Changes for efficiency

MANIFEST.in

@@ -0,0 +1,9 @@
+include requirements.txt
+include README.md
+include LICENSE
+include *.txt
+recursive-include grim *.py
+recursive-include grim *.txt
+recursive-include grim *.json
+recursive-include grim *.pyx
+recursive-include grim *.pyd

grim/__init__.py

@@ -26,4 +26,4 @@
 """Top-level package for py-grim."""
 
 __organization__ = "NMDP/CIBMTR Bioinformatics"
-__version__ = "0.0.4"
+__version__ = "0.0.6"

grim/conf/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library is distributed in the hope that it will be useful, but WITHOUT
+#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+__author__ = """Martin Maiers"""
+__email__ = 'mmaiers@nmdp.org'
+__version__ = '0.0.6'

grim/imputation/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library is distributed in the hope that it will be useful, but WITHOUT
+#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+__author__ = """Martin Maiers"""
+__email__ = 'mmaiers@nmdp.org'
+__version__ = '0.0.6'

grim/imputation/graph_generation/__init__.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library is distributed in the hope that it will be useful, but WITHOUT
+#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+
+
+__author__ = """Martin Maiers"""
+__email__ = 'mmaiers@nmdp.org'
+__version__ = '0.0.6'

grim/imputation/imputegl/__init__.py

@@ -24,4 +24,4 @@
 
 __author__ = """Martin Maiers"""
 __email__ = 'mmaiers@nmdp.org'
-__version__ = '0.0.4'
+__version__ = '0.0.6'

grim/imputation/imputegl/cutils.pyx

@@ -0,0 +1,65 @@
+import cython
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cpdef open_ambiguities(list hap, unsigned char loc, tuple split_loc):
+    cdef unsigned int k, i, p, j #hap_len, haps_len, splits_len
+    cdef Py_ssize_t hap_len, haps_len, splits_len
+    cdef list hap_new, hap1
+    # cdef np.ndarray[STR, ndim=1] hap_new, hap1
+    p = 0
+    if len(split_loc) > 1:
+        # This opens all allele ambiguities
+        hap_len = len(hap[0])
+        haps_len = len(hap)
+        splits_len = len(split_loc)
+        hap_new = [None] * (haps_len * splits_len)
+        # hap_new = np.empty(haps_len * splits_len, dtype=np.object)  # produces an empty list of haplotypes
+        hap1 = [None] * hap_len
+        # hap1 = np.empty(haps_len, dtype=np.object)
+        for k in range(haps_len):  # split a given locus in all haps.
+
+            for j in range(hap_len):
+                hap1[j] = hap[k][j]
+
+            for i in range(splits_len):
+                hap1[loc] = split_loc[i]
+                hap_new[p] = hap1[:]
+                p += 1
+        return hap_new
+    return hap
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cpdef create_hap_list(list all_haps, dict optionDict, unsigned int N_Loc):
+    cdef unsigned int i, j, count
+    cdef list hap_list = []
+    cdef list all_hap_split
+
+    for i in range(len(all_haps)):
+        all_hap_split = all_haps[i].split('~')
+        count = 0
+        for j in range(len(all_hap_split)):
+            if all_hap_split[j] not in optionDict:
+                break
+            else:
+                count += 1
+
+        if count == N_Loc:
+            hap_list.append(all_hap_split)
+    return hap_list
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cpdef deepcopy_list(list l):
+    cdef list copy_l
+    cdef unsigned int i, length
+    length = len(l)
+    copy_l = [None] * length
+    for i in range(length):
+        if isinstance(l[i], list):
+            copy_l[i] = deepcopy_list(l[i])
+        else:
+            copy_l[i] = l[i]
+    return copy_l