant or gamma
alfsim = alfsim
Statistical significance calculation and models of repeat evolution¶
[repeat_score]
evolutionary_model = lg # All models need to be available in /path/to/TandemRepeats/tandemrepeats/data/paml/
[[indel]]
indelRatePerSite = 0.01 # What magnitude is the indel rate compared to the substitution rate?
ignore_gaps = True # Shall trailing gaps be ignored / not penalised?
gaps = row_wise
zipf = 1.821
[[optimisation]]
start_min = 0.5
start_max = 1.5
nIteration = 14
[[K80]]
kappa = 2.59
[[TN93]]
alpha_1 = 0.3
alpha_2 = 0.4
beta = 0.7
[[score_calibration]]
scoreslist=phylo_gap01,
save_calibration = False
precision = 10
Creation of new Repeat list instances¶
[repeat_list]
output_characteristics = begin, msa_original, l_effective, n_effective, repeat_region_length, divergence, pvalue
model = phylo_gap01
Restrict Hmmer model size.¶
Set the maximum size of HMM for which the Viterbi algorithm is performed l_effective_max e.g. to ensure viable run-times on your system:
[hmm]
l_effective_max = 50
logging.ini - OPTIONAL¶
In this file, you can define the level of debugging per module (DEBUG, INFO, WARNING), and the format of the debugging message. Defaults to WARNING. The path to the file needs to be defined as
import logging
import logging.config
logging.config.fileConfig("path/to/your/home/.tral/logging.ini")