profile_enrichment

Contents

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

Overview

profile_enrichment is a program within the sortseq_tools package which calculates the log enrichment of each amino acid at each position. Pseudo counts are added to each entry during the calculation.

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

Command-line usage

usage: sortseq profile_enrichment [-h] [-s START] [-e END] [-w WTSEQ]
                                  [--pseudo PSEUDO] [-t {dna,rna,protein}]
                                  [-i I] [-o OUT]

Options:

-s=0, --start=0
	Position to start your analyzed region
-e, --end	Position to end your analyzed region
-w, --wtseq	Wild type sequence
--pseudo=1	Pseudo counts to add
-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

Input tables must be a table containing a column for sequences, counts before selection and counts after selection.

Example Input Table:

seq    ct_0    ct_1
GAPY   10      34
APFY   30      10
...

Example Output Table:

pos   le_A    le_C ...
0     .1      -.2
1     .4      -.3
...

The analysis can be run using the command:

sortseq profile_enrichment -i selected_library.txt

Where selected_library.txt is the file containing your input table.