oxymetag 1.1.1__py3-none-any.whl → 1.1.3__py3-none-any.whl

oxymetag/__init__.py

@@ -2,7 +2,7 @@
 OxyMetaG: Oxygen metabolism profiling from metagenomic data
 """
 
-__version__ = "1.1.1"
+__version__ = "1.1.3"
 __author__ = "Clifton P. Bueno de Mesquita"
 __email__ = "cliff.buenodemesquita@colorado.edu"
 

oxymetag/scripts/predict_oxygen.R

@@ -167,7 +167,7 @@ predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut
     
     gene.hit.length.correction <- gene.hits %>%
       left_join(pfam_gene_length, by = "Pfam") %>%
-      mutate(RPK = total_count / (1000 * Gene.length)) %>%
+      mutate(RPK = total_count / (Gene.length/1000)) %>%
       left_join(oxygen_pfams, by = "Pfam")
     
     # Sum by oxygen type
@@ -180,7 +180,7 @@ predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut
     anaerobe_rpk <- oxygen_rpk$RPKsum[oxygen_rpk$Oxygen == "anaerobic"]
     
     if (length(anaerobe_rpk) == 0 || anaerobe_rpk == 0) {
-      results$ratio[i] <- ifelse(length(aerobe_rpk) > 0 && aerobe_rpk > 0, Inf, 0)
+      results$ratio[i] <- ifelse(length(aerobe_rpk) > 0 && aerobe_rpk > 0, Inf, NA)
     } else {
       results$ratio[i] <- aerobe_rpk / anaerobe_rpk
     }
@@ -188,11 +188,18 @@ predict_oxygen <- function(input_dir, output_file, package_data_dir, mode, idcut
     message("Processed sample ", i, "/", length(files), ": ", sample_id)
   }
   
-  # Make predictions using the GAM model
+  # Make predictions using the GAM model, ratio NA are Per_anaerobe NA
+  results <- results %>%
+    mutate(ratio = ifelse(is.infinite(ratio), NA, ratio))
   new_data <- data.frame(ratio = results$ratio)
-  results$Per_aerobe <- predict(oxygen_model, newdata = new_data, type = "response")
+  results$Per_aerobe <- predict(oxygen_model, 
+                                newdata = new_data, 
+                                type = "response",
+                                na.action = na.exclude)
   
   # Constrain predictions to 0-100% and set to 100% if ratio > 35
+  # If NA, that means there were 0 aerobe or anaerobe genes found
+  # You can look at the gene counts to learn something about oxygen, but not calculate the Per_aerobe
   results <- results %>%
     mutate(Per_aerobe = pmax(0, pmin(100, Per_aerobe))) %>%
     mutate(Per_aerobe = ifelse(ratio > 35, 100, Per_aerobe))

{oxymetag-1.1.1.dist-info → oxymetag-1.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: oxymetag
-Version: 1.1.1
+Version: 1.1.3
 Summary: Oxygen metabolism profiling from metagenomic data
 Home-page: https://github.com/cliffbueno/oxymetag
 Author: Clifton P. Bueno de Mesquita

{oxymetag-1.1.1.dist-info → oxymetag-1.1.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-oxymetag/__init__.py,sha256=jmwbHrRvxQhdOGacT6-lojPH1Vf5r1BA0KWz2ycl0vk,441
+oxymetag/__init__.py,sha256=wfh3wanuq0rSf0mlXJjyxE4DDHINdRp1DtEFOfLl8Cs,441
 oxymetag/cli.py,sha256=GIXCxpBUQIRWgcSyQNudAWyuVWAAnxK1DRGXG8jpVzQ,4877
 oxymetag/core.py,sha256=zLLVT6XsNb7qFtDlobIh44xgnOzXauYBCL8nNLA4XSk,12496
 oxymetag/utils.py,sha256=fxzKYNUpsuBnYZxlh8QMIEg5wktV6BatoLasfawTeW8,3178
@@ -19,11 +19,12 @@ oxymetag/data/oxymetag_pfams_n117_db_h.dbtype,sha256=QvSuuBwe-B93Hz3oq8qdz2aQHFd
 oxymetag/data/oxymetag_pfams_n117_db_h.index,sha256=JQc2q-oSWwx-sv32muf51tZVgmDl0DgM6m1eJr5Z-V4,379408
 oxymetag/data/pfam_headers_table.txt,sha256=wMg4WvlST6Zi3EzVFudjFHyREqNk8kHDI9Q6th7FdFY,255832
 oxymetag/data/pfam_lengths.tsv,sha256=--0bGxDN2v_WiBo0rKFJMPeOPsOrbaNhyjPAoIF9E5A,366
-oxymetag/scripts/predict_oxygen.R,sha256=NUv23y0l7BQxFUoxHqttlKveh6LYmO2qgP8hciGdpMs,7657
+oxymetag/scripts/.Rhistory,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+oxymetag/scripts/predict_oxygen.R,sha256=L6FnPkeqil4TcMv53mKbqR86e6P-xrYlcSiiUAmt7Yk,8059
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-oxymetag-1.1.1.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-oxymetag-1.1.1.dist-info/METADATA,sha256=H6M4nnM-SOojWNgRCEJRMcCiS417gi0iIVvAAUlVryY,11898
-oxymetag-1.1.1.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-oxymetag-1.1.1.dist-info/entry_points.txt,sha256=-9xMAfrSPtFBEvQWRNVKROTM_3OjEik34mVEsYFwM2k,47
-oxymetag-1.1.1.dist-info/top_level.txt,sha256=G7EHL5Fpxne8CH3w5IDIkrsRmMzaEfOhmTngNovoYi8,15
-oxymetag-1.1.1.dist-info/RECORD,,
+oxymetag-1.1.3.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+oxymetag-1.1.3.dist-info/METADATA,sha256=5iHaKe2exnBf_LhJaOuU00CTWFVLxuHhJHDwsfV_Jdk,11898
+oxymetag-1.1.3.dist-info/WHEEL,sha256=WnJ8fYhv8N4SYVK2lLYNI6N0kVATA7b0piVUNvqIIJE,91
+oxymetag-1.1.3.dist-info/entry_points.txt,sha256=-9xMAfrSPtFBEvQWRNVKROTM_3OjEik34mVEsYFwM2k,47
+oxymetag-1.1.3.dist-info/top_level.txt,sha256=G7EHL5Fpxne8CH3w5IDIkrsRmMzaEfOhmTngNovoYi8,15
+oxymetag-1.1.3.dist-info/RECORD,,

{oxymetag-1.1.1.dist-info → oxymetag-1.1.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.2)
+Generator: setuptools (75.3.3)
 Root-Is-Purelib: true
 Tag: py3-none-any