9/18/18 RTK V0.1 2020-12-12 RTK V0.12. Minor updates.
Overview
The script seqs2ftab.py is used, in conjunction with "score definition" and sequence files, to generate sequence feature tables suitable for data analysis and machine learning.
Dependencies
The script requires pandas.
Background
The code parses the score definition file, then issues command line calls for each definition line and parses output(s) into a table. Each score definition line includes a command line specificiation, with program name and options separated by commas (rather than spaces), followed by one or more feature specifications (separated from the command specificiation and each other by spaces). When actually called, the command line is given a sequence filename as an additional agrument. Feature specifications take the form 'name=col' where the 'name' is a user-defined label for the feature (should be unique), and 'col' indicates which (command line) output column the feature is taken from.
Here is an example score definition line:
tm_util,-con,1e-7,-sal,0.2,-tmpey,-the 2=tmPey0_f 3=dGPey0_f 4=dHPey0_f 5=dSPey0_f
In this case, the script will call the program tm_util to get thermodynamic features. The command line specification and corresponding command line are as follows (using 'rand_seqs.dna' as the sequence filename):
# Command line specification from score definition file
tm_util,-con,1e-7,-sal,0.2,-tmpey,-the
# Actual command line; i.e. issued by script
tm_util -con 1e-7 -sal 0.2 -tmpey -the rand_seqs.dna
For this specific example, with the command line program tm_util (see NOTE2 below), the command line options -con and -sal set DNA and salt concentrations (to 1e-7 and 0.2 M, respectively); The -tmpey and -the options specify to use the Peyret thermodynamics algorithm, and to output all thermodynamic values. Output is dictated by the called command line code. In this case, we get melting temperature, Tm; free energy, dG; standard enthalpy, dH; and standard entropy, dS, terms, respectively.
There are four features indicated in the score definition line. These were chosen to match the output of the tm_util -the command; From col 2 we will get sequence melting temperature, Tm (named as 'tmPey0_f'), and from columns 3,4,5 we will get free energy ('dGPey0_f'), enthalpy ('dHPey0_f'), and entropy (dSPey0_f).
NOTE1: The output of called programs must have one line per input sequence. Blank lines and lines starting with "#" are ignored. Otherwise, each input sequence should have a corresponding output line with values to be extracted and compiled into score tables.
NOTE2: tm_util as well as other programs listed in the example score definition file (dna_util, alphcont, venpipe) are all part of the vertools collection; Source code is available here:
https://github.com/ryantkoehler/vertools
Usage
The script requires a score definition file and a sequence file.
Calling the script with --help will list options and (currently minimal!) usage instructions.
The following command line generates a table of features for sequences in the example 'rand_seqs.dna' file, using scores defined in the 'exam_score_defs.txt' file. In this example, the script 'exam_dna_prog.py' (included in this archive) is called; The output table has 10 features for 1000 sequences.
./seqs2ftab.py -s rand_seqs.dna -c exam_score_defs.txt -o rand_seqs.sco