diff --git a/README.md b/README.md index 8a11c0f..68adefb 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ NAME ==== -fatool +FA_TOOL VERSION ======= @@ -10,6 +10,8 @@ VERSION LICENSE ======= +Specified in LICENSE.md file + INTRODUCTION ============ @@ -36,10 +38,10 @@ facutter commands: {cut,extractNames,extractContigs,remContigs,join,split} each has own params cut split supplied sequence into smaller parts, according to given params - extractNames extracting contigs names only - extractContigs extracting contigs specified in file (output in new file) + extractNames extracting contigs names only into list txt file + extractContigs extracting contigs specified in file based on contigs names list (output in new file) join joining two or more files, yet not verifing duplicates - remContigs removing contigs specified in file (output in new file) + remContigs removing contigs specified in file based on contigs names list (output in new file) split each cotig saved into separate file cut: @@ -47,11 +49,11 @@ cut: usage: fatool.py cut [-h] -r RANGE [-o OUTPUT] [-s STEP] [--log LOG] optional arguments: - -h, --help show this help message and exit - -r RANGE, --range RANGE cutted sequence length + -h, --help show this help message and exit + -r RANGE, --range RANGE cutted sequence length -o OUTPUT, --output OUTPUT output file default: output.fa - -s STEP, --step STEP step length default: 1 - --log LOG log file if not supplied stdout + -s STEP, --step STEP step length default: 1 + --log LOG log file if not supplied stdout extractContigs: @@ -99,4 +101,4 @@ split: optional arguments: -h, --help show this help message and exit - -d OUTPUTDIR, --outputDir output directory where splited contigs will be saved \ No newline at end of file + -d OUTPUTDIR, --outputDir output directory where splited contigs will be saved