mgnify-pipelines-toolkit 1.2.8__py3-none-any.whl → 1.2.9__py3-none-any.whl

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Files changed (7) hide show
  1. mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py +4 -2
  2. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/METADATA +1 -1
  3. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/RECORD +7 -7
  4. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/WHEEL +0 -0
  5. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/entry_points.txt +0 -0
  6. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/licenses/LICENSE +0 -0
  7. {mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/top_level.txt +0 -0
mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py CHANGED
@@ -89,8 +89,10 @@ def main():
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  if iter_cds and feature["type"] == "CDS":
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  # Annotate CDS features
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- start = int(feature["location"].split(":")[0][1:])
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- end = int(feature["location"].split(":")[1].split("]")[0])
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+ # The > and < are removed to work with pseudogene outputs in Bakta
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+ # A feature["location"] example that can be seen in Bakta outputs: "[81883:>82231](+)"
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+ start = int(feature["location"].split(":")[0][1:].lstrip("<>"))
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+ end = int(feature["location"].split(":")[1].split("]")[0].lstrip("<>"))
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  strand = feature["location"].split("(")[1][0] # + or -
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  if not region_name or not (region_start <= end and start <= region_end):
{mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mgnify_pipelines_toolkit
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- Version: 1.2.8
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+ Version: 1.2.9
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  Summary: Collection of scripts and tools for MGnify pipelines
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  Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
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  License: Apache Software License 2.0
{mgnify_pipelines_toolkit-1.2.8.dist-info → mgnify_pipelines_toolkit-1.2.9.dist-info}/RECORD RENAMED
@@ -9,7 +9,7 @@ mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=Wu4t
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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/study_summary_generator.py,sha256=epVClL10QcllL8yu7YGjx0rXNVHL2GxHi-Ek0MOjsjo,13859
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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=vZdDIcG09hulgCp0FylwHXVSGSlwl2RsDU4_xvsrUC0,6732
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+ mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py,sha256=2Zkm3KJ1Borzch5XSZbsVNTPej3J5QYkqTQQACkRDVo,6944
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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=6gbCRlEX1eBqzFYjOt3og-961dZ--QsCJL-7l5nzg1k,33992
@@ -44,9 +44,9 @@ mgnify_pipelines_toolkit/schemas/schemas.py,sha256=he9igC80YTR32v1e5NslwTgtdVySm
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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-1.2.8.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- mgnify_pipelines_toolkit-1.2.8.dist-info/METADATA,sha256=RkF31O7GjADzb2k96oZxbyWOmDvN1bKzIThNTb0e7Qg,5775
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- mgnify_pipelines_toolkit-1.2.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- mgnify_pipelines_toolkit-1.2.8.dist-info/entry_points.txt,sha256=7TJ8GgbKoX1xnQsOdWwMvwhIv4uuHCx7pMxKmZabPOs,3228
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- mgnify_pipelines_toolkit-1.2.8.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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- mgnify_pipelines_toolkit-1.2.8.dist-info/RECORD,,
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/METADATA,sha256=hxvefbAKXzSx05LR0jTdW3iW2fHlr2hxmNhY4TCdJ_4,5775
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/entry_points.txt,sha256=7TJ8GgbKoX1xnQsOdWwMvwhIv4uuHCx7pMxKmZabPOs,3228
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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+ mgnify_pipelines_toolkit-1.2.9.dist-info/RECORD,,