Exposed Fast C counter to python

.gitignore

@@ -1,3 +1,11 @@
+# sequence files
+*.gb
+*.seq
+*.gz
+
+# autoenv
+.env
+
 # virtualenv
 .venv
 
@@ -7,7 +15,6 @@ __pycache__/
 
 # C extensions
 *.so
-*.c
 
 # Distribution / packaging
 .Python
@@ -56,3 +63,34 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
+
+## Directory-based project format
+.idea/
+# if you remove the above rule, at least ignore user-specific stuff:
+# .idea/workspace.xml
+# .idea/tasks.xml
+# and these sensitive or high-churn files:
+# .idea/dataSources.ids
+# .idea/dataSources.xml
+# .idea/sqlDataSources.xml
+# .idea/dynamic.xml
+
+## File-based project format
+*.ipr
+*.iws
+*.iml
+
+## Additional for IntelliJ
+out/
+
+# generated by mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# generated by JIRA plugin
+atlassian-ide-plugin.xml
+
+# generated by Crashlytics plugin (for Android Studio and Intellij)
+com_crashlytics_export_strings.xml
+

.travis.yml

@@ -1,9 +1,17 @@
 language: python
 python:
   - "2.7"
+  - "pypy"
 # command to install dependencies
 install:
   - "pip install -r requirements.txt"
-  - "python setup.py install"
+  - "wget https://raw.githubusercontent.com/biopython/biopython/master/Tests/GenBank/NC_005816.gb"
+  - "wget https://www.dropbox.com/s/n67qz6k262ghxuz/cow.seq"
+  - "make"
 # command to run tests
-script: "pep8 *.py*"
+script: 
+  - "python --version"
+  - "pep8 *.py*"
+  - "cat NC_005816.gb | python main.py -f genbank"
+  - "cat cow.seq | python bench.py"
+

CodonCountStruct.py

@@ -0,0 +1,70 @@
+from ctypes import Structure, c_longlong
+
+
+class CodonCount(Structure):
+    _fields_ = [
+        ('TTT', c_longlong),
+        ('TTC', c_longlong),
+        ('TTA', c_longlong),
+        ('TTG', c_longlong),
+        ('TCT', c_longlong),
+        ('TCC', c_longlong),
+        ('TCA', c_longlong),
+        ('TCG', c_longlong),
+        ('TAT', c_longlong),
+        ('TAC', c_longlong),
+        ('TAA', c_longlong),
+        ('TAG', c_longlong),
+        ('TGT', c_longlong),
+        ('TGC', c_longlong),
+        ('TGA', c_longlong),
+        ('TGG', c_longlong),
+        ('CTT', c_longlong),
+        ('CTC', c_longlong),
+        ('CTA', c_longlong),
+        ('CTG', c_longlong),
+        ('CCT', c_longlong),
+        ('CCC', c_longlong),
+        ('CCA', c_longlong),
+        ('CCG', c_longlong),
+        ('CAT', c_longlong),
+        ('CAC', c_longlong),
+        ('CAA', c_longlong),
+        ('CAG', c_longlong),
+        ('CGT', c_longlong),
+        ('CGC', c_longlong),
+        ('CGA', c_longlong),
+        ('CGG', c_longlong),
+        ('ATT', c_longlong),
+        ('ATC', c_longlong),
+        ('ATA', c_longlong),
+        ('ATG', c_longlong),
+        ('ACT', c_longlong),
+        ('ACC', c_longlong),
+        ('ACA', c_longlong),
+        ('ACG', c_longlong),
+        ('AAT', c_longlong),
+        ('AAC', c_longlong),
+        ('AAA', c_longlong),
+        ('AAG', c_longlong),
+        ('AGT', c_longlong),
+        ('AGC', c_longlong),
+        ('AGA', c_longlong),
+        ('AGG', c_longlong),
+        ('GTT', c_longlong),
+        ('GTC', c_longlong),
+        ('GTA', c_longlong),
+        ('GTG', c_longlong),
+        ('GCT', c_longlong),
+        ('GCC', c_longlong),
+        ('GCA', c_longlong),
+        ('GCG', c_longlong),
+        ('GAT', c_longlong),
+        ('GAC', c_longlong),
+        ('GAA', c_longlong),
+        ('GAG', c_longlong),
+        ('GGT', c_longlong),
+        ('GGC', c_longlong),
+        ('GGA', c_longlong),
+        ('GGG', c_longlong)
+    ]

Makefile

@@ -0,0 +1,26 @@
+UNAME := $(shell uname)
+
+prefix=${HOME}
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include
+
+# the build target executable:
+TARGET = counterc
+TRIE_CODON = trie_codon
+
+CC = gcc
+CFLAGS  = -shared -Wl,-soname,$(TARGET).so -Wl,--no-undefined -std=c99 -O3 -funroll-loops
+
+ifeq ($(UNAME), Darwin)
+CC = gcc
+CFLAGS  = -shared -Wl,-install_name,$(TARGET).so -O3 -funroll-loops
+endif
+
+all: $(TARGET)
+
+$(TARGET): $(TARGET).c
+	$(CC) $(CFLAGS) -o $(TARGET).so -fPIC $(TARGET).c $(TRIE_CODON).c
+
+clean:
+	$(RM) $(TARGET).so

README.md

@@ -12,9 +12,14 @@ Create a virtualenv and then run the following commands.
 
 ```bash
 pip install -r requirements.txt
-python setup.py install
+make
 ```
 
+C dependencies
+-----
+
+1. [C-Algorithms 1.2.0](http://c-algorithms.sourceforge.net)
+
 Usage
 -------
 

bench.py

@@ -0,0 +1,35 @@
+# !/usr/bin/python
+
+import sys
+import time
+
+from ctypes import *
+from CodonCountStruct import CodonCount
+
+""" Utility """
+CURRENT_MILLI_TIME = lambda: int(round(time.clock() * 1000))
+
+
+def getdict(struct):
+    return dict(
+        (field, getattr(struct, field)) for field, _ in struct._fields_
+        )
+
+
+def main(argv):
+    counterc = CDLL('./counterc.so')
+    counterc.countcodons.argtypes = (c_char_p,)
+    counterc.countcodons.restype = CodonCount
+
+    start = CURRENT_MILLI_TIME()
+
+    for line in sys.stdin:
+        cstruct = counterc.countcodons(line)
+    print getdict(cstruct)
+
+    end = CURRENT_MILLI_TIME()
+    print "Tokenize and Count in " + str(end - start) + " ms"
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])

counterc.c

@@ -0,0 +1,104 @@
+#include "counterc.h"
+
+CodonCount countcodons(char * sequence)
+{
+    char codon[4];
+    long seq_length = strlen(sequence) - 2;
+    const char * valid_characters = "ACTG";
+    char * c = codon;
+
+    Trie * codoncount = trie_new();     // You create it, you destroy it
+
+    for (int i = 0; i < seq_length; i+=3)
+    {
+        int invalid = 0;
+
+        strncpy(codon, sequence+i, 3);
+        codon[3] = '\0';                // Ensure codon ends at 3 characters
+
+        // Break out if invalid character detected
+        while (*c) {
+            if (!strchr(valid_characters, *c)) {
+                invalid = 1;
+                break;
+            }
+            c++;
+        }
+
+        if (invalid == 1) { continue; }
+
+        trie_increment(codoncount, codon);
+    }
+
+    // Prepare struct to return
+    // Trie is not an iterable structure, thus the length
+    struct CodonCount counts;
+    counts.TTT = (long long) trie_lookup(codoncount, "TTT");
+    counts.TTC = (long long) trie_lookup(codoncount, "TTC");
+    counts.TTA = (long long) trie_lookup(codoncount, "TTA");
+    counts.TTG = (long long) trie_lookup(codoncount, "TTG");
+    counts.TCT = (long long) trie_lookup(codoncount, "TCT");
+    counts.TCC = (long long) trie_lookup(codoncount, "TCC");
+    counts.TCA = (long long) trie_lookup(codoncount, "TCA");
+    counts.TCG = (long long) trie_lookup(codoncount, "TCG");
+    counts.TAT = (long long) trie_lookup(codoncount, "TAT");
+    counts.TAC = (long long) trie_lookup(codoncount, "TAC");
+    counts.TAA = (long long) trie_lookup(codoncount, "TAA");
+    counts.TAG = (long long) trie_lookup(codoncount, "TAG");
+    counts.TGT = (long long) trie_lookup(codoncount, "TGT");
+    counts.TGC = (long long) trie_lookup(codoncount, "TGC");
+    counts.TGA = (long long) trie_lookup(codoncount, "TGA");
+    counts.TGG = (long long) trie_lookup(codoncount, "TGG");
+    counts.CTT = (long long) trie_lookup(codoncount, "CTT");
+    counts.CTC = (long long) trie_lookup(codoncount, "CTC");
+    counts.CTA = (long long) trie_lookup(codoncount, "CTA");
+    counts.CTG = (long long) trie_lookup(codoncount, "CTG");
+    counts.CCT = (long long) trie_lookup(codoncount, "CCT");
+    counts.CCC = (long long) trie_lookup(codoncount, "CCC");
+    counts.CCA = (long long) trie_lookup(codoncount, "CCA");
+    counts.CCG = (long long) trie_lookup(codoncount, "CCG");
+    counts.CAT = (long long) trie_lookup(codoncount, "CAT");
+    counts.CAC = (long long) trie_lookup(codoncount, "CAC");
+    counts.CAA = (long long) trie_lookup(codoncount, "CAA");
+    counts.CAG = (long long) trie_lookup(codoncount, "CAG");
+    counts.CGT = (long long) trie_lookup(codoncount, "CGT");
+    counts.CGC = (long long) trie_lookup(codoncount, "CGC");
+    counts.CGA = (long long) trie_lookup(codoncount, "CGA");
+    counts.CGG = (long long) trie_lookup(codoncount, "CGG");
+    counts.ATT = (long long) trie_lookup(codoncount, "ATT");
+    counts.ATC = (long long) trie_lookup(codoncount, "ATC");
+    counts.ATA = (long long) trie_lookup(codoncount, "ATA");
+    counts.ATG = (long long) trie_lookup(codoncount, "ATG");
+    counts.ACT = (long long) trie_lookup(codoncount, "ACT");
+    counts.ACC = (long long) trie_lookup(codoncount, "ACC");
+    counts.ACA = (long long) trie_lookup(codoncount, "ACA");
+    counts.ACG = (long long) trie_lookup(codoncount, "ACG");
+    counts.AAT = (long long) trie_lookup(codoncount, "AAT");
+    counts.AAC = (long long) trie_lookup(codoncount, "AAC");
+    counts.AAA = (long long) trie_lookup(codoncount, "AAA");
+    counts.AAG = (long long) trie_lookup(codoncount, "AAG");
+    counts.AGT = (long long) trie_lookup(codoncount, "AGT");
+    counts.AGC = (long long) trie_lookup(codoncount, "AGC");
+    counts.AGA = (long long) trie_lookup(codoncount, "AGA");
+    counts.AGG = (long long) trie_lookup(codoncount, "AGG");
+    counts.GTT = (long long) trie_lookup(codoncount, "GTT");
+    counts.GTC = (long long) trie_lookup(codoncount, "GTC");
+    counts.GTA = (long long) trie_lookup(codoncount, "GTA");
+    counts.GTG = (long long) trie_lookup(codoncount, "GTG");
+    counts.GCT = (long long) trie_lookup(codoncount, "GCT");
+    counts.GCC = (long long) trie_lookup(codoncount, "GCC");
+    counts.GCA = (long long) trie_lookup(codoncount, "GCA");
+    counts.GCG = (long long) trie_lookup(codoncount, "GCG");
+    counts.GAT = (long long) trie_lookup(codoncount, "GAT");
+    counts.GAC = (long long) trie_lookup(codoncount, "GAC");
+    counts.GAA = (long long) trie_lookup(codoncount, "GAA");
+    counts.GAG = (long long) trie_lookup(codoncount, "GAG");
+    counts.GGT = (long long) trie_lookup(codoncount, "GGT");
+    counts.GGC = (long long) trie_lookup(codoncount, "GGC");
+    counts.GGA = (long long) trie_lookup(codoncount, "GGA");
+    counts.GGG = (long long) trie_lookup(codoncount, "GGG");
+
+    trie_free(codoncount);
+
+    return counts;
+}