• A Linux software for comprehensive DNA sequences compression

Version 1.3.0 Lasted edit time: 2021.6.5

Project for bi296 course

Dongchang Road 800, Minhang district, Shanghai, China.

Auto Install

./INSTALL

Manual Install

• make
• make install
• make clean
• cd bin
• ./main [Option] [Parameter] [Filename] ...

./main [Option] [Parameter] [Filename] ...

[OPTION]

-h, --help Obtain help from our doc

-v, --version Obtain version information

-c, --compress Compress mode

-d, --decompress Decompress mode

-t, --transfer Transfer file into fasta format (FILENAME.fq --> FILENAME.fq.transfer)

-e, --extract Extract sequences from standard fasta or transfered file (FILENAME.transfer)

-f, --MFC Compress .fa via MFC algorithm. The output file will be notes as suffix .mfc

-m, --huffman Compress .fa.ex or file containing only DNA sequences via huffman algorithm.

-o, --OEC Compress .fa.ex or file containing only DNA sequences via OEC algorithm.

-n, --Num Compress .fa.ex or file containing only DNA sequences via Num algorithm.

[Parameter]

MFC algorithm

-p, --parallel Choose the parallel progression of compression. Default progression is 2 (if parameter is not used).

-s, --speed Choose the compression speed (Default speed: 2).

		Speed 1: The fastest mode. Low compression rate and less memory cost.

		Speed 2: The balanced mode. Medium compression rate and medium memory cost.

		Speed 3: The slowest mode. High compression rate and high memory cost.

Huffman algorithm

[Encodefile] Compressing [Encodefile] with two output files: [Encodefile_hbin] and [Encodefile_table].

[Decodefile] Decompressing [Decodefile]. To simplify users input, users are allowed to input the filename of [Encodefile_hbin] or [Encodefile_table] only.

OEC algorithm

[Encodefile] Compressing [Encodefile] with two output files: [Encodefile_obin] and [Encodefile_dic].

[Decodefile] Decompressing [Decodefile]. To simplify users input, users are allowed to input the filename of [Encodefile_obin] or [Encodefile_dic] only.

Num algorithm

[Filename] Compressing and Decompressing [Filename]. Display outcome on prompt windows.

[Examples]

./main -c -s 3 -p 10 -f test.fa Utilized MFC algorithm to compress test.fa With speed 3 and parallel progression 10. Combinated parameters input style is also allowed. See: ./main -cs 3 -p 10 -f test.fa

./main -d -f -p 10 test.fa.mfc Utilized MFC algorithm to decompress test.fa.mfc With parallel progression 10.

./main -c -m test.fa.ex Compressing [test.fa.ex] (plain DNA sequences file) with two modes.

./main -d -m test.fa.ex Decompressing compressed file [test.fa.ex] as output file [test.fa.ex.hufde].