fixed typos, requirements and tests

databio · Oct 5, 2023 · 3f5894b · 3f5894b
1 parent 7f1cf69
commit 3f5894b
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Showing 4 changed files with 11 additions and 8 deletions.
diff --git a/bedboss/bedstat/bedstat.py b/bedboss/bedstat/bedstat.py
@@ -238,6 +238,9 @@ def bedstat(
             plot_id = plot["name"]
             del plot["name"]
             data.update({plot_id: plot})
+
+        # deleting md5sum, because it is record_identifier
+        del data["md5sum"]
         bbc.bed.report(
             record_identifier=bed_digest,
             values=data,

diff --git a/bedboss/bedstat/tools/regionstat.R b/bedboss/bedstat/tools/regionstat.R
@@ -234,13 +234,13 @@ doItAall <- function(query, fileId, genome, cellMatrix) {
         } else {
           if (genome %in% c("hg19", "hg38", "mm10")) {
             gp = calcPartitionsRef(query, genome)
-            plotBoth("paritions", plotPartitions(gp))
+            plotBoth("partitions", plotPartitions(gp))
           } else {
             partitionList = myPartitionList(gtffile)
             gp = calcPartitions(query, partitionList)
-            plotBoth("paritions", plotPartitions(gp))
+            plotBoth("partitions", plotPartitions(gp))
           }
-          plots = rbind(plots, getPlotReportDF("paritions", "Regions distribution over genomic partitions"))
+          plots = rbind(plots, getPlotReportDF("partitions", "Regions distribution over genomic partitions"))
           # flatten the result returned by the function above
           partiotionNames = as.vector(gp[,"partition"])
           partitionsList = list()

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -4,7 +4,7 @@ peppy>=0.40.0a4
 yacman>=0.8.4
 requests>=2.28.2
 piper>=0.13.3a1
-bbconf>=0.4.0a3
+bbconf>=0.4.0a5
 refgenconf>=0.12.2
 pandas>=1.5.3
 ubiquerg>=0.6.2
diff --git a/test/test_bedboss.py b/test/test_bedboss.py
@@ -121,8 +121,8 @@ def test_stat(self, bedfile, bigbed_file, genome, output_temp_dir):
         [
             f"{case_name}_cumulative_partitions.png",
             f"{case_name}_expected_partitions.pdf",
-            f"{case_name}_paritions.png",
-            f"{case_name}_paritions.pdf",
+            f"{case_name}_partitions.png",
+            f"{case_name}_partitions.pdf",
             f"{case_name}_cumulative_partitions.pdf",
             f"{case_name}_chrombins.pdf",
             f"{case_name}_widths_histogram.pdf",
@@ -191,8 +191,8 @@ def test_boss(self, input_file, genome, input_type, output_temp_dir):
         [
             f"{case_name}_cumulative_partitions.png",
             f"{case_name}_expected_partitions.pdf",
-            f"{case_name}_paritions.png",
-            f"{case_name}_paritions.pdf",
+            f"{case_name}_partitions.png",
+            f"{case_name}_partitions.pdf",
             f"{case_name}_cumulative_partitions.pdf",
             f"{case_name}_chrombins.pdf",
             f"{case_name}_widths_histogram.pdf",