{"id":26837011,"url":"https://github.com/ibchgenomic/proteogenomics","last_synced_at":"2025-03-30T16:35:07.913Z","repository":{"id":275190168,"uuid":"924331723","full_name":"IBCHgenomic/proteogenomics","owner":"IBCHgenomic","description":"proteogenomics for protein 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proteogenomics\n\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 - please see the last commit message and if it says compiled binary then it is completed or else still in development version. \n \n ```\n  cargo build \n ```\n\n ```\n gauravsablok@genome proteome-hmm main ? ./target/debug/proteogenomics -h\n proteome analyzers\n\n Usage: proteogenomics \u003cCOMMAND\u003e\n\n Commands:\n  target-hmm             select the targets from the hmm\n  score-hmm              select the scores from the hmm\n  evalue-hmm             select the evalues from the hmm\n  eval-target            select the targets based on evalue and target\n  targetcounts           prepare the unique counts of the domains\n  pdb-id\n  pdb-sequence           extract the sequence of the pdf file\n  euclidean-comparative  calculate the euclidean distance bettwen two chain coordinates\n  euclidean-all          calculates the euclidean distance for all chain atoms\n  help                   Print this message or the help of the given subcommand(s)\n\n Options:\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 Gaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fproteogenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fibchgenomic%2Fproteogenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fproteogenomics/lists"}