{"id":26450399,"url":"https://github.com/ibchgenomic/pacbio-polyatgc-remove","last_synced_at":"2025-03-18T15:25:49.995Z","repository":{"id":262142671,"uuid":"845193802","full_name":"IBCHgenomic/pacbio-polyATGC-remove","owner":"IBCHgenomic","description":"polyATGC pacbio/oxford nanopore estimator","archived":false,"fork":false,"pushed_at":"2024-08-20T19:47:45.000Z","size":2,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-11T23:15:34.800Z","etag":null,"topics":["bioinformatics","genome-analysis","genome-annotation","pacbio-data","pacbio-hifi-sequencing-reads","pacbio-sequencing","pacbiohifi"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/IBCHgenomic.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-08-20T19:09:34.000Z","updated_at":"2025-01-16T18:49:51.000Z","dependencies_parsed_at":"2024-11-10T20:18:24.273Z","dependency_job_id":"ae725e19-3ea6-4bf8-a91a-8a67541fb294","html_url":"https://github.com/IBCHgenomic/pacbio-polyATGC-remove","commit_stats":null,"previous_names":["applicativesystem/pacbio-nanopore-polyatgc-remove","sciencegenome/python-pacbio-nanopore-polyatgc-remove","sciencegenome/pacbio-polyatgc-remove","ibchgenomic/pacbio-polyatgc-remove"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpacbio-polyATGC-remove","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpacbio-polyATGC-remove/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpacbio-polyATGC-remove/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpacbio-polyATGC-remove/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IBCHgenomic","download_url":"https://codeload.github.com/IBCHgenomic/pacbio-polyATGC-remove/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244247616,"owners_count":20422632,"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","genome-analysis","genome-annotation","pacbio-data","pacbio-hifi-sequencing-reads","pacbio-sequencing","pacbiohifi"],"created_at":"2025-03-18T15:25:44.381Z","updated_at":"2025-03-18T15:25:49.988Z","avatar_url":"https://github.com/IBCHgenomic.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pacbio-nanopore-polyATGC-trimmer\n\n- A regular expression based polyATGC trimmer from the long reads or the fastq reads extremely fast and returns a fasta and also a dataframe for the sequence classification and this takes the current as 10 continuous bases.\n- A sample on how to run the code is given below. if you are using the long reads for machine learning then it directly returns a dataframe for ingestion to machine leaning.\n\n```\nlongreadpolyATGCtrimmer(\"/Users/gauravsablok/Desktop/CodeCheck/fasta_sample_datasets/test_sample_short.fasta\",\n                              polyATGCstretch_type=\"G\")\n\tids\tsequences\tstretch_count\ttrimmed_sequences_new\n0\t\u003e1\tGCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...\t[27, 30]\tGCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...\n1\t\u003e2\tGCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...\t[27, 30]\tGCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...\n2\t\u003e3\tGCAGCGTACGTGGTTGGATCAATTAGTGGGGCACATTTGAATCCAG...\t[27, 30]\tGCAGCGTACGTGGTTGGATCAATTAGTGCACATTTGAATCCAGCTT...\n3\t\u003e4\tCGAAAATTACTTCGGTACAATGCTTGTATACATGGGCAAAGCACAC...\t[33, 36]\tCGAAAATTACTTCGGTACAATGCTTGTATACATCAAAGCACACGGT...\n```\nGaurav Sablok \\\nAcademic Staff Member \\\nUniversity of Potsdam \\\nPotsdam,Germany\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fpacbio-polyatgc-remove","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fibchgenomic%2Fpacbio-polyatgc-remove","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fpacbio-polyatgc-remove/lists"}