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fix empty bin_info.tsv with --skip-abundances #127

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merged 2 commits into from
Aug 28, 2023
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fix empty bin_info.tsv with --skip-abundances #127

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935d531
fix empty bin_info.tsv with --skip-abundances
AroneyS Aug 28, 2023
8f4416e
switch to left join for taxa info
AroneyS Aug 28, 2023
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2 changes: 1 addition & 1 deletion aviary/modules/binning/scripts/finalise_stats.py
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Looks like you need to update the second merge as well. For safety, it should likely be a left join as well to keep all of the checkm output, also should change the column it is joining on to on=[merged_out.columns[0]] right?

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Just in case taxonomy is missing a genome?

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Yep, I know there are cases where GTDB-tk will randomly fail to assign taxonomy to genomes due to some pplacer issue. Not sure what happens to the gtdb-tk output in that case, like it might just end up missing from the file. Additionally, there probably exists a world where running gtdb-tk ends up being an optional step so making it a left join future proofs against that I suppose

Original file line number Diff line number Diff line change
Expand Up @@ -85,7 +85,7 @@ def get_taxonomy(rename_columns="Bin Id"):

taxa = get_taxonomy(checkm_output.columns[0])

merged_out = pd.merge(checkm_output, coverage_file, on=[checkm_output.columns[0]])
merged_out = pd.merge(checkm_output, coverage_file, on=[checkm_output.columns[0]], how="left")
merged_out = pd.merge(merged_out, taxa, on=[checkm_output.columns[0]])
merged_out.to_csv(snakemake.output.bin_stats, sep='\t', index=False)

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20 changes: 17 additions & 3 deletions test/test_integration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,12 @@ def test_short_read_recovery(self):
)
subprocess.run(cmd, shell=True, check=True)

self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
self.assertTrue(os.path.isfile(bin_info_path))
with open(bin_info_path) as f:
num_lines = sum(1 for _ in f)
self.assertTrue(num_lines > 1)

self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))
self.assertTrue(os.path.islink(f"{tmpdir}/aviary_out/assembly/final_contigs.fasta"))

Expand All @@ -97,7 +102,11 @@ def test_short_read_recovery_skip_binners(self):
)
subprocess.run(cmd, shell=True, check=True)

self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
self.assertTrue(os.path.isfile(bin_info_path))
with open(bin_info_path) as f:
num_lines = sum(1 for _ in f)
self.assertTrue(num_lines > 1)
self.assertFalse(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))


Expand All @@ -117,7 +126,12 @@ def test_short_read_recovery_skip_abundances(self):
)
subprocess.run(cmd, shell=True, check=True)

self.assertTrue(os.path.isfile(f"{tmpdir}/aviary_out/bins/bin_info.tsv"))
bin_info_path = f"{tmpdir}/aviary_out/bins/bin_info.tsv"
self.assertTrue(os.path.isfile(bin_info_path))
with open(bin_info_path) as f:
num_lines = sum(1 for _ in f)
self.assertEqual(num_lines, 3)

self.assertFalse(os.path.isfile(f"{tmpdir}/aviary_out/data/final_contigs.fasta"))


Expand Down