c++ lib started

barcode_detection/cseqlib/cseqlib.cpp

@@ -0,0 +1,43 @@
+#include<string>
+#include<vector>
+#include<iostream>
+
+
+
+char rev_comp_arr[256] = {' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', 'T', ' ', 'G', ' ', ' ', ' ', 'C', ' ', ' ', ' ', ' ', ' ', ' ', 'N', ' ', ' ', ' ', ' ', ' ', 'A', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', 't', ' ', 'g', ' ', ' ', ' ', 'c', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', 'a', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '};
+
+extern "C" {
+
+void rev_comp(const wchar_t* s, wchar_t* rc, int len) {
+    for (int i = len - 1; i >= 0; --i) {
+        int ri =  len - 1 - i;
+        rc[ri] = rev_comp_arr[s[i]];
+        /// std::cout << char(s[i]) << " " << char(rc[ri]) << std::endl;
+    }
+}
+
+}
+
+/*
+
+int main() {
+    std::string test[8] = {
+"GTGTACTTCGTTCAGTTACCAATTTGGGTGTTTAGCATGGTCATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGTGGGGGTTTTGAAAATGTCCTCGGCATAAAAGCGCCATTTTAATTTAAGAAAACGGGGAACTATGC", 
+"TCAGGATTGGATTTATATGACTGATCAGTTTCCTCTGCTGTTATCGAAAGCAGATATCAAATGGCTGTGGAGGAATGCAGGTGATTGGAGTTGGTCCAAAGGAAGTTGTGAGTTCTGGGAGAGGCAGAAGGAAAGCAGCTGCCATGTTCTGAAGGTTATCAGCACCTG", 
+"TTGGTGATAGAAACAGGCACAGAAGGTGTTAGCAGGTTCCTGTTTGTCCTCTCGCACCCCCTCCCTCCTGATGGTGACCTTGTCCCAGGTCTTCTACCAGGCCTTCTACCAGATGCCTTGCTGAGAATTCACAGAGGCCGTAGACCTGAAGAACCAACAACCTTCCAT", 
+"AGGCTTTGAGGTCCCACTCCGGCAGCAGGACGTGCTGGCTCCCAGGAATCACTGACATCAAGGCGTGTAAAATAACACAAAGAGGTTTGCAAAGTCCACAGCCCAAGAGGAGCCGGAGCGTCCTGTTTTTACCATCACGCTTCGTTGTTCACGTTGCTTGTGTGTGTA", 
+"AAACAGGGTACAATATTTAGAAACGGTGAAAGGAAATGACTGGCCTAAAACTCTTGTGATTCAGTGACTCAAGGATGATTGACACTGTGTAAAAACAGGCACATTAGACCAAGAGATAATTTGAAACCTTATTATTGGGTATTGTTTTTAAAAATTAAACCTATGGAC", 
+"ATGAATAAAATGAAAAACTTTATAAGCACAGCTTATTGAACTAAAGGGCCTTAAGACCATCACTTCCAACGGCCTCATTTTACAGGAGAGAAATCTGAGGACCAGGGAAACCAAGTGACTTTTCTGGGGTCACATGGAATGTCAACAGCAGAGCTGTGAAGGCGTTCA", 
+"GGTCTGCTAACCTCCCGGCTATGCTCATTCATGGAGAGTGCTTCGAAGAGTGTTTGCAACATTTAGTCACAGTTTATCTTTGGTTCCAATTCCACATTTACTCTATTTTTAATGTGTGTGAAAATGGCCCAGATTCATATGATTTGTTGCAGGTCAAACAGGTATTAG", 
+"AAAAACTGCCAAGCTTGCACCGCTTATGTATAGTTATTTGTTGTGTATGTGCAAGTGTTTGTATGTGTGTGAGCACATAAGCATAATCTCTTTACACACACACACACACACCATTCCTACATCAAAAAGCTCTGAAAATTAAACTTTTTCATAAATTTGTGACAAATT"};
+
+    int len = test[0].length();
+    for (int i = 0; i <= 1000000; ++i) {
+        char* rc = rev_comp(test[i % 8].c_str(), len);
+        delete rc;
+    }
+    return 0;
+}
+
+
+*/

barcode_detection/cseqlib/test.py

@@ -0,0 +1,24 @@
+from ctypes import cdll
+lib = cdll.LoadLibrary('./cseqlib.so')
+import ctypes
+
+
+TEST_SEQ = [
+"GTGTACTTCGTTCAGTTACCAATTTGGGTGTTTAGCATGGTCATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGTGGGGGTTTTGAAAATGTCCTCGGCATAAAAGCGCCATTTTAATTTAAGAAAACGGGGAACTATGC", 
+"TCAGGATTGGATTTATATGACTGATCAGTTTCCTCTGCTGTTATCGAAAGCAGATATCAAATGGCTGTGGAGGAATGCAGGTGATTGGAGTTGGTCCAAAGGAAGTTGTGAGTTCTGGGAGAGGCAGAAGGAAAGCAGCTGCCATGTTCTGAAGGTTATCAGCACCTG", 
+"TTGGTGATAGAAACAGGCACAGAAGGTGTTAGCAGGTTCCTGTTTGTCCTCTCGCACCCCCTCCCTCCTGATGGTGACCTTGTCCCAGGTCTTCTACCAGGCCTTCTACCAGATGCCTTGCTGAGAATTCACAGAGGCCGTAGACCTGAAGAACCAACAACCTTCCAT", 
+"AGGCTTTGAGGTCCCACTCCGGCAGCAGGACGTGCTGGCTCCCAGGAATCACTGACATCAAGGCGTGTAAAATAACACAAAGAGGTTTGCAAAGTCCACAGCCCAAGAGGAGCCGGAGCGTCCTGTTTTTACCATCACGCTTCGTTGTTCACGTTGCTTGTGTGTGTA", 
+"AAACAGGGTACAATATTTAGAAACGGTGAAAGGAAATGACTGGCCTAAAACTCTTGTGATTCAGTGACTCAAGGATGATTGACACTGTGTAAAAACAGGCACATTAGACCAAGAGATAATTTGAAACCTTATTATTGGGTATTGTTTTTAAAAATTAAACCTATGGAC", 
+"ATGAATAAAATGAAAAACTTTATAAGCACAGCTTATTGAACTAAAGGGCCTTAAGACCATCACTTCCAACGGCCTCATTTTACAGGAGAGAAATCTGAGGACCAGGGAAACCAAGTGACTTTTCTGGGGTCACATGGAATGTCAACAGCAGAGCTGTGAAGGCGTTCA", 
+"GGTCTGCTAACCTCCCGGCTATGCTCATTCATGGAGAGTGCTTCGAAGAGTGTTTGCAACATTTAGTCACAGTTTATCTTTGGTTCCAATTCCACATTTACTCTATTTTTAATGTGTGTGAAAATGGCCCAGATTCATATGATTTGTTGCAGGTCAAACAGGTATTAG", 
+"AAAAACTGCCAAGCTTGCACCGCTTATGTATAGTTATTTGTTGTGTATGTGCAAGTGTTTGTATGTGTGTGAGCACATAAGCATAATCTCTTTACACACACACACACACACCATTCCTACATCAAAAAGCTCTGAAAATTAAACTTTTTCATAAATTTGTGACAAATT"]
+
+
+
+for i in range(1000000):
+    s = TEST_SEQ[i % 8]
+    slen = len(s)
+    rc = ctypes.create_unicode_buffer(slen)
+    lib.rev_comp(s, rc, slen)
+    if i == 1:
+        print(rc.value)

misc/poly_perf.py

@@ -0,0 +1,73 @@
+RCARR = [''] * 256
+RCARR[ord('A')] = 'T'
+RCARR[ord('T')] = 'A'
+RCARR[ord('C')] = 'G'
+RCARR[ord('G')] = 'C'
+RCARR[ord('N')] = 'N'
+RCARR[ord('a')] = 't'
+RCARR[ord('t')] = 'a'
+RCARR[ord('c')] = 'g'
+RCARR[ord('g')] = 'c'
+RCARR[ord('g')] = 'c'
+
+
+
+RCDICT = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'N': 'N'}
+
+
+def rc_func(c):
+    if c == 'A': return 'T'
+    elif c == 'T': return 'A'
+    elif c == 'C': return 'G'
+    elif c == 'G': return 'C'
+    return ""
+
+
+def rev_comp_arr_map(seq):
+    return "".join(map(lambda x: RCARR[ord(x)], seq[::-1]))
+
+
+def rev_comp_arr_for(seq):
+    res = ""
+    for i in range(len(seq) - 1, -1, -1):
+        res += RCARR[ord(seq[i])]
+    return res
+
+
+def rev_comp_dict_map(seq):
+    return "".join(map(lambda x: RCDICT[x], seq[::-1]))
+
+
+def rev_comp_dict_for(seq):
+    res = ""
+    for i in range(len(seq) - 1, -1, -1):
+        res += RCDICT[seq[i]]
+    return res
+
+
+def rev_comp_func_map(seq):
+    return "".join(map(rc_func, seq[::-1]))
+
+
+def rev_comp_func_for(seq):
+    res = ""
+    for i in range(len(seq) - 1, -1, -1):
+        res += rc_func(seq[i])
+    return res
+
+
+
+TEST_SEQ = [
+"GTGTACTTCGTTCAGTTACCAATTTGGGTGTTTAGCATGGTCATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGTGGGGGTTTTGAAAATGTCCTCGGCATAAAAGCGCCATTTTAATTTAAGAAAACGGGGAACTATGC", 
+"TCAGGATTGGATTTATATGACTGATCAGTTTCCTCTGCTGTTATCGAAAGCAGATATCAAATGGCTGTGGAGGAATGCAGGTGATTGGAGTTGGTCCAAAGGAAGTTGTGAGTTCTGGGAGAGGCAGAAGGAAAGCAGCTGCCATGTTCTGAAGGTTATCAGCACCTG", 
+"TTGGTGATAGAAACAGGCACAGAAGGTGTTAGCAGGTTCCTGTTTGTCCTCTCGCACCCCCTCCCTCCTGATGGTGACCTTGTCCCAGGTCTTCTACCAGGCCTTCTACCAGATGCCTTGCTGAGAATTCACAGAGGCCGTAGACCTGAAGAACCAACAACCTTCCAT", 
+"AGGCTTTGAGGTCCCACTCCGGCAGCAGGACGTGCTGGCTCCCAGGAATCACTGACATCAAGGCGTGTAAAATAACACAAAGAGGTTTGCAAAGTCCACAGCCCAAGAGGAGCCGGAGCGTCCTGTTTTTACCATCACGCTTCGTTGTTCACGTTGCTTGTGTGTGTA", 
+"AAACAGGGTACAATATTTAGAAACGGTGAAAGGAAATGACTGGCCTAAAACTCTTGTGATTCAGTGACTCAAGGATGATTGACACTGTGTAAAAACAGGCACATTAGACCAAGAGATAATTTGAAACCTTATTATTGGGTATTGTTTTTAAAAATTAAACCTATGGAC", 
+"ATGAATAAAATGAAAAACTTTATAAGCACAGCTTATTGAACTAAAGGGCCTTAAGACCATCACTTCCAACGGCCTCATTTTACAGGAGAGAAATCTGAGGACCAGGGAAACCAAGTGACTTTTCTGGGGTCACATGGAATGTCAACAGCAGAGCTGTGAAGGCGTTCA", 
+"GGTCTGCTAACCTCCCGGCTATGCTCATTCATGGAGAGTGCTTCGAAGAGTGTTTGCAACATTTAGTCACAGTTTATCTTTGGTTCCAATTCCACATTTACTCTATTTTTAATGTGTGTGAAAATGGCCCAGATTCATATGATTTGTTGCAGGTCAAACAGGTATTAG", 
+"AAAAACTGCCAAGCTTGCACCGCTTATGTATAGTTATTTGTTGTGTATGTGCAAGTGTTTGTATGTGTGTGAGCACATAAGCATAATCTCTTTACACACACACACACACACCATTCCTACATCAAAAAGCTCTGAAAATTAAACTTTTTCATAAATTTGTGACAAATT"]
+
+
+
+for i in range(1000000):
+    s = rev_comp_dict_map(TEST_SEQ[i % 8])