biopipen 0.23.8__py3-none-any.whl → 0.24.0__py3-none-any.whl

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Files changed (29) hide show
  1. biopipen/__init__.py +1 -1
  2. biopipen/core/proc.py +7 -0
  3. biopipen/ns/cellranger.py +2 -2
  4. biopipen/ns/scrna.py +13 -20
  5. biopipen/ns/tcr.py +8 -6
  6. biopipen/scripts/scrna/SeuratClustering.R +102 -85
  7. biopipen/scripts/scrna/SeuratPreparing.R +13 -6
  8. biopipen/scripts/scrna/SeuratSubClustering.R +81 -97
  9. biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R +5 -5
  10. biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R +3 -3
  11. biopipen/scripts/tcr/Immunarch-basic.R +2 -3
  12. biopipen/scripts/tcr/Immunarch-clonality.R +2 -3
  13. biopipen/scripts/tcr/Immunarch-diversity.R +70 -49
  14. biopipen/scripts/tcr/Immunarch-geneusage.R +2 -3
  15. biopipen/scripts/tcr/Immunarch-kmer.R +2 -3
  16. biopipen/scripts/tcr/Immunarch-overlap.R +2 -3
  17. biopipen/scripts/tcr/Immunarch-spectratyping.R +2 -3
  18. biopipen/scripts/tcr/Immunarch-tracking.R +2 -3
  19. biopipen/scripts/tcr/Immunarch-vjjunc.R +2 -3
  20. biopipen/scripts/tcr/Immunarch.R +1 -1
  21. biopipen/scripts/tcr/ImmunarchLoading.R +2 -0
  22. biopipen/scripts/tcr/TCRClustering.R +6 -2
  23. biopipen/scripts/tcr/TESSA.R +3 -1
  24. biopipen/scripts/tcr/immunarch-patched.R +142 -0
  25. biopipen/utils/caching.R +44 -0
  26. {biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/METADATA +8 -7
  27. {biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/RECORD +29 -27
  28. {biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/WHEEL +0 -0
  29. {biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/entry_points.txt +0 -0
{biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: biopipen
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- Version: 0.23.8
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+ Version: 0.24.0
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  Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
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  License: MIT
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  Author: pwwang
@@ -14,9 +14,10 @@ Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Provides-Extra: runinfo
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- Requires-Dist: datar[pandas] (>=0.15.2,<0.16.0)
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- Requires-Dist: pipen-board[report] (>=0.13,<0.14)
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- Requires-Dist: pipen-cli-run (>=0.11,<0.12)
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- Requires-Dist: pipen-filters (>=0.10,<0.11)
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- Requires-Dist: pipen-runinfo (>=0.4,<0.5) ; extra == "runinfo"
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- Requires-Dist: pipen-verbose (>=0.9,<0.10)
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+ Requires-Dist: datar[pandas] (>=0.15.3,<0.16.0)
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+ Requires-Dist: pipen-board[report] (>=0.14,<0.15)
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+ Requires-Dist: pipen-cli-run (>=0.12,<0.13)
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+ Requires-Dist: pipen-filters (>=0.11,<0.12)
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+ Requires-Dist: pipen-poplog (>=0.0.2,<0.0.3)
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+ Requires-Dist: pipen-runinfo (>=0.5,<0.6) ; extra == "runinfo"
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+ Requires-Dist: pipen-verbose (>=0.10,<0.11)
{biopipen-0.23.8.dist-info → biopipen-0.24.0.dist-info}/RECORD RENAMED
@@ -1,16 +1,16 @@
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- biopipen/__init__.py,sha256=gx1o8BSQCB5X7Zn8JZ7cxhUiCNJydk8QQUY_fY1zEC8,23
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+ biopipen/__init__.py,sha256=DxtMZD542lg_xb6icrE2d5JOY8oUi-v34i2Ar63ddvs,23
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  biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
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  biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
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  biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
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  biopipen/core/filters.py,sha256=HLrjXGsvvjRtTWIAmg_f4IMymWaRD769HlDwsCTh170,12424
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- biopipen/core/proc.py,sha256=7TsjBM7EEtMMB-w4jbxV_CSRY8J970gM8320Ga1YeHU,717
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+ biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
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  biopipen/core/testing.py,sha256=5vR15kkCjfXM7Bx0HBzabNLtDLAEX4uU94TskCkPni8,1447
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  biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biopipen/ns/bam.py,sha256=5AsYrB0mtr_mH6mCL6gjJ5rC4NywpjFkpFjUrBGp7Fk,9301
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  biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
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  biopipen/ns/bed.py,sha256=UN38qUChDeE-ipuSBY8RVLwvJqM2wxSRmlhOiDo4JG0,5395
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- biopipen/ns/cellranger.py,sha256=0A6pCpBLg1zKm2Ve2cXvGvNNK4lMqdsek2iTer5X_TI,3679
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+ biopipen/ns/cellranger.py,sha256=vwyPNaiRIFMp1e8kSJ1UNsE9ZcUykNniakKE-BqZR60,3681
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  biopipen/ns/cnv.py,sha256=vq6dZfEOyuVuqg3nP6FQtNmQ-JocpBJMX9IYlZ0OPD0,6803
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  biopipen/ns/cnvkit.py,sha256=5mA2Q8-YDs4g1HoxtpB_NWnyZYwEThNr3s3wlubLQrQ,31130
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  biopipen/ns/cnvkit_pipeline.py,sha256=2fJLn70L2jJ81ZMNdnU84Sf3HoKA2CSnHuDzLGR8jmw,36854
@@ -20,10 +20,10 @@ biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
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  biopipen/ns/misc.py,sha256=fzn0pXvdghMkQhu-e3MMapPNMyO6IAJbtTzVU3GbFa0,3246
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  biopipen/ns/plot.py,sha256=yguxmErUOH-hOM10JfuI_sXw2p49XF8yGR_gXfbd5yQ,4066
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  biopipen/ns/rnaseq.py,sha256=l4vFeRasGhkexopGTM_VfSyIFewOxg-9L5niFzhWUNA,565
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- biopipen/ns/scrna.py,sha256=aV5HNM2TJW2LRAhE5ekEm4114rIeHXBio_nwI-bSPpQ,95883
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+ biopipen/ns/scrna.py,sha256=A3OcbCQzbOanPqn7_ZVeGvMpTAPDM24KM8ZFUUsWs6g,95467
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  biopipen/ns/scrna_metabolic_landscape.py,sha256=9s1NvH3aMaNDXyfwy9TdzGcSP_lIW4JqhLgknNZcIKE,28313
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  biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
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- biopipen/ns/tcr.py,sha256=IcP1uD8U9XD6UbOgdjA_Lk5PK6r4R84Gi7511uvXoy8,84411
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+ biopipen/ns/tcr.py,sha256=Pl6flJsgzcjExc3x9Eg_uiNkQprqmUTqKtmImM66zNY,84411
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  biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
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  biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
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  biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -131,22 +131,22 @@ biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=GTZfs1yOkuoMUM1Zb19i_My
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  biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=GVKIXFNS_syCuSN8oxoBkjxxAeI5LdSxh-qLVkUsbDA,2146
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  biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=CE9989SaO75_KYEEVqivEbUoTcUOtiTkRGWLNtWzxI8,6450
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  biopipen/scripts/scrna/SeuratClusterStats.R,sha256=PeXa3r2VTo0Q1rdXpSfAOIbYSJAcA8WUNM-tJkNUcPg,1284
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- biopipen/scripts/scrna/SeuratClustering.R,sha256=Q3XGg0Rq1xqswyQSsj8AmarmiT9ZFdoolXy2g9ibiTo,5185
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+ biopipen/scripts/scrna/SeuratClustering.R,sha256=kAvQq3RV86_KSv9NlUtUeQrPKkbhSsnv6Q4DoiTu8M0,6403
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  biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
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  biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
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  biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=tisYmoSaCX8Kl8y6euuuUroWdDsJ2NGI27J5AWr9Niw,4392
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  biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=Pp4GsF3hZ6ZC2vroC3LSBmVa4B1p2L3hbh981yaAIeQ,1093
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- biopipen/scripts/scrna/SeuratPreparing.R,sha256=plg8hn6lvVC630iXohTDiuszOuISQM44eQI5kWS3CP8,12565
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+ biopipen/scripts/scrna/SeuratPreparing.R,sha256=KNrBPibqANhCsCctOGCOMPLTjDDd-iDRpMSCXkPuUQU,12994
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  biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
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- biopipen/scripts/scrna/SeuratSubClustering.R,sha256=6b1J98YYK2gwJ_qkpuvYIdlj6uWxJA8IpUXvaCjgC_U,6334
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+ biopipen/scripts/scrna/SeuratSubClustering.R,sha256=L1SwKhNNKvsQGrcj0ZjScW9BLuvdO2pg7U48Ospsot8,6096
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  biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
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  biopipen/scripts/scrna/SeuratTo10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5wshqY,2679
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  biopipen/scripts/scrna/Write10X.R,sha256=OMhXvJwvaH-aWsMpijKrvXQVabc1qUu5ZEwiLAhkDeY,285
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  biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
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  biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=UbNoyspFB8166VgbkkFyTS6tkA-7ybylfvO50eqNnBU,4841
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- biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=dpyzIZU78zLHPLIEg9mAz8mK4XazxVuUm2CN33HGPpw,5233
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- biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=_iTOOByaaXyolMN8_IMY2qcEcC_EAZGCPoHyrOqiTKI,16245
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+ biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=Kv69CkVm67K3w5EEcPQr7SlaWFpPwqTI0DVSUn62Rj0,5230
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+ biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
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  biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
@@ -159,24 +159,24 @@ biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_Dg
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- biopipen/scripts/tcr/Immunarch-clonality.R,sha256=ZPOSPNAVamHyM6yskx2MVAMNw051yuTaZllj3mUwxEM,3927
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- biopipen/scripts/tcr/Immunarch-diversity.R,sha256=Wk7b7435r4y4g3ItReTEAleHHfRXZtabRi3nNtqfo4A,27597
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- biopipen/scripts/tcr/Immunarch-geneusage.R,sha256=30gJdMfe36enjIsn-tJayrU8YAowS_4EtVm5cj6FxUQ,6885
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- biopipen/scripts/tcr/Immunarch-kmer.R,sha256=VmuXKI9AplyAj2NUnGV7utjgyu-ZuKRnry2ghf-9eQ0,6302
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- biopipen/scripts/tcr/Immunarch-overlap.R,sha256=6RxXTjGhWzUC_1BxojMFrbrTq2PI_EAo9vpWxxbIs_o,7536
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- biopipen/scripts/tcr/Immunarch-tracking.R,sha256=j1w36v1YuzohW1Nd14m90wRtjzpJSD6OM5KbF_wVxcY,4443
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+ biopipen/scripts/tcr/Immunarch-clonality.R,sha256=48rbPCWka4eNEy-fjM0BlKDkMYdG2zlB8Sly1B4xdUI,3858
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+ biopipen/scripts/tcr/Immunarch-diversity.R,sha256=BDIhh1lbiaAEm-AQO0nb0mBmtQBA9yG_AP6N6zW8QOc,28330
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+ biopipen/scripts/tcr/Immunarch-geneusage.R,sha256=c0C8-KtKI2q6O9xZ9f5COefQbPlshT2hz1f36qpnW34,6817
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+ biopipen/scripts/tcr/Immunarch-kmer.R,sha256=4BUDiclarawetjUdBmrCTfHZOTjRpE5TDxDGI_CtYds,6229
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+ biopipen/scripts/tcr/Immunarch-overlap.R,sha256=GVt-qJPtd6NEe5njAqNStf2AP6pLkv7Ittw0YT_qdNY,7465
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- biopipen/scripts/tcr/TESSA.R,sha256=oh2P0RB4WoG-UA1wVafrb5RQDLndKq7I69kBbykHxMw,6784
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+ biopipen/scripts/tcr/TCRClustering.R,sha256=-BWbDqvDBEpfVaxrVvzVHK5bm6FCOFmGHydg1c3EgAM,8747
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+ biopipen/scripts/tcr/TESSA.R,sha256=bfOixWLZy8yi0MzXncP67KjtCukwXEzsK5fCdMzB5VM,6822
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@@ -205,6 +206,7 @@ biopipen/scripts/vcf/VcfSplitSamples.py,sha256=GraKi7WluzDAvVVGljwd3Yif6MriniF8s
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  biopipen/scripts/web/Download.py,sha256=WKC_t5ZEeJoKFyY9XwksHARcMbKmHMcxNEUDLMGJ0Cc,924
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  biopipen/scripts/web/DownloadList.py,sha256=cZvdi3LVzlATiTvAXe0uuDDXGqB5jcR2zHrMLCEb2U8,1130
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  biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biopipen/utils/caching.R,sha256=qANQqH8p-VpvD8V4VSoqSfp0TFr4esujC7x3OFZsJMw,1687
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  biopipen/utils/common_docstrs.py,sha256=ro9dUXeHMXBaqb-hTafwrG6xW5IOBEeiUM2_REjFoCo,5842
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  biopipen/utils/gene.R,sha256=BzAwlLA8hO12vF-3t6IwEuTEeLa_jBll4zm_5qe3qoE,1243
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  biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
@@ -218,7 +220,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
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  biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
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  biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
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  biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
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- biopipen-0.23.8.dist-info/METADATA,sha256=NDuFljfwMBKGx9__4fsjm2ZN7yAuW49L04kzmbxblmc,886
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- biopipen-0.23.8.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
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- biopipen-0.23.8.dist-info/entry_points.txt,sha256=16Apdku3RFwghe1nb0JR7eVo4IzLae6hCWjU1VxYUn0,525
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- biopipen-0.23.8.dist-info/RECORD,,
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+ biopipen-0.24.0.dist-info/METADATA,sha256=DNnxF-VG418LTtxJbvpZ9ebR8R7fgOaTb2mgFo9IBO8,932
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+ biopipen-0.24.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
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+ biopipen-0.24.0.dist-info/entry_points.txt,sha256=16Apdku3RFwghe1nb0JR7eVo4IzLae6hCWjU1VxYUn0,525
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+ biopipen-0.24.0.dist-info/RECORD,,