geniml

View on PyPIReverse Dependencies (3)

0.6.0 geniml-0.6.0-py3-none-any.whl

Wheel Details

Project: geniml
Version: 0.6.0
Filename: geniml-0.6.0-py3-none-any.whl
Download: [link]
Size: 156089
MD5: d4a4a7ebd5c1032b094b8c450924f602
SHA256: a849a6a0eca9a8d8c6155e631d97004d83284bcbabb6b9a962c1a398eaaaeb9f
Uploaded: 2025-01-03 16:47:47 +0000

dist-info

METADATA

Metadata-Version: 2.1
Name: geniml
Version: 0.6.0
Summary: Genomic interval toolkit
Author: Nathan Sheffield
Home-Page: https://docs.bedbase.org/geniml/
License: BSD2
Keywords: bioinformatics,sequencing,ngs
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: logmuse (>=0.2.8)
Requires-Dist: ubiquerg (>=0.6.3)
Requires-Dist: peppy (>=0.40.7)
Requires-Dist: requests (>=2.31.0)
Requires-Dist: botocore (>=1.34.54)
Requires-Dist: boto3 (>=1.34.54)
Requires-Dist: genomicranges (>=0.4.1)
Requires-Dist: gtars (>=0.1.1)
Requires-Dist: pybiocfilecache (>=0.6.0)
Requires-Dist: zarr (>=2.17.2)
Requires-Dist: pyyaml (>=6.0.1)
Requires-Dist: s3fs (>=2024.3.1)
Requires-Dist: pyarrow (>=17.0.0)
Requires-Dist: iranges (>=0.2.11)
Requires-Dist: numpy (>=1.24.0)
Requires-Dist: rich (>=13.9.4)
Requires-Dist: anndata (>0.9.0); extra == "ml"
Requires-Dist: fastembed (>=0.2.5); extra == "ml"
Requires-Dist: gensim (>=4.3.3); extra == "ml"
Requires-Dist: huggingface_hub (>=0.25.1); extra == "ml"
Requires-Dist: qdrant_client (>=1.11.2); extra == "ml"
Requires-Dist: hnswlib (>=0.8.0); extra == "ml"
Requires-Dist: paramiko (>=3.0.0); extra == "ml"
Requires-Dist: pyBigWig (>=0.3.23); extra == "ml"
Requires-Dist: scanpy (>=1.10.3); extra == "ml"
Requires-Dist: torch (>=2.3.0); extra == "ml"
Requires-Dist: lightning (>=2.4.0); extra == "ml"
Requires-Dist: langchain-huggingface (==0.0.2); extra == "ml"
Requires-Dist: hmmlearn (>=0.3.2); extra == "ml"
Requires-Dist: scipy (>=1.13.1); extra == "ml"
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-remotedata; extra == "test"
Requires-Dist: pytest-mock; extra == "test"
Requires-Dist: black; extra == "test"
Requires-Dist: ruff; extra == "test"
Requires-Dist: isort; extra == "test"
Provides-Extra: ml
Provides-Extra: test
Description-Content-Type: text/markdown
License-File: LICENSE.txt
[Description omitted; length: 949 characters]

WHEEL

Wheel-Version: 1.0
Generator: setuptools (75.6.0)
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
geniml/__init__.py sha256=blI-lJ0PxqdpWe_VF2D5iPU9Q4KPtrK1PBUiKJX44lY 124
geniml/_version.py sha256=cID1jLnC_vj48GgMN6Yb1FA3JsQ95zNmCHmRYE8TFhY 22
geniml/cli.py sha256=1DNJAGZDlukr82ehimLCfjPQ5x6M2jZY9mXSHRWr9wg 13198
geniml/const.py sha256=SWmgU6WmtRmq23gnewMalKXxjspYAr0pLDMFC49_GEM 38
geniml/exceptions.py sha256=jgGKCCNN5YL2nC47U3IhKl_0EZlICER8vfn8t6tPWvI 759
geniml/utils.py sha256=3yDp7znZCi7vc7NDMRUHbIUV8YDORc3Xjijb9FN1xh4 3144
geniml/assess/__init__.py sha256=-tJrIyTuYyPAteLC3kI5T6liK5T6y3I7ytwXOaXbUug 33
geniml/assess/assess.py sha256=HBck_moDAH0tGQGiUZGrKcLeLce5mCSpyVtsSF94f1Y 10937
geniml/assess/cli.py sha256=sJWjHw-gVFLRZAAlNDagp5RjrKc2wqjqEku2QTM275Y 2113
geniml/assess/distance.py sha256=ksDrWTGdoPjGSm7qstBzA5zwVKH6iiD6D3hLp2Dr1N4 11516
geniml/assess/intersection.py sha256=GB4grZVA3IjS_u6EQqX7MDt0ymORmrW_pldUTUWuy6c 8308
geniml/assess/likelihood.py sha256=1adDSbvu9TYJirlNumQ-LZ2mIb3DpQj0NZF9jb8pZ8A 12011
geniml/assess/utils.py sha256=YTppCzyFZ1tevX8mq4-3CyvaFudtKEIyhloVlJOS1Fc 2032
geniml/atacformer/__init__.py sha256=ZBiK4dsLdJCYYClBdpsVdf_UDivT_8IcbIYvUHS-QIo 88
geniml/atacformer/const.py sha256=0g3R6j0fZWnYXr_c9looq4n9tF3AXKCh_75lmJ1i6f4 656
geniml/atacformer/main.py sha256=J-DgYrW3Onb_bUhlAPWYIaoDLmDY0mcPq0lcjR94bIs 11948
geniml/atacformer/training.py sha256=Lkkn-D0czCBdCBAuHnhRbjf0Iwrm8lTQwZVY9G4qiAY 9533
geniml/atacformer/utils.py sha256=WEty2euaz7a2byy7kuSyKud66v6zy7X-KqBlRP0T2Ds 10269
geniml/bbclient/__init__.py sha256=ABZs57kcM4WzeWE5G-tnS1W1Mya7pElmySLpeb_EpnA 55
geniml/bbclient/bbclient.py sha256=nw2K31R6nBAoZJDfbuJwnlt24tp3m9fY01BfU_vDlFs 19553
geniml/bbclient/cli.py sha256=c0GlzYObIE2-8SKwdy5at9pVa5thIUsehfSk7OrIgYk 4070
geniml/bbclient/const.py sha256=P4rJokx_WH9OcmIj1LagcyAw_zZ5pEQjvhAFQNn4q2s 812
geniml/bbclient/utils.py sha256=nir7bYK0-GAZJeuNBWWp0hvVFuUBmmw7UrPcfzdgX8k 2531
geniml/bedshift/BedshiftYAMLHandler.py sha256=nNz6SnyqmJppDqjwLCQzGO_fBqmTGJL4l1U8Dlv7tPI 7451
geniml/bedshift/__init__.py sha256=2VVN1T8XP1ICrKeuv37npTAZN3OOi4ia718HpQBZcMg 221
geniml/bedshift/_version.py sha256=q8_5C0f-8mHWNb6mMw02zlYPnEGXBqvOmP3z0CEwZKM 22
geniml/bedshift/arguments.py sha256=QKsWujwOdT-gNAPjogen7tr7PCAfYr36WMX4FkLjv7I 3872
geniml/bedshift/bedshift.py sha256=sD8XdleJw5-IE7ob-8En99quhS0imi2zdnb1aSyekWQ 25951
geniml/bedspace/__init__.py sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs 1
geniml/bedspace/_version.py sha256=sXLh7g3KC4QCFxcZGBTpG2scR7hmmBsMjq6LqRptkRg 22
geniml/bedspace/argparsers.py sha256=txCbS9ISFXjVI-dO9aoGrJkf3uvO1pAioEvAEfIKCyY 3517
geniml/bedspace/cli.py sha256=6Ry-VE0CkpeOWxOJqpEeQb9aooa_Q1gxob58EFN5zHU 2637
geniml/bedspace/const.py sha256=t-0DeRDVa6Gj8ZmFt9SsSTaAHtJ0ytL4q1ive8xTSxI 489
geniml/eval/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
geniml/eval/cli.py sha256=72UB7TUdX5SxvKBFOzHvnRY8_hGLzgiEkpeSJ8Huloc 5091
geniml/eval/const.py sha256=ijliz4e-LxRmAec7iCdEEmpvNHwmocWHZhy_HtsE0dI 95
geniml/eval/ctt.py sha256=etbhkG-nNPU1oySbWw6DuMNrjNmF_-L0hgWXbS_K3X0 5405
geniml/eval/gdst.py sha256=xe0AapX0NRyLHmYzkU5TZ2PiQF6W7_09Daov9tPsttQ 8231
geniml/eval/npt.py sha256=7SHFQudo-fD3L04Mo7HFu0UhoB34wILKr1ILS83itm8 18314
geniml/eval/rct.py sha256=WtYbRYAeEVA5O011WmpYIN7JJ7qke06xAVGBqj2Kjbg 6286
geniml/eval/utils.py sha256=XnIM46W2mLoGAYZSguAQ8B8VjL4yJ1MfGTGpez_mJjc 8450
geniml/io/__init__.py sha256=KAoR2kO-0eikUzDKuLndGq6IWoj0rOR1rRWHJ_OHVKA 52
geniml/io/const.py sha256=ZnTYelXo9s0em4eROnXxEqYRB1w5l9OUd3DX1JlkUio 523
geniml/io/exceptions.py sha256=HVnKWbKoERHNaXLWR_6W8NFmT9KTugb8_dBsU3Ovzug 514
geniml/io/io.py sha256=zrPw-5PkF9KhFn36iqwS2cXJc1C2AW9XXUL_PEcBaT0 21712
geniml/io/utils.py sha256=32tPmnSwBkhhErINyEbSSEnT7uwExAN3DmdKOwCjddU 2836
geniml/likelihood/__init__.py sha256=-tJrIyTuYyPAteLC3kI5T6liK5T6y3I7ytwXOaXbUug 33
geniml/likelihood/build_model.py sha256=U_-XbkpDgWzMFcbLLwmwvB7oPfChSf81OmxLmlYIAdE 6655
geniml/likelihood/cli.py sha256=zmrrxtGTp3-KNdwn2u6wsYIC2XC8AXsf_aGYppLLqos 745
geniml/models/__init__.py sha256=XQBoSiVChlHI__DmjMi4HMgK6XMt8djSIMcjbTx7LiA 26
geniml/models/main.py sha256=HA-E3Hf5mhHPL8oWu0EsbIgGjtFB1li9XQFjaH8bG38 1070
geniml/nn/__init__.py sha256=zFlThrL2mnWqn_xVb5G17jr0ZkaEd56lAKgV_Bf6YGI 46
geniml/nn/main.py sha256=h1M0vbE8_9Yc6aB8YEdF7JirYs67KLrfWfmTRGQpX-8 1228
geniml/region2vec/__init__.py sha256=qpLk9W4cbyeCY02lFJb_-kDQXcB7UDGuSoMsZeAZqZY 90
geniml/region2vec/cli.py sha256=P314Zto0NhIsCStYg771abZakt7F7FaQw6K8IrpXu7I 2396
geniml/region2vec/const.py sha256=YJX2uFSm7vGelxKXF6A37YvxlwX3UOCrH2JMbErwkh8 776
geniml/region2vec/experimental.py sha256=dWFDnmWuqfPL2qOUuVB_i_egXd8MRKqXuDJJouFYxIU 9534
geniml/region2vec/main.py sha256=Qb5zGMAyZtrgoPoIhVtlzogGkyCDdgwBlcPbKoO5wKA 12584
geniml/region2vec/main_legacy.py sha256=s-ljKuvWOjZyGfPyxlDNnmlrbr6KscMiFF86U6exeZ8 6369
geniml/region2vec/models.py sha256=pyx9ZEmDZAW2Pu2jrhQAtja6mVdSOOCQNwH9MRdwiD8 2383
geniml/region2vec/pooling.py sha256=EIx_A4LPcMtAdnZDWV3X4ZtxExIagVLcBtVZjexYEQY 1102
geniml/region2vec/region2vec_train.py sha256=X_R7k7Pk3TR6W0YPjLx8_XhHkl4APFKH8DhijNFaUDQ 8295
geniml/region2vec/region_shuffling.py sha256=z_O_XB2asQK8DDV_9ILu17hQD91V-FNVJtWz4A7e2mU 9137
geniml/region2vec/utils.py sha256=esZNFJvZ5HxBpy1KGpyInI02oEjKFFdvK9SugVyID3U 19296
geniml/scembed/__init__.py sha256=xcGHHIMEyc_0vzHio6aEmCW_PRwNHdGzMFJ-7Tg2Cao 96
geniml/scembed/_version.py sha256=PNiDER4qM19h9zdsdfgKt2_dT4WgYK7EguJ8RU2qA_g 22
geniml/scembed/annotation.py sha256=vfv0OGQQ27Ry24A4rltkKbJUXTufqwawZdd0WqwTKf8 5805
geniml/scembed/argparser.py sha256=CgYifXD_SFsuTg7KXF9eA2m9J2W_KFoNTFTBtWv6Pvk 1910
geniml/scembed/cli.py sha256=sTciokU4-KRv9-h1vU0BnB2B7t8obMXq-9PoPvxUVZ4 2343
geniml/scembed/const.py sha256=uPIz0MDDeDTtmCLB3f3a9bvMcrj2zt6Tui8k3uthosY 127
geniml/scembed/exceptions.py sha256=L5ZIOKEOjh1SdhTY28eFoAcxkJLiGZ5J6G9GLpRmuv4 101
geniml/scembed/main.py sha256=vLGJ35orZsKONPCKnZ5loMzoQQRycN1P5eZ_FNgsH4o 11346
geniml/scembed/models.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
geniml/scembed/utils.py sha256=0oIupkJhvPhSASZfGNKAFqnMAeaWkbiweWJul5VPcwU 4207
geniml/search/__init__.py sha256=eHnRBKgqBIg3RA5byBxwBbQRdubi1bXinwrfw07r7oo 298
geniml/search/const.py sha256=bSCeyayKy5uB5zr42ijIOFthLS5D5-U2d_sH76QVrTw 1187
geniml/search/filebackend_tools.py sha256=bo_C-OAg_eSnH_ugbygOGFFIRbDqUj_pS7eW9moa-kM 1204
geniml/search/search_eval.py sha256=vCC69pcywuKX7PypDs6K1cKkJcGPAce9iId3Z5l1unY 2239
geniml/search/utils.py sha256=WvVRPwsjpCgXcgJU9GF0wBEq1Teiva9g1wCOpfhgiLQ 3275
geniml/search/backends/__init__.py sha256=0WYH67cPoRdh2oIBN7rT6JzVBgil0DmvUAtbOV3bK60 116
geniml/search/backends/abstract.py sha256=5RYwFAeITT-Crn2BuxyCDmU-5reNT7spjNQLmZxoeFQ 1606
geniml/search/backends/bivecbackend.py sha256=7vWEbS3MPjkeOtGvs1OjfVUctYsOb8Hbom1acDVude4 10496
geniml/search/backends/dbbackend.py sha256=gsGszgB11K8XjyXYYo2tNV4FZRhjEf7jR0TMN8TId2U 10748
geniml/search/backends/filebackend.py sha256=fBt_km0y8cPrT1SSKt3LMvszooeU1RQsFnQTaZidJgs 8208
geniml/search/interfaces/__init__.py sha256=OZ7NeDM-ai5hgoFXdqKgKL9H9CSlpJhhkOIgJTUwKbs 134
geniml/search/interfaces/abstract.py sha256=Z49YFq-PQfQVFuqQ5nr0D0htUtMztQYr2PuWtMtSlec 916
geniml/search/interfaces/bed2bed.py sha256=cAtSaeJW6GNTEJpka_RzQR3JsfB6C617WywTYSgj2cQ 1517
geniml/search/interfaces/mlfree.py sha256=tAXwxu67OcCEzuobLrdj158TLnSfAPfTC6H1q9qj17s 1788
geniml/search/interfaces/text2bed.py sha256=tT5hQmulaZf8H3QKDwKA613NfDvWWHHjlhACYhoq6Fg 3592
geniml/search/query2vec/__init__.py sha256=lAJJB8hNn0wUC_YsFl9wDQkdXtqgfU5E7IjfyeP6I0o 60
geniml/search/query2vec/abstract.py sha256=r6IapKTLSIucSO67rUDf2aq9TmAiZfSQ0JIBWrg-DqA 739
geniml/search/query2vec/bed2vec.py sha256=QvykSRa42ihdp3HEfGuSVaB-DPIVziDqDI0eAiuMjIw 1376
geniml/search/query2vec/text2vec.py sha256=FBA00bKnzkxcM18TXjJonhRCEilcAhROOuDNNYM9sAg 1652
geniml/text2bednn/__init__.py sha256=xdef8upOb_W5_nisQ3Ao31-2ezSytBugk8ydxg9lgWM 105
geniml/text2bednn/const.py sha256=JJ4CNbqrQMMD4C2ubTn6RL9pqN_aM3bAAPkxs4pO3iU 1229
geniml/text2bednn/text2bednn.py sha256=loaDH5LT5lfVxHh8aPRtsck0h0BZ1QSb9RuY_SVjsS8 16367
geniml/text2bednn/utils.py sha256=x73PbbgvMe9BYIDtNPGCNjPd6Lg4QIwTpHKwD0JAPPk 5986
geniml/tokenization/__init__.py sha256=uouB3d4ySupgt9m-G00yzw9hsnGXRwoVwx-TOWUZhE0 127
geniml/tokenization/bedtools_tokenizer.py sha256=u-p2UJZcPmt20bxq76Tt2Cwpo39anRMomF29zFPYjUs 2222
geniml/tokenization/cli.py sha256=MacK5brSaT7w-l-Oo_mU1LL9Yrdm3VGBXIC4uFGPmbM 936
geniml/tokenization/hard_tokenization_batch.py sha256=IKRhMzh6e6QmWF6AKJ8_ROpkwgRKlSbMbq0YzMKn6qw 4955
geniml/tokenization/main.py sha256=wPXEInjV_bpUhNEN9CNmK469hvNUzPGOmoXxTrlzAg4 18247
geniml/tokenization/split_file.py sha256=PsGjB4WSF3iunWiPqSuMom3kfY3219FZUzI0qpFr1D4 2205
geniml/tokenization/utils.py sha256=BN4KzjMAR_ygRuBlWmIIrU0UN7pTss69y2U2bc46OxM 2687
geniml/universe/__init__.py sha256=-tJrIyTuYyPAteLC3kI5T6liK5T6y3I7ytwXOaXbUug 33
geniml/universe/cc_universe.py sha256=EF7H9dYWsrykQYxJBM5vhKqngpBHu_WxMxuDxT__PoA 4134
geniml/universe/ccf_universe.py sha256=wppd6M8njIhicR1f3csQQTnojfA6lZp_DRxndhaCtHU 5879
geniml/universe/cli.py sha256=Z5V9HZl8YDKMYl1Xw7XEdD3SdAQ3WJBgueUgZIculQg 2340
geniml/universe/const.py sha256=QJCox3fisMPmibJwIbLKC5fhBwhCrh9ccKuIWZKRY4A 230
geniml/universe/custom_distribution.py sha256=mYf-_wueGcR7185s_johRF12vkuYXlhp8kDnecAKzFE 7613
geniml/universe/hmm_universe.py sha256=qzYG-KupNwylbXuuv-zIhzFCno1m2efL__MjR1xxx4E 5112
geniml/universe/ml_universe.py sha256=P2ERVYPV2hKIqLal2knI_tRAtNMiCfr34LFVtaiVINA 5433
geniml/universe/models.py sha256=nr2jNbQ99T10qKk81orIlf6Af-CIL9ZIgsKnBUwVFsk 6445
geniml/universe/utils.py sha256=niQAOmlEtquGM7oC8whb4yd6--rTmp-fyj-smmGWNWE 5062
geniml-0.6.0.dist-info/LICENSE.txt sha256=icA6c2AfOgBvINrm_KlxDyulzJyUi6UxJk2s1SH-vDI 1269
geniml-0.6.0.dist-info/METADATA sha256=zuTdQpfZtt-BXombaOO9n2nB1aBYbxu23P2lnGsOfy4 3075
geniml-0.6.0.dist-info/WHEEL sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U 91
geniml-0.6.0.dist-info/entry_points.txt sha256=wIN2CcxIGZDsbSnhpCV9Kijugo1LP-9TV4O0pvl3QEE 84
geniml-0.6.0.dist-info/top_level.txt sha256=VnqhfggQgcQLBPQCApNtNKWGfWsn8Pq05tu1T8Weg70 7
geniml-0.6.0.dist-info/RECORD

top_level.txt

geniml

entry_points.txt

bedshift = geniml.bedshift.bedshift:main
geniml = geniml.cli:main