oxymetag 1.1.2__tar.gz → 1.1.3__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {oxymetag-1.1.2/oxymetag.egg-info → oxymetag-1.1.3}/PKG-INFO +1 -1
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/__init__.py +1 -1
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/scripts/predict_oxygen.R +10 -3
- {oxymetag-1.1.2 → oxymetag-1.1.3/oxymetag.egg-info}/PKG-INFO +1 -1
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag.egg-info/SOURCES.txt +1 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/setup.py +1 -1
- oxymetag-1.1.3/tests/__init__.py +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/LICENSE +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/MANIFEST.in +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/README.md +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/environment.yml +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/cli.py +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/core.py +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/.DS_Store +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/Oxygen_pfams.csv +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/VTML20.out +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/nucleotide.out +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxygen_model.rds +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams.dmnd +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117.dmnd +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db.dbtype +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db.index +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db.lookup +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db.source +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db_h +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db_h.dbtype +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/oxymetag_pfams_n117_db_h.index +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/pfam_headers_table.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/data/pfam_lengths.tsv +0 -0
- /oxymetag-1.1.2/tests/__init__.py → /oxymetag-1.1.3/oxymetag/scripts/.Rhistory +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag/utils.py +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag.egg-info/dependency_links.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag.egg-info/entry_points.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag.egg-info/requires.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/oxymetag.egg-info/top_level.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/requirements.txt +0 -0
- {oxymetag-1.1.2 → oxymetag-1.1.3}/setup.cfg +0 -0
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@@ -180,7 +180,7 @@ predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut
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anaerobe_rpk <- oxygen_rpk$RPKsum[oxygen_rpk$Oxygen == "anaerobic"]
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if (length(anaerobe_rpk) == 0 || anaerobe_rpk == 0) {
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results$ratio[i] <- ifelse(length(aerobe_rpk) > 0 && aerobe_rpk > 0, Inf,
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results$ratio[i] <- ifelse(length(aerobe_rpk) > 0 && aerobe_rpk > 0, Inf, NA)
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} else {
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results$ratio[i] <- aerobe_rpk / anaerobe_rpk
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}
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@@ -188,11 +188,18 @@ predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut
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message("Processed sample ", i, "/", length(files), ": ", sample_id)
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}
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# Make predictions using the GAM model
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# Make predictions using the GAM model, ratio NA are Per_anaerobe NA
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results <- results %>%
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mutate(ratio = ifelse(is.infinite(ratio), NA, ratio))
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new_data <- data.frame(ratio = results$ratio)
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results$Per_aerobe <- predict(oxygen_model,
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results$Per_aerobe <- predict(oxygen_model,
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newdata = new_data,
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type = "response",
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na.action = na.exclude)
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# Constrain predictions to 0-100% and set to 100% if ratio > 35
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# If NA, that means there were 0 aerobe or anaerobe genes found
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# You can look at the gene counts to learn something about oxygen, but not calculate the Per_aerobe
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results <- results %>%
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mutate(Per_aerobe = pmax(0, pmin(100, Per_aerobe))) %>%
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mutate(Per_aerobe = ifelse(ratio > 35, 100, Per_aerobe))
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@@ -8,7 +8,7 @@ with open("requirements.txt", "r", encoding="utf-8") as fh:
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setup(
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name="oxymetag",
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version="1.1.
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version="1.1.3",
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author="Clifton P. Bueno de Mesquita",
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author_email="cliff.buenodemesquita@colorado.edu",
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description="Oxygen metabolism profiling from metagenomic data",
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