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I’m going to use these results to analyse different HMM models in the BioProspector package. Also, for maximum flexibility, I’m going to use my own biological training data set. As a general note, there is a limit of 1 million base pairs in a simulation setting, but we do not have this limit in real training data. The challenge is to build a model that fits training data well and also predicts accurately when the model is applied to new sequences. The final goal is not only to analyse different training data sets, but also to predict genes from an unknown genome. I will set the minimum cut-off probability to 10%. I will use the standard BioProspector training functions and visualise the results. We will use the software tools BFITTM to filter out uninformative bases (like 3 and 9), and NMF to reduce the size of the simulated training data set. Another important issue is to fit the model to the training data without using any parameter. The goal is to compare and validate how the trained models behave. The following picture shows the data set. Some of the sequences might be too long. The sequences are sorted by length. If we use too many base pairs, then the models will get out of memory or the computation will take too long. Only the first 5000 bases are shown in this picture. The figure on the right shows the base pair length distribution of the training set. The concentration of genes decreases towards the end of the training data, but we need to train a model of the entire genome in order to predict new genes. We will use the following codes.
python train.py -t -s 5000 -r 5000 -u 53552 –nme 0.6 –mfe 0.6 –aut 0 –ncols 1 –lend 1 –maxgene 1000 –minfreeprob 10 –maxfreeprob 1
The following codes are from the ViterbiHMM_jof.py.
Python Viterbi HMM code
We have the following files for building the model.
*result.hmm
(c) 2014, Rodrigo N
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A:
You have a broken package dependency.
It depends on version 0.7.4, but version 0.6.0-4 is installed. When installing it manually, it asks for version 0.6.2-4, but your package depends on 0.7.4.
You are likely to get the same error when you upgrade tomorrow.
Rather than try to manually resolve the package dependency, you should upgrade as soon as it becomes available.
Maybe something goes wrong during the upgrade and removes something necessary, but the point is:
Upgrade to a recent version
Use the updated version
Q:
Batch file to run command and store its output to files (optional)
I have a command that runs test cases from a directory (runs fine on windows and linux).
I am trying to write a batch file to run the test, then dump its output (pass/fail) to a text file. Then I want it to repeat the process on the files in a subdirectory.
So far I have this:
@ECHO OFF
:: Run test for all cases
FOR /R “%1” %%a in (*.txt) DO “%2″ &1 | findstr /L /C:”[PASSED]” > “%%a.log”
:: Dump results for each directory
FOR /R “%1” %%a in (*.txt) DO %3 “%%a”
A:
Try this:
@echo off
setlocal
:: Load output file
for /f %%a in (‘dir %~dp1 %%~fa *.log’) do set “output=%%a”
:: Read input file
for /r %1 %%a in (*.txt) do for /f %%b in (‘echo %%a^|findstr /rx B’) do (
if not defined output (
echo %%a^|findstr /L /C:”[PASSED]” > %output%
echo %%a^|findstr /L /C:”[FAILED]” > %output%
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