From 61b00d6013584a4913b3c58aa4778dad76ab718e Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 9 Oct 2018 16:41:14 +0200
Subject: [PATCH] Cython: fastq formatter

---
 python/obitools3/format/fastq.pxd | 10 ++++++++++
 python/obitools3/format/fastq.pyx | 32 +++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 python/obitools3/format/fastq.pxd
 create mode 100644 python/obitools3/format/fastq.pyx

diff --git a/python/obitools3/format/fastq.pxd b/python/obitools3/format/fastq.pxd
new file mode 100644
index 0000000..a32fa77
--- /dev/null
+++ b/python/obitools3/format/fastq.pxd
@@ -0,0 +1,10 @@
+from ..utils cimport bytes2str
+from .header cimport HeaderFormat
+from cython.view cimport array as cvarray
+
+cdef class FastqFormat:
+
+    cdef HeaderFormat headerFormatter
+    
+    cdef size_t  sequenceBufferLength
+    cdef char*   sequenceBuffer
diff --git a/python/obitools3/format/fastq.pyx b/python/obitools3/format/fastq.pyx
new file mode 100644
index 0000000..4bda2dc
--- /dev/null
+++ b/python/obitools3/format/fastq.pyx
@@ -0,0 +1,32 @@
+#cython: language_level=3
+
+cimport cython
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
+from obitools3.utils cimport bytes2str, str2bytes, tobytes
+
+
+# TODO quality offset option
+cdef class FastqFormat:
+	
+	def __init__(self, list tags=[], bint printNAKeys=False):
+		self.headerFormatter = HeaderFormat("fastq",
+										    tags,
+										    printNAKeys)
+		
+	@cython.boundscheck(False)	
+	def __call__(self, object data):
+		
+		cdef bytes quality
+		
+		if hasattr(data, "quality_str"):
+			quality = str2bytes(data.quality_str)    # TODO quality_bytes property
+		elif hasattr(data, "quality"):
+			quality = tobytes(data.quality)
+		else:
+			raise AttributeError("No quality when exporting to fastq")  # TODO discuss
+		
+		return bytes2str(self.headerFormatter(data) + 
+						b"\n" + 
+						data[NUC_SEQUENCE_COLUMN] +
+						b"\n+\n" + 
+						quality)