This program reformats column distance matrix into the input format for running web tool of Two-Sample Tests for Comparing Intra-Individual Genetic Sequence Diversity Between Populations. Click here for more information of the tool.
Input
Example:
seq1 seq10 0.01486108 seq1 seq2 0.00000000 seq1 seq3 0.00000000 seq1 seq4 0.00000000 seq1 seq5 0.00162075 seq1 seq6 0.01315215 seq1 seq7 0.01803690 seq1 seq8 0.01151463 seq1 seq9 0.01636412 seq2 seq10 0.01486108 seq2 seq3 0.00000000 seq2 seq4 0.00000000 seq2 seq5 0.00162075 seq2 seq6 0.01315215 seq2 seq7 0.01803690 seq2 seq8 0.01151463 seq2 seq9 0.01636412 seq3 seq10 0.01486108 seq3 seq4 0.00000000 seq3 seq5 0.00162075 seq3 seq6 0.01315215 seq3 seq7 0.01803690 seq3 seq8 0.01151463 seq3 seq9 0.01636412 seq4 seq10 0.01486108 seq4 seq5 0.00162075 seq4 seq6 0.01315215 seq4 seq7 0.01803690 seq4 seq8 0.01151463 seq4 seq9 0.01636412 seq5 seq10 0.01648743 seq5 seq6 0.01480351 seq5 seq7 0.01970637 seq5 seq8 0.01315187 seq5 seq9 0.01802527 seq6 seq10 0.00814550 seq6 seq7 0.01638615 seq6 seq8 0.00487810 seq6 seq9 0.00980428 seq7 seq10 0.01807237 seq7 seq8 0.01474021 seq7 seq9 0.01975881 seq8 seq10 0.00650614 seq8 seq9 0.00815682 seq9 seq10 0.01144043
Example:
group1 subject1 seq1 group1 subject1 seq2 group1 subject1 seq3 group1 subject1 seq4 group1 subject1 seq5 group2 subject2 seq6 group2 subject2 seq7 group2 subject2 seq8 group2 subject2 seq9 group2 subject2 seq10
Output
Example:
1 2 1 1 0.00000000 1 3 1 1 0.00000000 1 4 1 1 0.00000000 1 5 1 1 0.00162075 2 3 1 1 0.00000000 2 4 1 1 0.00000000 2 5 1 1 0.00162075 3 4 1 1 0.00000000 3 5 1 1 0.00162075 4 5 1 1 0.00162075 1 2 2 2 0.01638615 1 3 2 2 0.00487810 1 4 2 2 0.00980428 1 5 2 2 0.00814550 2 3 2 2 0.01474021 2 4 2 2 0.01975881 2 5 2 2 0.01807237 3 4 2 2 0.00815682 3 5 2 2 0.00650614 4 5 2 2 0.01144043
Example:
Subject index Subject 1 subject1 2 subject2 Group index Group 1 group1 2 group2
How to run
chmod +x ColumnDist2diverstest.pl
Create a subdirectory in your working directory to hold input and output files. In the subdirectory, type following command:
perl ../ColumnDist2diverstest.pl InputColumnDistanceFile InputGroupFile OutputDistanceFile OutputInfoFile