mgnify-pipelines-toolkit 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

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Files changed (18) hide show
  1. mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py +5 -1
  2. mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py +84 -21
  3. mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py +11 -0
  4. mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py +25 -7
  5. mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py +13 -9
  6. mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py +211 -0
  7. mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py +162 -0
  8. mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py +230 -0
  9. mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py +119 -0
  10. mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py +6 -3
  11. mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +1 -1
  12. mgnify_pipelines_toolkit/constants/thresholds.py +1 -1
  13. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/METADATA +19 -27
  14. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/RECORD +18 -14
  15. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/WHEEL +1 -1
  16. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/entry_points.txt +5 -0
  17. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/licenses/LICENSE +0 -0
  18. {mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/top_level.txt +0 -0
{mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/RECORD RENAMED
@@ -12,22 +12,26 @@ mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=B
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  mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=Wu4tRtuRkgd3hoeuwPl_E5ghxIW7e_1vrcvFGWv_U4A,3173
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  mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py,sha256=yLpzkRJXAeXRUNgz60zopEwHcdprM2UDjquE-GkrFys,1722
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  mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_matching.py,sha256=K6gniytuItq5WzHLi1BsaUCOdP4Zm0_ZzW2_ns7-BTI,11114
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- mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py,sha256=HarDM6ay0MbyDfGGjmxP8epjsXciAJHOmqe8G64gLuM,4258
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+ mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py,sha256=NZSNY2bqs_TQyz8riDqiEFPLKcwTgzh1C7DeVHT6V8Q,4366
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  mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py,sha256=wXrw1B-z4hOu5oA27Vp1WYxGP2Mk6ZY4i_T5jDZgek0,6954
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  mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py,sha256=Pq-9RSt3RCxzDMQVW1VHlHF4NtpVwCWFbg2CMkvpZZc,19089
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  mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py,sha256=2T4T7aXMGPac-LZUXJF3lOUzZZF50dAKkKTSaO-4idQ,3587
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- mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py,sha256=IlkeP4DuN7rXJIHa7o2sONHAXLhV9nGP-5Y1_0u8YQo,31393
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- mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py,sha256=8kv_6KWznOVRkeAtghLf4pxKPhAqdn36LOK4MsTz9hU,3282
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- mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py,sha256=uUIo97gmzO2zzN-pYF5paIzeHWBsmmjFp7zGAhf4PKY,5021
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+ mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py,sha256=6gbCRlEX1eBqzFYjOt3og-961dZ--QsCJL-7l5nzg1k,33992
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+ mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py,sha256=_4J31wAjK5B15p9lDzTG2wmZdyoZkOgmy7Kp_w8lTeE,3812
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+ mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py,sha256=n2rbS8UHevF8OB4umo7QivS6v4avlgsCaRwrBbVmZ24,5398
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  mgnify_pipelines_toolkit/analysis/assembly/go_utils.py,sha256=eay9e3Xdc8XxnlC_4SHHjN89k-M9i_cFMc2lI_ZFxqY,5596
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- mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py,sha256=1nAgfjb1pT80Q82FZ2hSkWCGVD6BoKVP4MIqsFTmQ1c,4024
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+ mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py,sha256=uex2T6GagtYFBIc39-Xm4SFHL06KAQ5v0_loOmY_eaw,4289
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+ mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py,sha256=dlsXfLPvm1qXRQplM0d5q0JMv9AuD9ytZn3utgYDYAM,7712
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+ mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py,sha256=61zVSuQ6Jw2hZU6QOa05lNcrr8Ylzpy2Tes-QaX8kFw,5888
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+ mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py,sha256=eRAQ0vFbqnWreiBdtFuwLKve9WwYwv9dYQtD1pumaZs,10776
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  mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py,sha256=TPaKlYkoy37_XgYNOskWCCoXtPNku_k5ygSeK4fT1VQ,6689
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+ mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py,sha256=65szj-H8Hxy_eXy3TyTs48EhPJbJ2w1skHlVbH2YeVM,4538
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  mgnify_pipelines_toolkit/analysis/genomes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  mgnify_pipelines_toolkit/analysis/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py,sha256=0Ot1j4LPsEPyPbySSAh6n9s5Dilm_8_M9YQvTnQ-1PQ,4415
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+ mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py,sha256=kAGU5kQyj-Hlcdx32i-xOJSuHYYUDj-kqnyYHMohHGc,4477
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  mgnify_pipelines_toolkit/analysis/shared/dwc_summary_generator.py,sha256=hggPqv9QawWAccm5tmru4VF9VnQAHF5LCXnqyLw_BWI,6727
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  mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py,sha256=ye0Jka6_lNn4dQGb2QG3YT46y7QK0QvyaIitIaS8JVQ,4026
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- mgnify_pipelines_toolkit/analysis/shared/get_subunits.py,sha256=j_UN3hItF7KhJrhGrSqjvZMg-ZwKAMc2sc0vHdJzjQw,4908
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+ mgnify_pipelines_toolkit/analysis/shared/get_subunits.py,sha256=UrU0CpZj3pfHZWI7Uuhv2a_C0JsO8pnVErY0sWGgNdw,4920
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  mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py,sha256=EH5RyzesLqsonnTQbSDs7kAOV6IskS4oyqZYlex1tAY,1934
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  mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py,sha256=6Ck2NhwRWw66GctUtKDdPT5fwJhWFR_YOZq-Vxwoa8A,1996
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  mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py,sha256=7-U0DN1joVu0ifLOoDUK2Pfqy8rb1RDKT6khVg3jky0,5559
@@ -38,15 +42,15 @@ mgnify_pipelines_toolkit/constants/ncrna.py,sha256=a_5hWp446S7BhRbe_JcydFgZM7sgP
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  mgnify_pipelines_toolkit/constants/regex_ambiguous_bases.py,sha256=7nEOODQq35y9wx9YnvJuo29oBpwTpXg_kIbf_t7N4TQ,1093
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  mgnify_pipelines_toolkit/constants/regex_fasta_header.py,sha256=G-xrc9b8zdmPTaOICD2b3RCVeFAEOVkfRkIfotQ7gek,1193
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  mgnify_pipelines_toolkit/constants/tax_ranks.py,sha256=kMq__kOJcbiwsgolkdvb-XLo3WMnJdEXgedjUyMOYjI,1081
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- mgnify_pipelines_toolkit/constants/thresholds.py,sha256=guDE7c4KrVJEfg_AcO_cQoJM6LGGaRlmo_U2i8d4N7g,1157
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+ mgnify_pipelines_toolkit/constants/thresholds.py,sha256=V_xDBk0RhS3hHeWqOacKzth2gM6zJABRPgwHy-Ciqfk,1157
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  mgnify_pipelines_toolkit/constants/var_region_coordinates.py,sha256=0bM4MwarFiM5yTcp5AbAmQ0o-q-gWy7kknir9zJ9R0A,1312
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  mgnify_pipelines_toolkit/schemas/schemas.py,sha256=pnH8LUH8i2ACNvFNWyG-n-eIHZcI5O9UDYulkh43mec,7692
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  mgnify_pipelines_toolkit/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  mgnify_pipelines_toolkit/utils/fasta_to_delimited.py,sha256=lgYIR1S4crURY7C7nFtgE6QMV4u4zCNsUrVkcRnsEEo,3996
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  mgnify_pipelines_toolkit/utils/get_mpt_version.py,sha256=aS9bWrC9CP7tpxoEVg6eEYt18-pmjG7fJl5Mchz4YOU,798
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- mgnify_pipelines_toolkit-1.0.3.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- mgnify_pipelines_toolkit-1.0.3.dist-info/METADATA,sha256=9_2fpTUZw_ers9JvGS41z9rnvasCWl_Dnh4to-pfSV0,6203
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- mgnify_pipelines_toolkit-1.0.3.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
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- mgnify_pipelines_toolkit-1.0.3.dist-info/entry_points.txt,sha256=QZ6vY4w3lYG8Xmll_s9SIsOpkxa5gBVEIxU3GvoCF4I,2946
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- mgnify_pipelines_toolkit-1.0.3.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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- mgnify_pipelines_toolkit-1.0.3.dist-info/RECORD,,
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/METADATA,sha256=fp1mfamjDfteh42zghP_y8br_zRaEYGzAhbDB7O72mc,5810
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/entry_points.txt,sha256=T8soGT2to8c_qafw-0itqCn4sjOnxlfaNWHIaHz4H54,3416
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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+ mgnify_pipelines_toolkit-1.0.5.dist-info/RECORD,,
{mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (78.0.2)
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+ Generator: setuptools (78.1.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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{mgnify_pipelines_toolkit-1.0.3.dist-info → mgnify_pipelines_toolkit-1.0.5.dist-info}/entry_points.txt RENAMED
@@ -18,6 +18,7 @@ genomes_extract_trnas = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_tr
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  get_mpt_version = mgnify_pipelines_toolkit.utils.get_mpt_version:main
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  get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main
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  get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main
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+ gff_toolkit = mgnify_pipelines_toolkit.analysis.assembly.gff_toolkit:main
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  krona_txt_from_cat_classification = mgnify_pipelines_toolkit.analysis.assembly.krona_txt_from_cat_classification:main
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  library_strategy_check = mgnify_pipelines_toolkit.analysis.shared.library_strategy_check:main
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  make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main
@@ -25,8 +26,12 @@ mapseq2biom = mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main
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  mapseq_to_asv_table = mgnify_pipelines_toolkit.analysis.amplicon.mapseq_to_asv_table:main
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  markergene_study_summary = mgnify_pipelines_toolkit.analysis.shared.markergene_study_summary:main
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  primer_val_classification = mgnify_pipelines_toolkit.analysis.amplicon.primer_val_classification:main
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+ process_dbcan_cazys = mgnify_pipelines_toolkit.analysis.assembly.process_dbcan_result_cazys:main
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+ process_dbcan_clusters = mgnify_pipelines_toolkit.analysis.assembly.process_dbcan_result_clusters:main
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  remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main
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  rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main
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  standard_primer_matching = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main
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  study_summary_generator = mgnify_pipelines_toolkit.analysis.shared.study_summary_generator:cli
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+ summarise_antismash_bgcs = mgnify_pipelines_toolkit.analysis.assembly.summarise_antismash_bgcs:main
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  summarise_goslims = mgnify_pipelines_toolkit.analysis.assembly.summarise_goslims:main
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+ summarise_sanntis_bgcs = mgnify_pipelines_toolkit.analysis.assembly.summarise_sanntis_bgcs:main