{"id":20393940,"url":"https://github.com/stewsquared/rosalind-long-python","last_synced_at":"2025-08-26T09:18:28.632Z","repository":{"id":67764619,"uuid":"71482142","full_name":"stewSquared/rosalind-long-python","owner":"stewSquared","description":"Solution to http://rosalind.info/problems/long/","archived":false,"fork":false,"pushed_at":"2016-11-29T00:51:15.000Z","size":334,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"optimized","last_synced_at":"2025-03-05T00:41:29.981Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/stewSquared.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-10-20T16:24:54.000Z","updated_at":"2019-03-14T18:06:34.000Z","dependencies_parsed_at":"2023-02-21T07:30:40.373Z","dependency_job_id":null,"html_url":"https://github.com/stewSquared/rosalind-long-python","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/stewSquared/rosalind-long-python","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stewSquared%2Frosalind-long-python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stewSquared%2Frosalind-long-python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stewSquared%2Frosalind-long-python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stewSquared%2Frosalind-long-python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stewSquared","download_url":"https://codeload.github.com/stewSquared/rosalind-long-python/tar.gz/refs/heads/optimized","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stewSquared%2Frosalind-long-python/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272202204,"owners_count":24891164,"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","status":"online","status_checked_at":"2025-08-26T02:00:07.904Z","response_time":60,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-11-15T03:51:15.204Z","updated_at":"2025-08-26T09:18:28.606Z","avatar_url":"https://github.com/stewSquared.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Usage\n\nMark executable or run with `python2 rosalind.py`. Takes a filename\n(defaults to \"rosalind_long.txt\") and prints assembled strand.\n\n\n## Caveats\n\n`find_overlap` assumes (without loss of correctness) that left and\nright are roughly the same length. Complexity is O(len(left)) rather\nthan O(min_overlap). Superstring relationships are not detected.\n\n`adjacency_list` is not technically an adjacency list, whose type\nwould map `String -\u003e List[String]` rather than `String -\u003e String`.\nThis is fine for our case, where the path is linear and unique.\n\nI could return some sort of overlap object/tuple/datastructure that\nstores the length of overlap, rather than just a string, so I don't\nhave to recompute overlap during assembly. I don't for two reasons:\n\n - find_overlap is only called O(N) times during assembly vs O(N^2)\n   times during adjacency. Not likely to make 1% difference.\n\n - By not overdesigning for this special-case optimization, code is\n   cleaner, more intuitive, and more re-useable.\n\nI call `find_overlap` in `assemble` without first performing a None\ncheck. This is safe, because of the pre-computed `adj`. But the\ncompiler doesn't know that. Renegade for life ;)\n\nThere are no tests; I used the REPL to develop. That said, code is\nmodular and testable, since this is TDD with tests thrown out.\n\nDocumentation is just comments with Scala type signatures. Sorry.\n\n\n### Performance\n(`time` 50, 500, and 5000 reads on a Xeon processor)\n```\nreal    0m0.016s    0m0.232s    0m20.159s\nuser    0m0.010s    0m0.223s    0m20.140s\nsys     0m0.003s    0m0.007s    0m0.017s\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstewsquared%2Frosalind-long-python","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstewsquared%2Frosalind-long-python","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstewsquared%2Frosalind-long-python/lists"}