Definitely fix the "new-line error"

micca/api/_convert.py

@@ -49,9 +49,9 @@ def add_phred_quality(records, defaultq):
                          "quality file")
 
     # parse records
-    input_handle = open(input_fn, 'r')
+    input_handle = open(input_fn, 'rU')
     if input_fmt == "fasta-qual":
-        qual_handle = open(qual_fn, 'r')
+        qual_handle = open(qual_fn, 'rU')
         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, "r") as input_handle:
+    with open(input_fn, "rU") 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, "r") as input_handle:
+    with open(input_fn, "rU") as input_handle:
         for title, seq, qualstr in FastqGeneralIterator(input_handle):
 
             seqlen = len(seq)

micca/api/classify.py

@@ -90,7 +90,7 @@ def get_cons_tax(tax, minfrac):
         os.remove(hits_temp_fn)
         raise
 
-    with open(hits_temp_fn, 'rb') as hits_temp_handle:
+    with open(hits_temp_fn, 'rU') as hits_temp_handle:
         with open(output_fn, 'wb') as output_handle:
             hits_temp_reader = csv.reader(hits_temp_handle, delimiter='\t')
             output_writer = csv.writer(

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, "r") as input_handle:
+    with open(input_fn, "rU") 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, "r")
+    input_handle = open(input_fn, "rU")
     output_handle = open(output_fn, "wb")
 
     for title, seq in SimpleFastaParser(input_handle):
@@ -233,7 +233,7 @@ def nast(input_fn, template_fn, output_fn, notaligned_fn=None, hits_fn=None,
     hits_out_handle = open(hits_out_fn, "wb")
 
     # set up hits reader
-    hits_temp_handle = open(hits_temp_fn, 'rb')
+    hits_temp_handle = open(hits_temp_fn, 'rU')
     hits_temp_reader = csv.reader(hits_temp_handle, delimiter='\t')
 
     # set MSA coverage to zero
@@ -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, "r")
+        output_temp_handle = open(output_temp_fn, "rU")
         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, "r")
+    input_handle = open(input_fn, "rU")
     otuids_handle = open(otuids_fn, "wb")
     tmp_handle = open(tmp_fn, "wb")
 
@@ -65,14 +65,14 @@ def _rename_seqids(input_fn, otuids_fn, prefix=""):
 
 def _hits_to_otutable(hits_fn, otuids_fn, otutable_fn):
 
-    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 = [(row[1], row[0]) for row in otuids_reader]
     ordered_otuids = [otuid[1] for otuid in otuids]
     otuids_dict = dict(otuids)
 
     otutable_dict = {}
-    with open(hits_fn, 'rb') as hits_handle:
+    with open(hits_fn, 'rU') as hits_handle:
         hits_reader = csv.reader(hits_handle, delimiter='\t')
         for row in hits_reader:
             match = re.search("(^|;)sample=([^;]+)", row[0])
@@ -97,7 +97,7 @@ def _uc_to_hitssqlite(uc_fn, sqlite_fn):
     cur = con.cursor()
     cur.execute('CREATE TABLE hits (query text, target text, ident real)')
 
-    with open(uc_fn, 'rb') as uc_handle:
+    with open(uc_fn, 'rU') as uc_handle:
         uc_reader = csv.reader(uc_handle, delimiter='\t')
         for row in uc_reader:
             rtype, ident, query, target = row[0], row[3], row[8], row[9]
@@ -343,15 +343,15 @@ def open_ref(input_fn, ref_fn, output_dir, ident=0.97, threads=1, mincov=0.75,
             raise
 
         with open(otus_fn, 'a') as otus_handle:
-            with open(denovo_otus_fn, 'r') as denovo_otus_handle:
+            with open(denovo_otus_fn, 'rU') as denovo_otus_handle:
                 otus_handle.write(denovo_otus_handle.read())
 
         with open(otuids_fn, 'a') as otuids_handle:
-            with open(denovo_otuids_fn, 'r') as denovo_otuids_handle:
+            with open(denovo_otuids_fn, 'rU') as denovo_otuids_handle:
                 otuids_handle.write(denovo_otuids_handle.read())
 
         with open(hits_fn, 'a') as hits_handle:
-            with open(denovo_hits_fn, 'r') as denovo_hits_handle:
+            with open(denovo_hits_fn, 'rU') as denovo_hits_handle:
                 hits_handle.write(denovo_hits_handle.read())
 
         os.remove(denovo_otus_fn)
@@ -462,7 +462,7 @@ def strip_size(s):
 
     # write the OTUs file and store the OTU ids
     otuids = []
-    otus_nochim_handle = open(otus_nochim_fn, "rb")
+    otus_nochim_handle = open(otus_nochim_fn, "rU")
     otus_handle = open(otus_fn, "wb")
     for i, (title, seq) in enumerate(SimpleFastaParser(otus_nochim_handle)):
         otuid = strip_size(title.split()[0])
@@ -474,7 +474,7 @@ def strip_size(s):
     os.remove(otus_nochim_fn)
 
     # write the hits file
-    swarms_temp_handle = open(swarms_temp_fn, 'rb')
+    swarms_temp_handle = open(swarms_temp_fn, 'rU')
     swarms_temp_reader = csv.reader(swarms_temp_handle, delimiter=' ')
     hits_handle = open(hits_fn, 'wb')
     hits_writer = csv.writer(hits_handle, delimiter='\t', lineterminator='\n')