mgnify-pipelines-toolkit 0.1.7__tar.gz → 0.1.8__tar.gz

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  1. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/PKG-INFO +1 -1
  2. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +3 -1
  3. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/PKG-INFO +1 -1
  4. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/pyproject.toml +1 -1
  5. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/LICENSE +0 -0
  6. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/README.md +0 -0
  7. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/__init__.py +0 -0
  8. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/__init__.py +0 -0
  9. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py +0 -0
  10. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py +0 -0
  11. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py +0 -0
  12. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py +0 -0
  13. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py +0 -0
  14. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py +0 -0
  15. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py +0 -0
  16. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py +0 -0
  17. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py +0 -0
  18. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py +0 -0
  19. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_matching.py +0 -0
  20. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/__init__.py +0 -0
  21. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py +0 -0
  22. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py +0 -0
  23. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py +0 -0
  24. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py +0 -0
  25. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py +0 -0
  26. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/constants/regex_ambiguous_bases.py +0 -0
  27. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/constants/regex_fasta_header.py +0 -0
  28. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/constants/tax_ranks.py +0 -0
  29. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/constants/thresholds.py +0 -0
  30. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/constants/var_region_coordinates.py +0 -0
  31. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/utils/__init__.py +0 -0
  32. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/utils/fasta_to_delimited.py +0 -0
  33. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/utils/get_mpt_version.py +0 -0
  34. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt +0 -0
  35. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/dependency_links.txt +0 -0
  36. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/entry_points.txt +0 -0
  37. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/requires.txt +0 -0
  38. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/top_level.txt +0 -0
  39. {mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/setup.cfg +0 -0
{mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: mgnify_pipelines_toolkit
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- Version: 0.1.7
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+ Version: 0.1.8
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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-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py RENAMED
@@ -277,6 +277,8 @@ def main():
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  taxa_df = taxa_df.fillna("0")
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  taxa_df = order_df(taxa_df)
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+ asv_list = taxa_df.ASV.to_list()
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+
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  amp_reads = [read.strip() for read in list(open(amp, "r"))]
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  headers = [read.split(" ")[0][1:] for read in list(open(headers, "r"))]
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  amp_region = ".".join(amp.split(".")[1:3])
@@ -288,7 +290,7 @@ def main():
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  counter += 1
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  line_fwd = line_fwd.strip()
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- if line_fwd == "0":
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+ if line_fwd == "0" or f"seq_{line_fwd}" not in asv_list:
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  continue
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  if headers[counter] in amp_reads:
{mgnify_pipelines_toolkit-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/mgnify_pipelines_toolkit.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: mgnify_pipelines_toolkit
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- Version: 0.1.7
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+ Version: 0.1.8
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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-0.1.7 → mgnify_pipelines_toolkit-0.1.8}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "mgnify_pipelines_toolkit"
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- version = "0.1.7"
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+ version = "0.1.8"
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  readme = "README.md"
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  license = {text = "Apache Software License 2.0"}
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  authors = [