Added method for single record analysis.

ggirelli · Apr 6, 2018 · 7d2e007 · 7d2e007
1 parent 2cb2ba5
commit 7d2e007
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Showing 2 changed files with 35 additions and 19 deletions.
diff --git a/bin/melt_duplex b/bin/melt_duplex
@@ -181,25 +181,8 @@ def run_fasta(fpath, **kwargs):
     # Iterate FASTA records
     print_header(**kwargs)
     for record in SimpleFastaParser(IH):
-        record = list(record)
-        kwargs.update([('name', record[0].split(" ")[0]), ('seq', record[1])])
-
-        # Calculate Tm
-        output = OligoMelt.Duplex.calc_tm(**kwargs)
-
-        # Prepare output
-        if kwargs['fasta_like']:
-            d = kwargs['fasta_delim']
-
-            # Add Tm field to record header
-            fields = dict(re.findall(r'(tm)%s(.*?);' % d, record[0]))
-            if "tm" in fields.keys():
-                record[0] = re.sub(r'(tm)%s(.*?);' % d,
-                    'tm%s%.2f;' % output[4], record[0])
-            else: record[0] += " tm%s%.2f;" % (d, output[4])
-
-            # Output
-            print(">%s\n%s" % tuple(record))
+        output = OligoMelt.Duplex.calc_tm_record(record, **kwargs)
+        if kwargs['fasta_like']: print(">%s\n%s" % tuple(output))
         else: print("%s\t%f\t%f\t%f\t%f\t%s" % output)
 
     # Close connection to input file

diff --git a/oligo_melting/duplex.py b/oligo_melting/duplex.py
@@ -771,6 +771,39 @@ def calc_tm(seq, name = None, oligo_conc = None, na_conc = None, mg_conc = None,
         if not silent: print(output)
         return(output)
 
+def calc_tm_record(record, **kwargs):
+    '''Calculate Tm for a single FASTA record read with SimpleFastaParser.
+
+    Args:
+        record (tuple): (header, seq) tuple.
+        kwargs: additional arguments to pass to calc_tm
+
+    Returns:
+        tuple: the output of calc_tm.
+        tuple: (header, seq) if kwargs['fasta_like'].
+    '''
+    record = list(record)
+    kwargs.update([('name', record[0].split(" ")[0]), ('seq', record[1])])
+
+    # Calculate Tm
+    output = OligoMelt.Duplex.calc_tm(**kwargs)
+
+    # Prepare output
+    if kwargs['fasta_like']:
+        d = kwargs['fasta_delim']
+
+        # Add Tm field to record header
+        fields = dict(re.findall(r'(tm)%s(.*?);' % d, record[0]))
+        if "tm" in fields.keys():
+            record[0] = re.sub(r'(tm)%s(.*?);' % d,
+                'tm%s%.2f;' % output[4], record[0])
+        else: record[0] += " tm%s%.2f;" % (d, output[4])
+
+        # Output
+        return(record)
+    else:
+        return(output)
+
 # END ==========================================================================
 
 ################################################################################