From 1cd35b33591c71340d5fc545a5c49e13ac7b5c4a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 31 Mar 2016 10:47:12 +0200
Subject: [PATCH] firt version of a fastq parser

---
 python/obitools3/parsers/__init__.py |  0
 python/obitools3/parsers/fastq.pxd   |  8 +++++
 python/obitools3/parsers/fastq.pyx   | 41 ++++++++++++++++++++++++
 python/obitools3/parsers/header.pxd  |  5 +++
 python/obitools3/parsers/header.pyx  | 47 ++++++++++++++++++++++++++++
 5 files changed, 101 insertions(+)
 create mode 100644 python/obitools3/parsers/__init__.py
 create mode 100644 python/obitools3/parsers/fastq.pxd
 create mode 100644 python/obitools3/parsers/fastq.pyx
 create mode 100644 python/obitools3/parsers/header.pxd
 create mode 100644 python/obitools3/parsers/header.pyx

diff --git a/python/obitools3/parsers/__init__.py b/python/obitools3/parsers/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python/obitools3/parsers/fastq.pxd b/python/obitools3/parsers/fastq.pxd
new file mode 100644
index 0000000..d1546d1
--- /dev/null
+++ b/python/obitools3/parsers/fastq.pxd
@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+from .header cimport parseHeader
+from ..files.universalopener cimport uopen
+from ..files.linebuffer cimport LineBuffer
+
+
+    
\ No newline at end of file
diff --git a/python/obitools3/parsers/fastq.pyx b/python/obitools3/parsers/fastq.pyx
new file mode 100644
index 0000000..0e44cf8
--- /dev/null
+++ b/python/obitools3/parsers/fastq.pyx
@@ -0,0 +1,41 @@
+#cython: language_level=3
+
+'''
+Created on 30 mars 2016
+
+@author: coissac
+'''
+
+
+
+def fastqIterator(lineiterator, int buffersize=100000000):
+    cdef LineBuffer lb
+    cdef str        ident
+    cdef str        definition
+    cdef dict       tags
+    
+    if isinstance(lineiterator,(str,bytes)):
+        lineiterator=uopen(lineiterator)
+    
+    if isinstance(lineiterator, LineBuffer):
+        lb=lineiterator
+    else:
+        lb=LineBuffer(lineiterator,buffersize)
+        
+    i = iter(lb)
+    for line in i:
+        ident,tags,definition = parseHeader(line)
+        sequence  = next(i)[0:-1]
+        next(i)
+        quality   = next(i)[0:-1]
+
+        yield { "id"         : ident,
+                "definition" : definition,
+                "sequence"   : sequence,
+                "quality"    : quality,
+                "tags"       : tags,
+                "annotation" : {}
+              }
+        
+        
+        
\ No newline at end of file
diff --git a/python/obitools3/parsers/header.pxd b/python/obitools3/parsers/header.pxd
new file mode 100644
index 0000000..b09a418
--- /dev/null
+++ b/python/obitools3/parsers/header.pxd
@@ -0,0 +1,5 @@
+#cython: language_level=3
+
+cdef object __etag__(str x)
+
+cpdef tuple parseHeader(str header)
diff --git a/python/obitools3/parsers/header.pyx b/python/obitools3/parsers/header.pyx
new file mode 100644
index 0000000..e0099e6
--- /dev/null
+++ b/python/obitools3/parsers/header.pyx
@@ -0,0 +1,47 @@
+#cython: language_level=3
+
+'''
+Created on 25 mars 2016
+
+@author: coissac
+'''
+
+import re
+
+__ret__ = re.compile('''(([^ ]+)=('[^']*'|"[^"]*"|[^;]+); *)+?''')
+
+cdef object __etag__(str x):
+    try:
+        v = eval(x,{},{})
+    except:
+        v = x
+    return v
+
+cpdef tuple parseHeader(str header):
+    cdef list m 
+    cdef dict tags 
+    cdef str definition
+    cdef str ident
+    cdef str second
+    
+    m=header[1:-1].split(maxsplit=1)
+
+    ident=m[0]
+    
+    if len(m)==1:
+        tags={}
+        definition='' 
+    else:
+        second=m[1]
+        m = __ret__.findall(second)
+        
+        if m:
+            tags = dict([(a[1],__etag__(a[2])) for a in m])
+            definition = second.split(m[-1][0],1)[1].strip()
+        else:
+            tags = {}
+            definition = second.strip() 
+        
+    return ident,tags,definition
+    
+