{"id":15018235,"url":"https://github.com/pseudogene/genetic-mapper","last_synced_at":"2025-10-30T19:30:52.842Z","repository":{"id":79848606,"uuid":"47559073","full_name":"pseudogene/genetic-mapper","owner":"pseudogene","description":"SVG Genetic Map Drawer","archived":true,"fork":false,"pushed_at":"2020-05-22T07:54:31.000Z","size":48,"stargazers_count":10,"open_issues_count":0,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-24T02:19:30.044Z","etag":null,"topics":["bioinformatics","genetic-maps","genetics","perl-script","svg"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pseudogene.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-12-07T15:02:44.000Z","updated_at":"2024-10-31T07:40:30.000Z","dependencies_parsed_at":null,"dependency_job_id":"ac7376d5-410f-4ee8-9b30-4696786329fd","html_url":"https://github.com/pseudogene/genetic-mapper","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Fgenetic-mapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Fgenetic-mapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Fgenetic-mapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Fgenetic-mapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pseudogene","download_url":"https://codeload.github.com/pseudogene/genetic-mapper/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239036821,"owners_count":19571571,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","genetic-maps","genetics","perl-script","svg"],"created_at":"2024-09-24T19:51:42.886Z","updated_at":"2025-10-30T19:30:47.579Z","avatar_url":"https://github.com/pseudogene.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"Genetic-mapper - Vectorial Genetic Map Drawer\n\n[![Build Status](https://travis-ci.org/pseudogene/genetic-mapper.svg?branch=master)](https://travis-ci.org/pseudogene/genetic-mapper) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/9ca9d97b26f94b27911cbf6e6e95f55a)](https://www.codacy.com/manual/pseudogene/genetic-mapper?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=pseudogene/genetic-mapper\u0026amp;utm_campaign=Badge_Grade)\n\n# Genetic-mapper\n\nGenetic-mapper is a perl script able to draw publication-ready vectorial genetic maps.\n\n## Description\n\nPerl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like [Inkscape](https://inkscape.org/) and [Abobe Illustrator(R)](http://www.adobe.com/uk/products/illustrator.html).\n\nThe input file must be a text file with at least the marker name (ID), linkage group (LG) and the position (POS) separeted by tabulations. Additionally a logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.\n\n```plaintext\nmap.tsv\n\nID\u003ctab\u003eLG\u003ctab\u003ePOS\u003ctab\u003eLOD\n13519  12     0       0.250840894\n2718   12     1.0     0.250840893\n11040  12     1.6     0.252843341\n...\n```\n\n## How to cite Genetic-mapper\n\n\u003e**Genetic-Mapper: vectorial genetic map drawer**.\n\u003eBekaert M.\n\u003e_F1000Research_. 2016, 5:1301 (poster).\n\n[![DOI](https://img.shields.io/badge/DOI-10.7490%2Ff1000research.1112266.1-blue.svg)](http://dx.doi.org/10.7490/f1000research.1112266.1)\n\n## Installation (optional)\n\nYou can directly use the script `script/genetic_mapper.pl` or install it in your system using:\n\n```sh\ngit clone https://github.com/pseudogene/genetic-mapper.git\ncd genetic-mapper\nperl Makefile.pl\nmake\nmake test\nsudo make install\n```\n\n## Usage\n\n```plaintext\n..:: Vectorial Genetic Map Drawer ::..\n\nUsage: ./genetic_mapper.pl [options] --map=\u003cmap.tsv\u003e\n\nOptions\n --map \u003cgenetic map file\u003e\n       The input file must be a text file with at least the marker name (ID), linkage\n       group (LG) and the position (POS) separeted by tabulations. Additionally a\n       logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.\n         ID     LG    POS     LOD\n         M19    12    0.01    0.45068\n         M18    12    1.14    0.00014\n         M40    12    11.48   0.25284\n  --chr \u003cstring\u003e\n       Draw only the specified chromosome/linkage group.\n  --delim \u003ccharacter\u003e\n       Use \u003ccharacter\u003e as the field delimiter character instead of the tab character.\n  --bar\n       Use a coloured visualisation with a dark bar at the marker position.\n  --plot\n       Rather than a list of marker names, it plots a circle. If the LOD-score is provided\n       a dark disk fills the circle proportionality to its value.\n  --species\n       Rather than a list of marker names, it plots a coloured circle. The option --col\n       must be used to specify the species name (incompatible with --plot or --bar).\n  --var\n       If specified with --bar or --plot the size of the bar/circle is proportional to the\n       number of markers.\n  --col\n       If --plot is specified and if more that one LOD-score column is available specify\n       the column number [default 1 (first LOD-score column)].\n  --square\n       Small squares are used rather than names (incompatible with --plot).\n  --pos\n       The marker positions are indicated on the left site of the chromosome.\n  --compact\n       A more compact chromosome is used (incompatible with --bar).\n  --karyotype=\u003ckaryotype.file\u003e\n       Specify a karytype to scale the physical chromosme. Rather than using genetic\n       distances, expect nucleotide position in the map file.\n        FORMAT: \"chr - ID LABEL START END COMMENT\"\n  --scale= ]0,+oo[\n       Change the scale of the figure [default x10].\n  --split\n       If multiple markers have the same position, split the markers on multiple links\n       rather than on a long list on name.\n  --horizontal\n       Rotate the figure by 90 degrees.\n  --verbose\n       Become chatty.\n```\n\n## Examples\n\n```sh\n# compact (stylish)\n./genetic_mapper.pl --var --compact --plot --map=map.tsv \u003e lg.svg\n\n# Classic publication style\n./genetic_mapper.pl --pos --chr=13 --map=map.tsv \u003e lg13.svg\n```\n\n![LG13](lg13.png \"LG13 compact or classic\")\n\n## License\nThe content of this project itself is licensed under the [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/), and the source code presented is licensed under the [GPLv3 license](http://www.gnu.org/licenses/gpl-3.0.html).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Fgenetic-mapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpseudogene%2Fgenetic-mapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Fgenetic-mapper/lists"}