{"id":33926581,"url":"https://github.com/rustcodepro/proteogenomics","last_synced_at":"2025-12-12T10:23:38.045Z","repository":{"id":275190168,"uuid":"924331723","full_name":"rustcodepro/proteogenomics","owner":"rustcodepro","description":"proteogenomics for protein analysis","archived":false,"fork":false,"pushed_at":"2025-09-29T11:35:26.000Z","size":6988,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-11-29T20:17:17.801Z","etag":null,"topics":["bioinformatics","euclidean-algorithm","euclidean-distances","genome-analysis","genome-annotation","hmm","hmm-model","hmmer","pdb","pdb-files"],"latest_commit_sha":null,"homepage":"","language":"Rust","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/rustcodepro.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-01-29T20:11:51.000Z","updated_at":"2025-09-29T11:35:29.000Z","dependencies_parsed_at":"2025-01-31T19:24:07.030Z","dependency_job_id":"747bda38-a920-450d-8980-2f0c74c34fa0","html_url":"https://github.com/rustcodepro/proteogenomics","commit_stats":null,"previous_names":["sciencegenome/proteome-model","ibchgenomic/proteogenomics","sciencegenome/proteogenomics","sciencegenome/proteome-hmm","codebiogenomics/proteogenomics","genomicssport/proteogenomics","omicscode/proteogenomics","rustcodepro/proteogenomics"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/rustcodepro/proteogenomics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fproteogenomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fproteogenomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fproteogenomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fproteogenomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rustcodepro","download_url":"https://codeload.github.com/rustcodepro/proteogenomics/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rustcodepro%2Fproteogenomics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27680802,"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":"2025-12-12T02:00:06.775Z","response_time":129,"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":["bioinformatics","euclidean-algorithm","euclidean-distances","genome-analysis","genome-annotation","hmm","hmm-model","hmmer","pdb","pdb-files"],"created_at":"2025-12-12T10:23:33.989Z","updated_at":"2025-12-12T10:23:38.038Z","avatar_url":"https://github.com/rustcodepro.png","language":"Rust","readme":"# proteogenomics\n - rust crate for hmm domain search, selection and annotation mapper.\n - it reports only chains with atoms for the id and sequence and euclidean distance for all irrespective of chain and atoms.\n - Euclidean distance chain comparsion for two point coordinate protein.\n - Euclidean distance chain coordinate comparsion for all protein atoms of the chain.\n\n\n ```\n  cargo build\n ```\n\n ```\n _                                                               _\n_ __    _ __    ___   | |_    ___    ___     __ _    ___   _ __     ___    _ __ ___   (_)   ___   ___\n| '_ \\  | '__|  / _ \\  | __|  / _ \\  / _ \\   / _` |  / _ \\ | '_ \\   / _ \\  | '_ ` _ \\  | |  / __| / __|\n| |_) | | |    | (_) | | |_  |  __/ | (_) | | (_| | |  __/ | | | | | (_) | | | | | | | | | | (__  \\__ \\\n| .__/  |_|     \\___/   \\__|  \\___|  \\___/   \\__, |  \\___| |_| |_|  \\___/  |_| |_| |_| |_|  \\___| |___/\n|_|                                          |___/\n\nhmm proteome analyze\n************************************************\nAuthor Gaurav Sablok,\nEmail: codeprog@icloud.com\n************************************************\n\nUsage: proteogenomics \u003cCOMMAND\u003e\n\nCommands:\ntarget-hmm             select the targets from the hmm\nscore-hmm              select the scores from the hmm\nevalue-hmm             select the evalues from the hmm\neval-target            select the targets based on evalue and target\ntargetcounts           prepare the unique counts of the domains\npdb-id\npdb-sequence           extract the sequence of the pdf file\neuclidean-comparative  calculate the euclidean distance bettwen two chain coordinates\neuclidean-all          calculates the euclidean distance for all chain atoms\nhelp                   Print this message or the help of the given subcommand(s)\n\nOptions:\n-h, --help     Print help\n-V, --version  Print version\n```\n\n ```\n score-hmm ./sample-file/samplehmmalignment.txt 12.5\n ==\u003e filtered-scores-with-all-targets.txt \u003c==\n HTH_26  63      WP_003872347.1  189     0.00000000000023        37.9    1       60      14      72      14      75      Cro/C1-type\n HTH_24  48      WP_003872375.1  193     0.0000023       13.8    17      37      34      54      33      54      Winged\n HTH_24  48      WP_003872469.1  148     0.00000000000000000054  55.1    1       48      4       51      4       51      Winged\n HTH_24  48      WP_003872548.1  161     0.0000062       13.1    7       47      47      87      43      88      Winged\n HTH_26  63      WP_003872666.1  178     0.00000000058   27.2    2       62      5       64      5       65      Cro/C1-type\n\n ==\u003e filtered-score.txt \u003c==\n HTH_XRE 56      WP_003872292.1  132     0.00000003      20.9    17      56      35      75      35      75      -\n HTH_XRE 56      WP_003872307.1  249     0.00000048      17.1    2       34      149     187     148     195     -\n HTH_XRE 56      WP_003872347.1  189     0.0000000000000000000022        63.4    1       56      14      69      14      69      -\n HTH_26  63      WP_003872347.1  189     0.00000000000023        37.9    1       60      14      72      14      75      Cro/C1-type\n HTH_24  48      WP_003872375.1  193     0.0000023       13.8    17      37      34      54      33      54      Winged\n ```\n ```\n target-hmm ./sample-file/samplehmmalignment.txt Winged\n\n head -n 3 filtered-target.txt\n HTH_24  48      WP_003872375.1  193     0.0000023       13.8    17      37      34      54      33      54      Winged\n HTH_24  48      WP_003872375.1  193     0.0000023       -3.9    23      31      180     188     178     189     Winged\n HTH_24  48      WP_003872469.1  148     0.00000000000000000054  55.1    1       48      4       51      4       51      Winged\n\n evalue-hmm ./sample-file/samplehmmalignment.txt 1.3e-5\n\n==\u003e ./sample-file/evalue-filter-with-all-targets.txt \u003c==\n HTH_XRE 56      210     WP_003872175.1  0.000023        10.9    3       30      10      56      8       84      -\n HTH_XRE 56      210     WP_003872175.1  0.000023        -2.6    14      24      139     149     138     150     -\n HTH_XRE 56      210     WP_003872175.1  0.000023        -3.4    44      53      187     196     185     198     -\n HTH_24  48      253     WP_003872618.1  0.000016        11.5    22      47      43      68      42      69      Winged\n\n==\u003e ./sample-file/evalues-filter-with-target-annotated.txt \u003c==\n HTH_24  48      WP_003872618.1  0.000016        11.5    22      47      43      68      42      69      Winged\n HTH_24  48      WP_003872618.1  0.000016        -3.9    32      39      117     124     116     127     Winged\n HTH_24  48      WP_003872953.1  0.000023        10.1    19      43      47      71      41      72      Winged\n HTH_24  48      WP_003872953.1  0.000023        -1.6    31      42      192     203     191     204     Winged\n\n```\n```\n eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Winged\n head -n 3 evalue-filter-with-all-targets.txt\n HTH_24  48      253     WP_003872618.1  0.000016        11.5    22      47      43      68      42      69      Winged\n HTH_24  48      253     WP_003872618.1  0.000016        -3.9    32      39      117     124     116     127     Winged\n HTH_24  48      245     WP_003872953.1  0.000023        10.1    19      43      47      71      41      72      Winged\n\n eval-target ./sample-file/samplehmmalignment.txt 1.3e-5 Cro/C1-type\n head -n 1 evalue-filter-with-all-targets.txt\n HTH_26  63      213     WP_003876921.1  0.000033        11.4    10      36      42      67      40      77      Cro/C1-type\n\n```\n```\n targetcounts ./sample-file/samplehmmalignment.txt\n The domain aligned targets for the enrichment are: {\"Winged\": 1, \"Cro/C1-type\": 1, \"Domain\": 1}\n\n```\n```\n euclidean-comparative sample.pdb A 10 10 N CA\n The eucledian distance between to given coordinates of the same chain is 1.4656264\n euclidean-comparative sample.pdb A 1 1 N CA\n The eucledian distance between to given coordinates of the same chain is 1.4909409\n```\n```\n euclidean-all sample.pdb A\n  The vector containing the eucleadian distance for those chain atoms are:\n   [1.4909409, 1.5401275, 1.254727, 3.479588, 1.4994173, 1.4884146 ...]\n\n and will write a eucledian file as\n 32.231  15.281  -13.143 32.184  14.697  -11.772 1.4909409\n 32.184  14.697  -11.772 33.438  13.89   -11.387 1.5401275\n 33.438  13.89   -11.387 34.102  13.07   -12.066 1.254727\n 34.102  13.07   -12.066 30.797  14.065  -11.625 3.479588\n 30.797  14.065  -11.625 30.976  12.589  -11.819 1.4994173\n 30.976  12.589  -11.819 29.608  12.016  -11.694 1.4884146\n 29.608  12.016  -11.694 28.942  12.335  -12.945 1.4526931\n 28.942  12.335  -12.945 27.67   12.696  -13.05  1.3263968\n 27.67   12.696  -13.05  26.901  12.777  -11.999 1.3048087\n 26.901  12.777  -11.999 27.161  12.963  -14.255 2.2785378\n\n```\n\n- To install windows version:\n```\nrustup component add llvm-tools\nrustup target add x86_64-pc-windows-msvc\ngit clone https://github.com/IBCHgenomic/varlinker.git\ncd ensemblcov\ncargo xwin build --target x86_64-pc-windows-msvc\n```\n\nGaurav Sablok \\\ncodeprog@icloud.com\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fproteogenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frustcodepro%2Fproteogenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fproteogenomics/lists"}