Merge branch 'release_0.6'

maxplanck-ie · Nov 14, 2017 · cd37d23 · cd37d23
2 parents 409552c + 1c65858
commit cd37d23
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/shared/rules/ChIP_qc_report.snakefile b/shared/rules/ChIP_qc_report.snakefile
@@ -17,7 +17,7 @@ if paired:
         benchmark:
             "QC_report/.benchmark/qc_report.{sample}.benchmark"
         shell:
-            "python " + os.path.join(workflow_tools, "sample_qc_report_PE.py") + " "
+            os.path.join(workflow_tools, "sample_qc_report_PE.py") + " "
             "{input.alignment_summary_metrics} {input.mark_duplicates_metrics} {input.insert_size_metrics} {input.macs2_xls} {input.macs2_qc_txt} "
             ">{output} 2>{log} "
 else:
@@ -36,7 +36,7 @@ else:
         benchmark:
             "QC_report/.benchmark/qc_report.{sample}.benchmark"
         shell:
-            "python " + os.path.join(workflow_tools, "sample_qc_report_SE.py") + " "
+            os.path.join(workflow_tools, "sample_qc_report_SE.py") + " "
             "{input.alignment_summary_metrics} {input.mark_duplicates_metrics} {input.macs2_xls} {input.macs2_qc_txt} "
             ">{output} 2>{log} "
 

diff --git a/shared/tools/sample_qc_report_PE.py b/shared/tools/sample_qc_report_PE.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 
 # paired-end ONLY!
@@ -28,7 +28,7 @@
     with open(infile_AlignmentSummaryMetrics) as f:
         lines = f.readlines()
 
-    columns = filter(lambda x: x.startswith("PAIR"), lines)[0].strip().split("\t")
+    columns = list(filter(lambda x: x.startswith("PAIR"), lines))[0].strip().split("\t")
 
     # PF_READS: The number of PF reads where PF is defined as passing Illumina's filter.
     total_reads = int(columns[2])
@@ -57,7 +57,7 @@
 try:
     with open(infile_MarkDuplicates) as f:
         lines = f.readlines()
-    columns = filter(lambda x: x.startswith("Unknown Library"), lines)[0].strip().split("\t")
+    columns = list(filter(lambda x: x.startswith("Unknown Library"), lines))[0].strip().split("\t")
 
     dup_mapped_pairs = int(columns[5])
     fdup_mapped_pairs = 1.0 * dup_mapped_pairs / mapped_pairs
@@ -79,7 +79,7 @@
     elif os.path.isfile(infile_MACS2_xls):
         with open(infile_MACS2_xls) as f:
             lines = f.readlines()
-        columns = filter(lambda x: x.startswith("# d"), lines)[0].strip()
+        columns = list(filter(lambda x: x.startswith("# d"), lines))[0].strip()
         fragment_size = int(columns.split(" = ")[1])
     else:
         fragment_size = "NA"

diff --git a/shared/tools/sample_qc_report_SE.py b/shared/tools/sample_qc_report_SE.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 
 # single-end ONLY!
@@ -24,7 +24,7 @@
 try:
     with open(infile_AlignmentSummaryMetrics) as f:
         lines = f.readlines()
-    columns = filter(lambda x: x.startswith("UNPAIRED"), lines)[0].strip().split("\t")
+    columns = list(filter(lambda x: x.startswith("UNPAIRED"), lines))[0].strip().split("\t")
 
     # PF_READS: The number of PF reads where PF is defined as passing Illumina's filter.
     total_reads = int(columns[2])
@@ -45,7 +45,7 @@
 try:
     with open(infile_MarkDuplicates) as f:
         lines = f.readlines()
-    columns = filter(lambda x: x.startswith("Unknown Library"), lines)[0].strip().split("\t")
+    columns = list(filter(lambda x: x.startswith("Unknown Library"), lines))[0].strip().split("\t")
 
     # UNPAIRED_READ_DUPLICATES: The number of fragments that were marked as duplicates.
     dup_mapped_reads = int(columns[4])
@@ -66,7 +66,7 @@
 try:
     with open(infile_MACS2_xls) as f:
         lines = f.readlines()
-    columns = filter(lambda x: x.startswith("# d"), lines)[0].strip()
+    columns = list(filter(lambda x: x.startswith("# d"), lines))[0].strip()
     fragment_size = int(columns.split(" = ")[1])
 except OSError:
     fragment_size = "NA"