mgnify-pipelines-toolkit 1.2.1__py3-none-any.whl → 1.2.2__py3-none-any.whl

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Files changed (7) hide show
  1. mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py +18 -17
  2. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/METADATA +1 -1
  3. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/RECORD +7 -7
  4. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/WHEEL +0 -0
  5. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/entry_points.txt +0 -0
  6. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/licenses/LICENSE +0 -0
  7. {mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/top_level.txt +0 -0
mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py CHANGED
@@ -300,23 +300,24 @@ def main():
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  if paired_end:
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  rev_fr.close()
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- ref_db = ""
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-
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- if len(taxa_df.columns) == 9:
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- tax_assignment_dict = make_tax_assignment_dict_silva(taxa_df, asv_dict)
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- ref_db = "silva"
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- elif len(taxa_df.columns) == 10:
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- tax_assignment_dict = make_tax_assignment_dict_pr2(taxa_df, asv_dict)
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- ref_db = "pr2"
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-
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- with open(f"./{sample}_{amp_region}_{ref_db}_asv_krona_counts.txt", "w") as fw:
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- for tax_assignment, count in tax_assignment_dict.items():
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- fw.write(f"{count}\t{tax_assignment}\n")
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-
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- asv_count_df = generate_asv_count_dict(asv_dict)
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- asv_count_df.to_csv(
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- f"./{sample}_{amp_region}_asv_read_counts.tsv", sep="\t", index=False
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- )
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+ if asv_dict: # if there are matches between taxonomic and ASV annotations
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+ ref_db = ""
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+
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+ if len(taxa_df.columns) == 9:
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+ tax_assignment_dict = make_tax_assignment_dict_silva(taxa_df, asv_dict)
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+ ref_db = "silva"
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+ elif len(taxa_df.columns) == 10:
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+ tax_assignment_dict = make_tax_assignment_dict_pr2(taxa_df, asv_dict)
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+ ref_db = "pr2"
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+
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+ with open(f"./{sample}_{amp_region}_{ref_db}_asv_krona_counts.txt", "w") as fw:
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+ for tax_assignment, count in tax_assignment_dict.items():
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+ fw.write(f"{count}\t{tax_assignment}\n")
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+
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+ asv_count_df = generate_asv_count_dict(asv_dict)
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+ asv_count_df.to_csv(
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+ f"./{sample}_{amp_region}_asv_read_counts.tsv", sep="\t", index=False
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+ )
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  if __name__ == "__main__":
{mgnify_pipelines_toolkit-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.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: 1.2.1
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+ Version: 1.2.2
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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-1.2.1.dist-info → mgnify_pipelines_toolkit-1.2.2.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
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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=W0ob9z_8sjrB1Ck48Ac-_5Vw2kyoRFalcxhrR6KSXpI,20196
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- mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=soTewFddtebW-EcejGh9whs3cBLWJrGCYdPc0KukoAw,8756
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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/primer_val_classification.py,sha256=Bmc4Yu8inpT6AVTG1zwxp9F9mknIDLY33-UuFdaZuq0,3756
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  mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=Wu4tRtuRkgd3hoeuwPl_E5ghxIW7e_1vrcvFGWv_U4A,3173
@@ -42,9 +42,9 @@ 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-1.2.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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- mgnify_pipelines_toolkit-1.2.1.dist-info/METADATA,sha256=CIH7XH5WIzQMc0e2MfYFlWCnV1hokgYaQskYsfobzao,5775
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- mgnify_pipelines_toolkit-1.2.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- mgnify_pipelines_toolkit-1.2.1.dist-info/entry_points.txt,sha256=d7r4_VUS1hWNMnTJOy8u2kTRSFcy-sDN5NLRUXz-IhU,3041
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- mgnify_pipelines_toolkit-1.2.1.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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- mgnify_pipelines_toolkit-1.2.1.dist-info/RECORD,,
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/METADATA,sha256=MRDDDp1xhJhoIc-rU1IKWASfleAvFXsJLyhaoG8FLUg,5775
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/entry_points.txt,sha256=d7r4_VUS1hWNMnTJOy8u2kTRSFcy-sDN5NLRUXz-IhU,3041
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
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+ mgnify_pipelines_toolkit-1.2.2.dist-info/RECORD,,