mgnify-pipelines-toolkit 1.2.4__py3-none-any.whl → 1.2.6__py3-none-any.whl

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Files changed (8) hide show
  1. mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +1 -1
  2. mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +3 -0
  3. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/METADATA +1 -1
  4. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/RECORD +8 -8
  5. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/WHEEL +0 -0
  6. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/entry_points.txt +0 -0
  7. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/licenses/LICENSE +0 -0
  8. {mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/top_level.txt +0 -0
mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py CHANGED
@@ -454,7 +454,7 @@ def retrieve_regions(
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  temp_seq_counter[determine_domain(model) + " " + reg] = (
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  len(model_regions) * freq
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  )
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- if total_useful_sequences / len(data) < 0.95 and run_status != "ambiguous":
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+ if total_useful_sequences / len(data) < 0.75 and run_status != "ambiguous":
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  failed_run_counter += 1
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  logging.info("No output will be produced - too few useful sequences")
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  continue
mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py CHANGED
@@ -110,6 +110,9 @@ def main():
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  beg = float(line_lst[5])
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  end = float(line_lst[6])
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+ if "variant" not in primer_name:
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+ continue
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+
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  cleaned_primer_name = "_".join(primer_name.split("_")[0:-3])
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  if cleaned_primer_name in matched_primers_list:
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  continue
{mgnify_pipelines_toolkit-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.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: 1.2.4
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+ Version: 1.2.6
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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-1.2.4.dist-info → mgnify_pipelines_toolkit-1.2.6.dist-info}/RECORD RENAMED
@@ -1,10 +1,10 @@
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  mgnify_pipelines_toolkit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  mgnify_pipelines_toolkit/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=nUvboLz08RyqRE8Thfh8NRlmgJk0kVdXcSvgmAfKip0,20649
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+ mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=8yFhmHQXVDPXvRX8oWSANV3VMu0X-zNnz12u1fcGwTE,20649
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  mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=ohguvrMSg7GuiiZ5aHj1DvCnfThKFUG4s13LUSMM0mo,8892
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  mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py,sha256=BLqhflblUegCvuQic16PrFXfIXlFWmGkmWJyl4wJoLQ,5040
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  mgnify_pipelines_toolkit/analysis/amplicon/permute_primers.py,sha256=1aGOJX9tC7M1rnd0U2PeJ681sUo02wxk7_ycJqeVt6s,2216
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- mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=I9JfkM_o6Wp4VINOMO6ff9mHqghdJw1kDIfiF37JtLo,5185
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+ mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=-W_QmdmKAIqVC5n-RS8LX11hEQM4xdp5r1jkITB1CI8,5256
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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/study_summary_generator.py,sha256=epVClL10QcllL8yu7YGjx0rXNVHL2GxHi-Ek0MOjsjo,13859
@@ -43,9 +43,9 @@ mgnify_pipelines_toolkit/schemas/schemas.py,sha256=pyDZvCuWbwccQF0D7c5BN1vv36wQd
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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-1.2.4.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- mgnify_pipelines_toolkit-1.2.4.dist-info/METADATA,sha256=UXCHFcEcjuPMZvUgtzITSY_iIG-j_nfGVBMGCWjBjjA,5775
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- mgnify_pipelines_toolkit-1.2.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- mgnify_pipelines_toolkit-1.2.4.dist-info/entry_points.txt,sha256=sHDxlHizt_iZPtkNp0EDuohDGvC4O12B57JtpUmHwYk,3123
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- mgnify_pipelines_toolkit-1.2.4.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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- mgnify_pipelines_toolkit-1.2.4.dist-info/RECORD,,
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/METADATA,sha256=5XvhGHG2Zc5p8PNmR5ZYHUuRG1G6IIWT67t_FxkXkus,5775
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/entry_points.txt,sha256=sHDxlHizt_iZPtkNp0EDuohDGvC4O12B57JtpUmHwYk,3123
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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+ mgnify_pipelines_toolkit-1.2.6.dist-info/RECORD,,