added reverse complement

python/README.rst

@@ -139,8 +139,8 @@ the following format:
 It is effectively the PAF format without the QueryName and QueryLength columns
 (the first two columns in PAF).
 
-Function mappy.fastx_read
+Miscellaneous Functions
-~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
@@ -149,3 +149,11 @@ Function mappy.fastx_read
 This generator function opens a FASTA/FASTQ file and *yields* a
 :code:`(name,seq,qual)` tuple for each sequence entry. The input file may be
 optionally gzip'd.
+
+.. code:: python
+
+	mappy.revcomp(seq)
+
+Return the reverse complement of DNA string :code:`seq`. This function
+recognizes IUB code and preserves the letter cases. Uracil :code:`U` is
+complemented to :code:`A`.

python/cmappy.h

@@ -101,4 +101,16 @@ static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const
 	}
 }
 
+static inline uint8_t *mappy_revcomp(int len, uint8_t *seq)
+{
+	int i;
+	for (i = 0; i < len>>1; ++i) {
+		uint8_t t = seq_comp_table[seq[i]];
+		seq[i] = seq_comp_table[seq[len - 1 - i]];
+		seq[len - 1 - i] = t;
+	}
+	if (len&1) seq[len>>1] = seq_comp_table[seq[len>>1]];
+	return seq;
+}
+
 #endif

python/cmappy.pxd

@@ -116,5 +116,6 @@ cdef extern from "cmappy.h":
 	void mm_fastx_close(kseq_t *ks)
 	int kseq_read(kseq_t *seq)
 
+	uint8_t *mappy_revcomp(int l, uint8_t *seq)
 	int mm_verbose_level(int v)
 	void mm_reset_timer()

python/mappy.pyx

@@ -164,6 +164,11 @@ def fastx_read(fn):
 		yield name, seq, qual
 	cmappy.mm_fastx_close(ks)
 
+def revcomp(seq):
+	cdef uint8_t *s
+	s = cmappy.mappy_revcomp(len(seq), str.encode(seq))
+	return s if isinstance(s, str) else s.decode()
+
 def verbose(v=None):
 	if v is None: v = -1
 	return cmappy.mm_verbose_level(v)