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# kff-tools

This repository contains a list of tools that are used to manipulate kff files.
kff file format is [described here](https://github.com/yoann-dufresne/kmer_file_format).

kff-tools is a program containing a set of small programs allowing kff files manipulations.
Each following part describes one of these tools.

## Install

git clone https://github.com/Kmer-File-Format/kff-tools.git --recursive
    cd kff-tools && mkdir build && cd build && cmake .. && make -j 4

## `kff-tools instr`

Convert a text kmer file or a text sequence file into a kff file. ACTG encoding is used.
Kmer files must contain 1 kmer per line.
Example (k=3):
```
  ACC
  CCT
  GTA
```
Sequence files must contains 1 sequence of compacted kmers per line.
Example (k=3):
```
  ACCT   # contains the 2 kmers ACC and CCT
  TGC
```
If data_size is non 0, then instr is looking for n integers at the end of the line (n: the number of kmer in the sequence).
The sequence and the data are separated by a one char delimiter (default ' ').
kmer data are separated by another one char delimiter (default ',').
Example (k=3):
```
  ACCC 12,31
  CCT 1
  GTAA 42,3
```

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to translate.
* **-o &lt;output.kff&gt;** \[required\]: Output kff file.
* **-k kmer_size** \[required\]: kmer size.

* **-d nb_bytes**: Data size in Bytes (Default 0, max 8).
* **-c**: Read counts at the end of the lines in a kmer txt file.
* **-m max_size**: Set the maximum number of kmer per sequence in the kff file. Set to 0 when 1 kmer per line. Split the sequences that are too long when reading a sequence file.

Usage:
```bash
  # Read 1 kmer per line
  kff-tools instr -i kmers.txt -o kmers.kff -k 12
  # Read 1 kmer per line with its counts (up to 255)
  kff-tools instr -i counts.txt -o counts.kff -k 12 -c -d 1
  # Read sequences and split them if the contains more than 256 kmers
  kff-tools instr -i sequences.txt -o sequences.kff -k 12 -m 256
```

## `kff-tools outstr`

Read a kff file and print to stdout the kmers and data as strings (one kmer per line)

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to print.
* **-c**: Print the encoding lexicagraphic minimal string between each kmer and its reverse complement (can affact the computation time).

Usage:
```bash
  kff-tools outstr -i file.kff
```

## `kff-tools validate`

Read a kff file and exit raising an error if a file corruption is detected.
Print details of the file on verbose mode.

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to read.
* **-v** : Verbose mode.

Usage:
```bash
  kff-tools validate -i file.kff -v
```

## `kff-tools bucket`

A tool that split each raw section into multiple minimizer sections.
Each section contains only kmers sharing the same minimizer (ie the same substring of size m minimizing the encoding order).

* **-i &lt;input.kff&gt;** \[required\]: File to bucketize.
* **-o &lt;output.kff&gt;** \[required\]: A file containing only minimizer sections (no raw). Each previous raw section is splitted into on minimizer section per bucket.
* **-m minimizer_size** \[required\]: The size of the minimizer to use.
* **-s**: Do not search for the minimizer on the reverse complements.

## `kff-tools compact`

Compact kmers into super-kmers (group of overlapping kmers sharing a minimizer).
One block per super-kmer generated is written.
Only the kmers inside of minimizer sections are compacted.
Each minimizer section is compacted separatly.
The compaction is linear in time and needs an amount of memory proportional to the largest minimizer section (larger in terms of number of kmers).

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to compact.
* **-o &lt;output.kff&gt;** \[required\]: Compacted file.

Usage:
```bash
  kff-tools compact -i to_compact.kff -o compacted.kff
```

## `kff-tools disjoin`

The disjoin tool is the opposite of the compact tool.
Each block containing a sequence of n kmers will be splitted in n blocks of 1 kmer.
The number of kmers inside of each section is preserved.

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: Input kff file.
* **-o &lt;output.kff&gt;** \[required\]: Dijoint file..

Usage:
```bash
  kff-tools disjoin -i input.kff -o disjoin.kff
```

## `kff-tools split`

Split a kff file into one kff file per section.

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: Input file to split.
* **-o &lt;path&gt;**: Directory where the split output files are written (Default ./).

Usage:
```bash
  kff-tools split -i to_split.kff -o split_dir/
```

## `kff-tools merge`

Merge a list of kff files into only one.
The order of the input file will be preserved in the merged output.

Parameters:
* **-i &lt;input1.kff&gt; &lt;input2.kff&gt; ...** \[required\]: Input file list to merge.
All the files must share the same encoding.
If not, please first translate them (you can use the translate subprogram of kff-tools).
* **-o &lt;output.kff&gt;** \[required\]: Name of the merged kff file.

Usage:
```bash
  kff-tools merge -i to_merge_1.kff to_merge_2.kff to_merge_3.kff -o merged.kff
```

## `kff-tools translate`

Read and rewrite a kff file changing the nucleotide encoding.

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to translate.
* **-o &lt;output.kff&gt;** \[required\]: Translated file.
* **-e &lt;encoding&gt;** \[required\]: 4 chars encoding. All the letters A, C, G and T must be present in the encoding order.
For example, AGTC represent the encoding A=0, G=1, T=2, C=3.

Usage:
```bash
  kff-tools translate -i to_encode.kff -o encoded.kff -e AGTC
```

## `kff-tools data-rm`

Read a kff file and write the same one with a data size of 0.
It means that all the data are removed and the file only preserve sequences.

Parameters:
* **-i &lt;input.kff&gt;** \[required\]: File to copy.
* **-o &lt;output.kff&gt;** \[required\]: Copied file without data.

Usage:
```bash
  kff-tools data-rm -i file.kff -o file_nodata.kff
```

# Testing the code

Run functional tests from the root of the project

```bash
  python3 -m unittest discover -s tests/
```

Run unit tests from the root of the project

```bash
  ./bin/tests
```

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