Open in 'r' mode with biopython and in 'rU' with csv

micca/api/_convert.py

@@ -49,9 +49,9 @@ def add_phred_quality(records, defaultq):
                          "quality file")
 
     # parse records
-    input_handle = open(input_fn, 'rb')
+    input_handle = open(input_fn, 'r')
     if input_fmt == "fasta-qual":
-        qual_handle = open(qual_fn, 'rb')
+        qual_handle = open(qual_fn, 'r')
         records = PairedFastaQualIterator(input_handle, qual_handle)
     else:
         records = SeqIO.parse(input_handle, input_fmt)

micca/api/_filterstats.py

@@ -39,7 +39,7 @@ def _stats(input_fn, topn=None, maxeerates=[0.25, 0.5, 0.75, 1, 1.25, 1.5],
     eerate_minlen = np.array([], dtype=np.int, order='C')
     eerate_trunclen = np.array([], dtype=np.int, order='C')
 
-    with open(input_fn, "rb") as input_handle:
+    with open(input_fn, "r") as input_handle:
         for title, seq, qualstr in FastqGeneralIterator(input_handle):
             seqlen = len(seq)
             if (seqlen < 1):

micca/api/_stats.py

@@ -41,7 +41,7 @@ def _stats(input_fn, topn=None):
     qual_sum = np.array([], dtype=np.int, order='C')
     eerate_sum = np.array([], dtype=np.float, order='C')
 
-    with open(input_fn, "rb") as input_handle:
+    with open(input_fn, "r") as input_handle:
         for title, seq, qualstr in FastqGeneralIterator(input_handle):
 
             seqlen = len(seq)

micca/api/_tobiom.py

@@ -65,7 +65,7 @@ def tobiom(input_fn, output_fn, tax_fn=None, sampledata_fn=None,
 
     # replace the OTU ids with the original sequence ids when found in otuids
     if otuids_fn is not None:
-        with open(otuids_fn, "rb") as otuids_handle:
+        with open(otuids_fn, "rU") as otuids_handle:
             otuids_reader = csv.reader(otuids_handle, delimiter="\t")
             otuids = dict([(row[0], row[1]) for row in otuids_reader])
 

micca/api/classify.py

@@ -131,7 +131,7 @@ def rdp(input_fn, output_fn, gene="16srrna", maxmem=2, minconf=0.8):
     queryids = [record.id for record in SeqIO.parse(input_fn, "fasta")]
 
     rdp_temp_dict = dict()
-    with open(rdp_temp_fn, 'rb') as rdp_temp_handle:
+    with open(rdp_temp_fn, 'rU') as rdp_temp_handle:
         rdp_temp_reader = csv.reader(rdp_temp_handle, delimiter='\t')
 
         for row in rdp_temp_reader:
@@ -170,7 +170,7 @@ def otuid(input_fn, ref_tax_fn, output_fn):
 
     tax_dict = micca.tax.read(ref_tax_fn)
 
-    input_handle = open(input_fn, 'rb')
+    input_handle = open(input_fn, 'rU')
     input_reader = csv.reader(input_handle, delimiter='\t')
 
     output_handle = open(output_fn, 'wb')

micca/api/msa.py

@@ -108,7 +108,7 @@ def _nast_core(template, template_aln, candidate_aln):
 def _msa_count_columns(input_fn):
     """Count columns in a MSA in FASTA format.
     """
-    with open(input_fn, "rb") as input_handle:
+    with open(input_fn, "r") as input_handle:
         parser = SimpleFastaParser(input_handle)
         try:
             title, seq = parser.next()
@@ -127,7 +127,7 @@ def _msa_remove_gaps(input_fn, output_fn):
     """Write a new file without gap characters (-).
     """
 
-    input_handle = open(input_fn, "rb")
+    input_handle = open(input_fn, "r")
     output_handle = open(output_fn, "wb")
 
     for title, seq in SimpleFastaParser(input_handle):
@@ -313,7 +313,7 @@ def nast(input_fn, template_fn, output_fn, notaligned_fn=None, hits_fn=None,
     if nofilter:
         os.rename(output_temp_fn, output_fn)
     else:
-        output_temp_handle = open(output_temp_fn, "rb")
+        output_temp_handle = open(output_temp_fn, "r")
         output_handle = open(output_fn, "wb")
         for title, seq in SimpleFastaParser(output_temp_handle):
             seqout = "".join(np.array(list(seq))[msa_cov > 0])

micca/api/otu.py

@@ -46,7 +46,7 @@ def _rename_seqids(input_fn, otuids_fn, prefix=""):
     output_dir = os.path.dirname(input_fn)
 
     tmp_fn = micca.ioutils.make_tempfile(output_dir)
-    input_handle = open(input_fn, "rb")
+    input_handle = open(input_fn, "r")
     otuids_handle = open(otuids_fn, "wb")
     tmp_handle = open(tmp_fn, "wb")