Merge pull request #70 from maxplanck-ie/fix_python3_again

Fix python3 again
maxplanck-ie · Nov 16, 2017 · 340ad12 · 340ad12
2 parents 3d07d82 + 6682ae4
commit 340ad12
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Showing 2 changed files with 28 additions and 17 deletions.
diff --git a/shared/tools/sample_qc_report_PE.py b/shared/tools/sample_qc_report_PE.py
@@ -16,6 +16,9 @@
 infile_AlignmentSummaryMetrics = sys.argv[1]    # sample_name.alignment_summary_metrics.txt
 infile_MarkDuplicates = sys.argv[2]             # sample_name.mark_duplicates_metrics.txt
 input_InsertSizeMetrics = sys.argv[3]
+
+infile_MACS2_xls = ""
+infile_MACS2_qc_txt = ""
 try:
     infile_MACS2_xls = sys.argv[4]              # sample_name.filtered.BAM_peaks.xls (optional)
     infile_MACS2_qc_txt = sys.argv[5]           # ample_name.filtered.BAM_peaks.qc.txt (optional)
@@ -88,17 +91,19 @@
 
 
 # get peak qc from MACS2_peak_qc output #######################################
+peak_count = "NA"
+frip = "NA"
+peak_genome_coverage = "NA"
+
 try:
-    with open(infile_MACS2_qc_txt) as f:
-        columns = map(lambda x: float(x), f.readlines()[1].split())
-        peak_count = int(columns[0])
-        frip = round(float(columns[1]), 3)
-        peak_genome_coverage = round(columns[2], 3)
+    if os.path.isfile(infile_MACS2_qc_txt):
+        with open(infile_MACS2_qc_txt) as f:
+            columns = list(map(lambda x: float(x), f.readlines()[1].split()))
+            peak_count = int(columns[0])
+            frip = round(float(columns[1]), 3)
+            peak_genome_coverage = round(columns[2], 3)
 except OSError:
-    peak_count = "NA"
-    frip = "NA"
-    peak_genome_coverage = "NA"
-
+    pass
 
 # Output to stdout ###########################################################
 print("{sample_name}\t{read_pairs}\t{mapped_pairs}\t{fmapped_pairs:.3f}\t{dup_mapped_pairs}\t{fdup_mapped_pairs:.3f}\t{dupfree_mapped_pairs}\t{fdupfree_mapped_pairs:.3f}\t{fhq_mapped_reads:.3f}\t{fmapped_singletons:.3f}\t{fragment_size}\t{peak_count}\t{frip}\t{peak_genome_coverage}".format(

diff --git a/shared/tools/sample_qc_report_SE.py b/shared/tools/sample_qc_report_SE.py
@@ -13,6 +13,9 @@
 # Input files ################################################################
 infile_AlignmentSummaryMetrics = sys.argv[1]    # sample_name.alignment_summary_metrics.txt
 infile_MarkDuplicates = sys.argv[2]             # sample_name.mark_duplicates_metrics.txt
+
+infile_MACS2_xls = ""
+infile_MACS2_qc_txt = ""
 try:
     infile_MACS2_xls = sys.argv[3]              # sample_name.filtered.BAM_peaks.xls (optional)
     infile_MACS2_qc_txt = sys.argv[4]           # ample_name.filtered.BAM_peaks.qc.txt (optional)
@@ -73,16 +76,19 @@
 
 
 # get peak qc from MACS2_peak_qc output #######################################
+peak_count = "NA"
+frip = "NA"
+peak_genome_coverage = "NA"
+
 try:
-    with open(infile_MACS2_qc_txt) as f:
-        columns = map(lambda x: float(x), f.readlines()[1].split())
-        peak_count = int(columns[0])
-        frip = round(float(columns[1]), 3)
-        peak_genome_coverage = round(columns[2], 3)
+    if os.path.isfile(infile_MACS2_qc_txt):
+        with open(infile_MACS2_qc_txt) as f:
+            columns = list(map(lambda x: float(x), f.readlines()[1].split()))
+            peak_count = int(columns[0])
+            frip = round(float(columns[1]), 3)
+            peak_genome_coverage = round(columns[2], 3)
 except OSError:
-    peak_count = "NA"
-    frip = "NA"
-    peak_genome_coverage = "NA"
+    pass
 
 # Output to stdout ###########################################################
 print("{sample_name}\t{total_reads}\t{mapped_reads}\t{fmapped_reads:.3f}\t{dup_mapped_reads}\t{fdup_mapped_reads}\t{dupfree_mapped_reads}\t{fdupfree_mapped_reads}\t{fhq_mapped_reads:.3f}\t{fragment_size}\t{peak_count}\t{frip}\t{peak_genome_coverage}".format(