smehringer / chopper-old

A tool to partition a set of sequences into similar batches.

Chopper - partition your sequences

System requirements

• GCC Version >= 7
• CMake Version >= 3.8 && <= 3.18

General setup

Set up the repository:

git clone --recurse-submodules https://github.com/smehringer/Chopper

Set up the build directory

mkdir chopper_build
cd chopper_build
cmake ../Chopper

Build the test to check if everything works

make test

Chopper pack

This submodule uses a hierarchical DP algorithm to pack user bins into a given number technical bins, optimizing the space consumption of a Hierarchical Binning Directory.

The app chopper pack needs an input file with filenames and weights as input (see chopper count if you want to use kmer counts as weights).

The file has to be tab separated and looks like this:

file_path1    500
file_path2    1000
file_path3    10
...

It can also contain meta information like taxonomic ids which you can group by later on:

file_path1    500    taxID_1
file_path2    1000   taxID_2
file_path2    10     taxID_2
...

If you have the file you can use chopper pack like this:

./chopper pack -f fata.tsv --technical-bins 2 -o output_filename.txt

Given the example tsv file with the 3 lines above, it will create a file output_filename.txt which looks like this:

#MERGED_BIN_0 max_bin_id:0
#HIGH_LEVEL_IBF max_bin_id:SPLIT_BIN_1
#BIN_ID SEQ_IDS NUM_TECHNICAL_BINS  ESTIMATED_MAX_TB_SIZE
MERGED_BIN_0_0  file_path1  62  9
MERGED_BIN_0_62 file_path2  2   5
SPLIT_BIN_1 file_path2  1   1000

Every line that starts with # is a header line and is needed for chopper split and chopper build.

The output file has the following columns:

1. BIN_ID: An identification of the bin. MERGED/SPLIT indicates a bin that has been merged/split. Note that MERGED bins with the same number belong together. In the example MERGED_BIN_0_0 and MERGED_BIN_0_62 both belong to MERGED_BIN_0.
2. SEQ_IDS: The file paths that belong to this bin.
3. NUM_TECHNICAL_BINS: The number of technical bins. For SPLIT bins, this indicates the number of technical bins in the High-Level IBF. For MERGED bins, this indicates the number of technical bins in the Low-Level IBF (MERGED bins have always exactly one bin in the High-Level IBF).
4. ESTIMATED_MAX_TB_SIZE: The estimated maximum bin size of this bin (can be neglected and is used for internal calculations).

To be continued...

More Examples and descriptions will follow soon.