{"id":17285307,"url":"https://github.com/ewels/niceliftover","last_synced_at":"2025-04-12T22:44:08.429Z","repository":{"id":15666665,"uuid":"18404090","full_name":"ewels/niceLiftOver","owner":"ewels","description":"Wrapper script to take an input file and liftOver the co-ordinates in place, leaving all other data in tact. 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These are core packages and typically come with most Perl installations.\n\nniceLiftOver is a wrapper script for the [UCSC liftOver tool](http://genome.ucsc.edu/cgi-bin/hgLiftOver) ([download here](http://hgdownload.cse.ucsc.edu/admin/exe/)). `liftOver` must be installed and added to your PATH.\n\nInstallation\n------------\nniceLiftOver is best used when added to your `PATH` environment. It is suitable for use with environment modules.\nIf you are not using environment modules, you can install niceLiftOver by adding the following to the `.bashrc` file in your home directory: `export PATH=\"$PATH\":\u003cinstallation directory\u003e/niceLiftOver`\n\nUsage\n-----\nTypical useage for niceLiftOver is `niceLiftOver \u003cchain ID\u003e *.files`\n\nniceLiftOver will look at the first line of the first file supplied and try to determine the delimeter between columns and then which column holds the chromosome and which hold the start and end positions. These can all be manually specified, see below.\n\nliftOver needs a chain file. These are kept in `\u003cinstallation directory\u003e/chainfiles/`. Available chain files can be seen by running `niceLiftOver --listchains`\n\nAdditional chain files can be downloaded from the [UCSC](http://hgdownload.cse.ucsc.edu/downloads.html)\n\n\nParameters\n---------\n* `--listchains`\n\t* List the available chain file IDs.\n\t* These are stored in `\u003cinstallation directory\u003e/chainfiles/`\n\t* Files must end in .over.chain\n\n* `--skip \u003cint\u003e`\n\t* Skip `n` lines at the start of each file\n\n* `--chr \u003cint\u003e`\n\t* Integer to specify which column should be used for the chromosome\n\t* 1 based index, eg. First column = 1 (not 0)\n\t* Defaults to searching the first line for the first occurance of \"chr\"\n\n* `--start \u003cint\u003e`\n\t* Integer to specify which column should be used for the start position\n\t* 1 based index, eg. First column = 1 (not 0)\n\t* Defaults to searching the first line for the first occurance of \"start\"\n\n* `--end \u003cint\u003e`\n\t* Integer to specify which column should be used for the end position\n\t* 1 based index, eg. First column = 1 (not 0)\n\t* Defaults to searching the first line for the first occurance of \"end\"\n\n* `--delim \u003cstr\u003e`\n\t* String delimiter to use to split columns\n\t* If not specified, niceLiftOver will try to split the first line using\n\t* tabs, commas and whitespace (in that order)\n\n* `--repdomain`\n\t* Shortcut to specify repdomain.com file format\n\n* `--version`\n\t* Print the version of the software\n\n* `--help`\n\t* Print this help message.\n\n\nAuthor\n------\nniceLiftOver was written by Phil Ewels at the Babraham Institute, Cambridge, UK\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fewels%2Fniceliftover","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fewels%2Fniceliftover","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fewels%2Fniceliftover/lists"}