profile_counts

Contents

• profile_counts
  • Overview
  • Command-line usage
  • Example Input and Output

Overview

profile_counts is a program within the sortseq_tools package which tallies the occurance of each base or amino acid at each position and outputs them in a table.

After you install `sortseq_tools`_, this program will be available to run at the command line.

Command-line usage

usage: sortseq profile_counts [-h] [-b BIN] [-w WTSEQ] [-t {dna,rna,protein}]
                              [-i I] [-o OUT]

Options:

-b, --bin	Bin where mutation rate will be measured. If left blank, total mutation rate will be measured.
-w, --wtseq	Wild Type Sequence
-t=dna, --type=dna
	Undocumented Possible choices: dna, rna, protein
-i, --i	Input file, otherwise input through the standard input.
-o, --out	Undocumented

Example Input and Output

The input table must have at least a column for sequences, and a column with counts.

Example input table:

seq       ct
ACAGGT    10
ACGGTT    9
...

Alternatively by using the –bin k option, another bin can be profiled.

Then the example table must at least have a column of sequences and a column labeled ct_k:

seq       ct_1
ACAGGT    10
ACGGTT    9
...

An example command to run the analysis is

sortseq profile_counts -i input_table.txt