Merge pull request #70 from databio/dev

Dev
databio · Mar 27, 2020 · 5e5ada4 · 5e5ada4
2 parents dbdd8a4 + feb91d6
commit 5e5ada4
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Showing 6 changed files with 24 additions and 12 deletions.
diff --git a/PEPPROr/R/PEPPROr.R b/PEPPROr/R/PEPPROr.R
@@ -552,17 +552,23 @@ calcFRiF <- function(bedFile, total, reads) {
         bedFile <- bedFile[order(-bedFile$bases),]
     }
 
-    bedFile <- bedFile[apply(bedFile != 0, 1, all),]
+    bedFile <- bedFile[bedFile$count > 0,]
+    if (nrow(bedFile) != 0) {
+        if (reads) {
+            bedFile <- cbind(bedFile, cumsum=cumsum(bedFile$count))
+        } else {
+            bedFile <- cbind(bedFile, cumsum=cumsum(bedFile$bases))
+        }
 
-    if (reads) {
-        bedFile <- cbind(bedFile, cumsum=cumsum(bedFile$count))
+        bedFile <- cbind(bedFile, cumSize=cumsum(bedFile$size))
+        bedFile <- cbind(bedFile, frip=bedFile$cumsum/as.numeric(total))
+        bedFile <- cbind(bedFile, numfeats=as.numeric(1:nrow(bedFile)))
     } else {
-        bedFile <- cbind(bedFile, cumsum=cumsum(bedFile$bases))
+        bedFile$cumsum = integer()
+        bedFile$frip = integer()
+        bedFile$numfeats = integer()
     }
-
-    bedFile <- cbind(bedFile, cumSize=cumsum(bedFile$size))
-    bedFile <- cbind(bedFile, frip=bedFile$cumsum/as.numeric(total))
-    bedFile <- cbind(bedFile, numfeats=as.numeric(1:nrow(bedFile)))
+
     return(bedFile)
 }
 

diff --git a/docs/annotation.md b/docs/annotation.md
@@ -33,7 +33,7 @@ refgenie build -g GENOME -a refgene_anno --files refgene=/path/to/refGene.txt.gz
 ```
 
 ## 5: Build the feat_annotation asset
-The `feat_annotation` asset includes feature annotations used to calculate the [FRiF](glossary.md) and [PRiF](glossary.md). `Refgenie` can automatically build this after you have the above assets installed:
+The `feat_annotation` asset includes feature annotations used to calculate the FRiF and cFRiF. `Refgenie` can automatically build this after you have the above assets installed:
 
 ```console
 refgenie build -g GENOME -a feat_annotation

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,6 +1,12 @@
 # Change log
 All notable changes to this project will be documented in this file.
 
+## [0.9.5] -- 2020-03-26
+
+## Changed
+ - Updated FRiF calculation to only account for the `count` column
+ - Updated FRiF calculation to check if results are empty
+
 ## [0.9.4] -- 2020-03-25
 
 ## Changed

diff --git a/docs/usage.md b/docs/usage.md
@@ -25,7 +25,7 @@ usage: peppro.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V]
                  [--coverage] [--keep] [--noFIFO] [--no-complexity]
                  [--prioritize] [-V]
 
-PEPPRO version 0.9.4
+PEPPRO version 0.9.5
 
 optional arguments:
   -h, --help            show this help message and exit

diff --git a/pipelines/peppro.py b/pipelines/peppro.py
@@ -5,7 +5,7 @@
 
 __author__ = ["Jason Smith", "Nathan Sheffield", "Mike Guertin"]
 __email__ = "[email protected]"
-__version__ = "0.9.4"
+__version__ = "0.9.5"
 
 from argparse import ArgumentParser
 import os

diff --git a/usage.txt b/usage.txt
@@ -17,7 +17,7 @@ usage: peppro.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V]
                  [--coverage] [--keep] [--noFIFO] [--no-complexity]
                  [--prioritize] [-V]
 
-PEPPRO version 0.9.4
+PEPPRO version 0.9.5
 
 optional arguments:
   -h, --help            show this help message and exit