Usage - Genetalks/gtz GitHub Wiki

1:Compress the sample.fq to the current directory.
	gtz sample.fq    

2:Compress the file sample.fq into the out folder of the current directory.
	gtz sample.fq -o ./out/sample.fq.gtz    

***If the species is not specified by the '--bin-file' , GTZ will automatically recognize the species to compress.  ***  

3.GTZ performs high compression by specifying bin files in the Homo folder under the current directory.  
	gtz sample.fq --bin-file ./Homo/Homo_sapiens_bcacac9064331276504f27c6cf40e580.bin  

1.Deompress the file sample.fq to the current directory.If there is no species rbin file under "\~/.config/ gtz/", GTZ will be automatically downloaded from the Cloud to "\~/.config/ gtz /".  
	gtz -d sample.fq.gtz 

2.Specify the directory of the rbin path “~/Homo” for decompress sample.fq.gtz.  
	gtz -d sample.fq.gtz --rbin-path ~/Homo 

3.Decompress sample.fq.gtz to the Homo folder in the current path  
	gtz -d sample.fq.gtz --out-dir ./Homo    

usage: gtz [-h] [-o OUT] [-b INDEX_BIN] [-d DECOMPRESS] [-O OUT_DIR]  

-h, --help                                      show this help message and exit  
-o OUT, --out OUT                               specify the GTZ file name after compression  
-b BIN_FILE, --bin-file BIN_FILE                specify the bin file name for high compression  
-d DECOMPRESS, --decompress DECOMPRESS          decompress  
-O OUT_DIR, --out-dir OUT_DIR                   specify the save path of the extracted file 
-c, --stdout                                    decompress to terminal
-z, --fastq-to-fastq-gz                         decompress fastq to fastq.gz, it's valid only for FASTQ
-r RBIN_PATH, --rbin-path RBIN_PATH             specify the path where the rbin file resides  
-p PARALLEL_NUM,--parallel			specify parallel number for compression or decompression, 
						default equal CPU logical cores
-f, --force                                     force overwrite of output file  
-e, --no-keep                                   don't keep input files  
-v, --version                                   display version number  

Interaction mode:  
	gtz_index  
	
Show supported species and you can gradually create bin files through human-machine interaction mode.  

Manual mode  
1:Show supported species list，the index number is the input of the gtz_index download command.  
	gtz_index list  
	
2:Download the rbin file in the species list with No.1 index  
	gtz_index download 1  
	
3:Make BIN,rec file by specifying the rbin file". /Homo/Homo_sapiens_bcacac9064331276504f27c6cf40e580.rbin "  
	gtz_index makeindex ./Homo/Homo_sapiens_bcacac9064331276504f27c6cf40e580.rbin  
	

gtz_index <command> [options]
	list					show species which current support
	download <index> <path_to>		download species reference sequence rbin file , path_to is not necessary.  
	makeindex <rbin_path>			making reference sequence  

Step 1:  
Run the following command to extract the embeded programe gtz_reborn to current directory:  
	sed -e 's/\[GTZ_REBORN_BEGIN\]/\n&/;' sample.fq.gtz | sed -n '/\[GTZ_REBORN_BEGIN\]/,/\[GTZ_REBORN_END\]/p' | sed -e 's/.*\[GTZ_REBORN_BEGIN\]//g' -e 's/\[GTZ_REBORN_END\].*//g' | tar -zxvf -

Step2:  
If sample.fq.gtz is a high compression file, download the corresponding fasta file according to the prompt, and then extract the file.  
If sample.fq.gtz is not a high compression file, the FASTQ file can be extracted directly  
	./gtz_reborn -d sample.fq.gtz