{"id":17278197,"url":"https://github.com/mojaveazure/pseudoscaffold_annotator","last_synced_at":"2025-03-26T14:23:12.015Z","repository":{"id":33265198,"uuid":"36909739","full_name":"mojaveazure/Pseudoscaffold_Annotator","owner":"mojaveazure","description":"A Python package for creating an annotation file for a pseudoscaffold","archived":false,"fork":false,"pushed_at":"2017-03-21T21:56:54.000Z","size":14763,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-31T15:40:37.388Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"Jessie365/accedia-git-workshop-intermediate","license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mojaveazure.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-06-05T03:26:52.000Z","updated_at":"2015-08-20T13:41:25.000Z","dependencies_parsed_at":"2022-09-10T14:50:06.984Z","dependency_job_id":null,"html_url":"https://github.com/mojaveazure/Pseudoscaffold_Annotator","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mojaveazure%2FPseudoscaffold_Annotator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mojaveazure%2FPseudoscaffold_Annotator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mojaveazure%2FPseudoscaffold_Annotator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mojaveazure%2FPseudoscaffold_Annotator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mojaveazure","download_url":"https://codeload.github.com/mojaveazure/Pseudoscaffold_Annotator/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245668687,"owners_count":20653015,"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":[],"created_at":"2024-10-15T09:11:02.991Z","updated_at":"2025-03-26T14:23:06.996Z","avatar_url":"https://github.com/mojaveazure.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pseudoscaffold_annotator\n### A program to annotate an assembled pseudoscaffold\n___\n___\n\n**If this program fails on you, revert back to a previous release using the commands**\n```shell\ngit checkout -f\ngit reset --hard 25543ca66a9a1a7cc1ab8dc72f4c6e237e797478\n```\n\nThis is a program for annotating an assembled pseudoscaffold using a reference genome and annotation file. Currently, this only supports using GFF3 files as input, but can output both GFF3 files and 3-column BED files. Increased support for the BED format will come later.\n\nRunning this program to annotate a pseudoscaffold is done using the following command:\n\n```shell\n./pseudoscaffold_annotator.py annotate -r REFERENCE_FASTA -a ORIGINAL_ANNOTATION -p PSEUDOSCAFFOLD_FASTA -o OUTFILE_NAME -c BLAST_CONFIG_FILE\n```\n\nThe BLAST configuration file can be run using the following command:\n\n```shell\n./pseudoscaffold_annotator.py blast-config\n```\nUse the `-h` flag to see all options for configuring.\n\n**IMPORTANT**\n\npseudoscaffold_annotator.py requires no new lines within the sequence of the pseudoscaffold. The following is not an allowed sequence:\n\n        \u003epseudoscaffold\n        ACTGTCAG\n        GCTATCGA\n\nThe 'fix' subroutine removes new lines\nbetween sequence data, creating a fasta\nfile that reads like:\n        \u003epseudoscaffold\n        ACTGTCAGGCTATCGA\n\nTo fix a pseudoscaffold, run the following command:\n\n```shell\n./pseudoscaffold_annotator.py fix -p PSEUDOSCAFFOLD_FASTA -n FIXED_FASTA\n```\n\nThis program requires Python 2.7 or higher, or the [`argparse`](https://pypi.python.org/pypi/argparse) module installed for Python 2.6\n\n**NOTE: this has NOT been tested on Python 3.x**\n\nOther dependencies include:\n - [BEDTools](http://bedtools.readthedocs.org/en/latest/)\n - [NCBI's BLAST+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs\u0026DOC_TYPE=Download)\n - [BioPython](http://biopython.org/wiki/Main_Page)\n\n**NOTE: This program has only been tested with the _Morex_ (Barley) genome, please use with caution**\n\n## TODO\n\n - Add support for extracting information from BED file\n - Add parallelization support\n - Add BED to GFF annotating capabilities\n - Add GFF to BED annotating capabilities\n - ~~Finish GFF to GFF annotation capabilities~~ DONE!\n - Add BED to BED annotating capabilities\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmojaveazure%2Fpseudoscaffold_annotator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmojaveazure%2Fpseudoscaffold_annotator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmojaveazure%2Fpseudoscaffold_annotator/lists"}