profile_freqs is a program within the sortseq_tools package which calculates the fractional occurrence of each base or amino acid at each position.
After you install `sortseq_tools`_, this program will be available to run at the command line.
usage: sortseq profile_freqs [-h] [-b BIN] [-i I] [-w WTSEQ]
[-t {dna,rna,protein}] [-o OUT]
| -b, --bin | Bin where mutation rate will be measured. If left blank, total mutation rate will be measured. |
| -i, --i | Input file, otherwise input through the standard input. |
| -w, --wtseq | Wild Type Sequence |
| -t=dna, --type=dna | |
Undocumented Possible choices: dna, rna, protein | |
| -o, --out | Undocumented |
Input tables must contain a position column (labeled ‘’pos’‘) and columns for each base or amino acid (labeled ct_A, ct_C...).
Example Input Table:
pos ct_A ct_C ct_G ct_T
0 10 20 40 30
...
Example Output Table:
pos freq_A freq_C freq_G freq_T
0 .1 .2 .4 .3
...
An example command to run the analysis is
sortseq profile_freqs -i counts_table.txt