Imported Upstream version 0.2.1

[tabix.git] / tabix.py

diff --git a/tabix.py b/tabix.py
new file mode 100755 (executable)
index 0000000..8b5c7c8
--- /dev/null
+++ b/tabix.py
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+
+# Author: Heng Li and Aaron Quinlan
+# License: MIT/X11
+
+import sys
+from ctypes import *
+from ctypes.util import find_library
+import glob, platform
+
+def load_shared_library(lib, _path='.', ver='*'):
+    """Search for and load the tabix library. The
+    expectation is that the library is located in
+    the current directory (ie. "./")
+    """
+    # find from the system path
+    path = find_library(lib)
+    if (path == None): # if fail, search in the custom directory
+        s = platform.system()
+        if (s == 'Darwin'): suf = ver+'.dylib'
+        elif (s == 'Linux'): suf = '.so'+ver
+        candidates = glob.glob(_path+'/lib'+lib+suf);
+        if (len(candidates) == 1): path = candidates[0]
+        else: return None
+    cdll.LoadLibrary(path)
+    return CDLL(path)
+
+def tabix_init():
+    """Initialize and return a tabix reader object
+    for subsequent tabix_get() calls.  
+    """
+    tabix = load_shared_library('tabix')
+    if (tabix == None): return None
+    tabix.ti_read.restype = c_char_p
+    # on Mac OS X 10.6, the following declarations are required.
+    tabix.ti_open.restype = c_void_p
+    tabix.ti_querys.argtypes = [c_void_p, c_char_p]
+    tabix.ti_querys.restype = c_void_p
+    tabix.ti_query.argtypes = [c_void_p, c_char_p, c_int, c_int]
+    tabix.ti_query.restype = c_void_p
+    tabix.ti_read.argtypes = [c_void_p, c_void_p, c_void_p]
+    tabix.ti_iter_destroy.argtypes = [c_void_p]
+    tabix.ti_close.argtypes = [c_void_p]
+    # FIXME: explicit declarations for APIs not used in this script
+    return tabix
+
+# OOP interface
+class Tabix:
+    def __init__(self, fn, fnidx=0):
+        self.tabix = tabix_init();
+        if (self.tabix == None):
+            sys.stderr.write("[Tabix] Please make sure the shared library is compiled and available.\n")
+            return
+        self.fp = self.tabix.ti_open(fn, fnidx);
+
+    def __del__(self):
+        if (self.tabix): self.tabix.ti_close(self.fp)
+
+    def fetch(self, chr, start=-1, end=-1):
+        """Generator function that will yield each interval
+        within the requested range from the requested file.
+        """
+        if (self.tabix == None): return
+        if (start < 0): iter = self.tabix.ti_querys(self.fp, chr) # chr looks like: "chr2:1,000-2,000" or "chr2"
+        else: iter = self.tabix.ti_query(self.fp, chr, start, end) # chr must be a sequence name
+        if (iter == None):        
+            sys.stderr.write("[Tabix] Malformatted query or wrong sequence name.\n")
+            return
+        while (1): # iterate
+            s = self.tabix.ti_read(self.fp, iter, 0)
+            if (s == None): break
+            yield s   
+        self.tabix.ti_iter_destroy(iter)
+
+# command-line interface
+def main():
+    if (len(sys.argv) < 3):
+        sys.stderr.write("Usage: tabix.py <in.gz> <reg>\n")
+        sys.exit(1)
+    
+    # report the features in the requested interval
+    tabix = Tabix(sys.argv[1])
+    for line in tabix.fetch(sys.argv[2]):
+        print line
+
+if __name__ == '__main__':
+    main()