Fixed stdout output

versions of python

python/obitools3/commands/ngsfilter.pyx

@@ -24,6 +24,9 @@ from cpython.exc cimport PyErr_CheckSignals
 from io import BufferedWriter
 
 
+MAX_PAT_LEN = 31
+
+
 __title__="Assign sequence records to the corresponding experiment/sample based on DNA tags and primers"
 
 
@@ -84,6 +87,8 @@ class Primer:
         @type direct:
         '''
         
+        assert len(sequence) <= MAX_PAT_LEN, "Primer %s is too long, 31 bp max" % sequence
+        
         assert sequence not in Primer.collection        \
             or Primer.collection[sequence]==taglength,  \
             "Primer %s must always be used with tags of the same length" % sequence
@@ -271,7 +276,7 @@ cdef tuple annotate(sequences, infos, no_tags, verbose=False):
 
     if not_aligned:
         sequences[1] = sequences[1].clone()
-        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq             # used by alignpairedend tool
+        sequences[0][REVERSE_SEQUENCE_COLUMN] = sequences[1].seq        # used by alignpairedend tool
         sequences[0][REVERSE_QUALITY_COLUMN] = sequences[1].quality     # used by alignpairedend tool
 
     for seq in sequences:

python/obitools3/dms/taxo/taxo.pyx

@@ -325,8 +325,9 @@ cdef class Taxonomy(OBIWrapper) :
         cdef Taxon taxon
         try:
             taxon = self.get_taxon_by_taxid(taxid)
-        except:
-            raise StopIteration
+        except Exception as e:
+            print('\n'+e, file=sys.stderr)
+            return 
         if taxon is not None:
             while taxon.taxid != 1:
                 yield taxon
@@ -334,7 +335,7 @@ cdef class Taxonomy(OBIWrapper) :
                 taxon = taxon.parent
             yield taxon
         else:
-            raise StopIteration
+            return
 
 
     def is_ancestor(self, int ancestor_taxid, int taxid):

python/obitools3/format/tab.pyx

@@ -23,15 +23,16 @@ cdef class TabFormat:
     @cython.boundscheck(False)    
     def __call__(self, object data):
         
-        cdef set ktags
+        cdef object ktags
         cdef list tags = [key for key in data]
         
         line = []
-        
-        if self.tags is not None and self.tags:
-            ktags = self.tags
+        if self.tags != None and self.tags:
+            ktags = list(self.tags)
         else:
-            ktags = set(tags)            
+            ktags = list(set(tags))   
+                     
+        ktags.sort()
                         
         if self.header and self.first_line:
             for k in ktags:

python/obitools3/parsers/fastq.pyx

@@ -103,7 +103,11 @@ def fastqWithQualityIterator(lineiterator,
         yield seq
 
         read+=1
-        hline = next(i)
+        try:
+            hline = next(i)
+        except StopIteration:
+            return
+
     
 
 def fastqWithoutQualityIterator(lineiterator, 
@@ -174,5 +178,7 @@ def fastqWithoutQualityIterator(lineiterator,
         yield seq
     
         read+=1
-        hline = next(i)
-        
+        try:
+            hline = next(i)
+        except StopIteration:
+            return        

python/obitools3/parsers/tab.pyx

@@ -99,7 +99,10 @@ def tabIterator(lineiterator,
         
         read+=1
         
-        line = next(iterator)
+        try:
+            line = next(iterator)
+        except StopIteration:
+            return 
     
         
         

python/obitools3/uri/decode.pyx

@@ -280,7 +280,7 @@ def open_uri(uri,
             iseq = urib
             objclass = bytes
     else:  # TODO update uopen to be able to write? 
-        if config['obi']['outputformat'] == b'metabaR':
+        if 'outputformat' in config['obi'] and config['obi']['outputformat'] == b'metabaR':
             if 'metabarprefix' not in config['obi']:
                 raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
             else:

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '1b22'
+serial= '1b26'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/obi_ecopcr.c

@@ -365,8 +365,6 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
 
 	int32_t i;
 
-	// TODO add check for primer longer than MAX_PAT_LEN (32)
-
 	// Get sequence id
 	seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
 
@@ -751,6 +749,20 @@ int obi_ecopcr(const char* i_dms_name,
 	o1c = complementPattern(o1);
 	o2c = complementPattern(o2);
 
+	// check for primers equal or longer than MAX_PAT_LEN (32)
+	if (strlen(primer1) >= MAX_PAT_LEN)
+	{
+		obi_set_errno(OBI_ECOPCR_ERROR);
+		obidebug(1, "\nError: first primer is too long, needs to be < 32bp (%s)", primer1);
+		return -1;
+	}
+	if (strlen(primer2) >= MAX_PAT_LEN)
+	{
+		obi_set_errno(OBI_ECOPCR_ERROR);
+		obidebug(1, "\nError: second primer is too long, needs to be < 32bp (%s)", primer2);
+		return -1;
+	}
+
 	// Open input DMS
 	i_dms = obi_open_dms(i_dms_name, false);
 	if (i_dms == NULL)