passing tests

Author: lpantano

mirtop/gff/convert.py

@@ -81,11 +81,11 @@ def convert_gff_counts(args):
             if extra == "Invalid":
                 continue
             logger.debug("COUNTS::EXTRA:%s" % extra)
-            cols_variants = [cols_variants] + _expand(extra, True)
-        #import pdb; pdb.set_trace()   
+            cols_variants = cols_variants + _expand(extra, True)
         summary = [UID, Read,  mirna, variant] + cols_variants + expression
         logger.debug(summary)
         all_lines.append(summary)
+    #import pdb; pdb.set_trace()   
     df = pd.DataFrame(all_lines, columns = ['UID', 'Read', 'miRNA', 'Variant'] + variant_header + samples)
     df = df.drop_duplicates()
     df.to_csv(out_file, sep="\t", index=False)

mirtop/gff/stats.py

@@ -107,13 +107,13 @@ def _add_missing(df):
     # ref_miRNA_mean
     category = "ref_miRNA_mean"
     if sum(df['category']==category) == 0:
-        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
-        df = df.append(df2, ignore_index = True)
+        df2 = pd.DataFrame({'category': category, 'sample': df['sample'].iat[0], 'counts': 0}, index=[0])
+        df = pd.concat([df, df2], ignore_index = True)
 
     category = "isomiR_sum"
     if sum(df['category']==category) == 0:
-        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
-        df = df.append(df2, ignore_index = True)
+        df2 =  pd.DataFrame({'category': category, 'sample': df['sample'].iat[0], 'counts': 0}, index=[0])
+        df = pd.concat([df, df2], ignore_index = True)
 
     return df
 

mirtop/mirna/realign.py

@@ -1,5 +1,5 @@
 import re
-from Bio.Align import PairwiseAligner
+from Bio import pairwise2
 from Bio.Seq import Seq
 from collections import defaultdict
 
@@ -94,7 +94,7 @@ def formatGFF(self):
             value.append("iso_3p:%s%s" % (direction, size))
         if not value:
             value = ["NA"]
-        return ",".join(sorted(list(set(value))))
+        return ",".join(list(set(value)))
 
     def format(self, sep="\t"):
         """Create tabular line from variant fields."""