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Fix issue #5 - GL-file-association-table #6

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merged 1 commit into from
Jun 14, 2024
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Fix issue #5 - GL-file-association-table #6

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8 changes: 4 additions & 4 deletions bin/GL-gen-file-associations-table
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Original file line number Diff line number Diff line change
Expand Up @@ -512,13 +512,13 @@ def gen_and_write_out_metagenomics_filenames_table(unique_filename_prefixes, map

if os.path.exists(bins_dir + output_prefix + f"bins-overview_{assay_suffix}.tsv"):
bins_overview = [file_prefix + output_prefix + f"bins-overview_{assay_suffix}.tsv"]
bins_dir_files = [file for file in os.listdir(bins_dir) if file.endswith(".fasta")]
bins_zip_files = [file for file in os.listdir(bins_dir) if file.endswith(".zip")]
else:
bins_overview = [""]

if os.path.exists(MAGs_dir + output_prefix + f"MAGs-overview_{assay_suffix}.tsv"):
MAGs_overview = [file_prefix + output_prefix + f"MAGs-overview_{assay_suffix}.tsv"]
MAGs_dir_files = [file for file in os.listdir(MAGs_dir) if file.endswith(".fasta")]
MAGs_zip_files = [file for file in os.listdir(MAGs_dir) if file.endswith(".zip")]
else:
MAGs_overview = [""]

Expand Down Expand Up @@ -605,12 +605,12 @@ def gen_and_write_out_metagenomics_filenames_table(unique_filename_prefixes, map
curr_read_mapping = [""]

if bins_overview[0] == file_prefix + output_prefix + f"bins-overview_{assay_suffix}.tsv":
curr_bins = bins_overview + [file_prefix + file for file in bins_dir_files if file.startswith(sample)]
curr_bins = bins_overview + [file_prefix + file for file in bins_zip_files if file.startswith(sample)]
else:
curr_bins = [""]

if MAGs_overview[0] == file_prefix + output_prefix + f"MAGs-overview_{assay_suffix}.tsv":
curr_MAGs = MAGs_overview + [file_prefix + file for file in MAGs_dir_files if file.startswith(sample)] + MAG_KO_files_list
curr_MAGs = MAGs_overview + [file_prefix + file for file in MAGs_zip_files if file.startswith(sample)] + MAG_KO_files_list
else:
curr_MAGs = [""]

Expand Down