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csmap - Conservation score mapper

Usage

Indexing and packing score files

Firstly, you need to index and pack score files:

$ packwig.py scores chr2L.wig chr2R.wig chr3L.wig chr3R.wig chr3.wig chrX.wig

This will generate a tar file named 'scores.tar'.

If you have more than one score files and want to pack all of them, you can do that:

$ packwig.py output *.wig

Before your packing, please check the identity of chromosome names in score file and in fasta file.

Score mapping

Here is an example of fasta header in 'input.fa' file for score mapping:

>dm3_xenoRefGene_NM_068112 range=chr4:1009965-1125359 5'pad=0 3'pad=0 strand=+ repeatMasking=none

$ csmap.py input.fa scores.tar.bz2 result.txt

This script identified a keyword 'range=X:A-B' (where X is chromosome name, A is start position and B is stop position), and generated a file named 'result.txt'. Bases with the range of 1009965 to 1125359 were mapped.

Column descriptions

  • sequence_name: sequence name in fasta
  • avg_conservation_score: conservation score on average