add bipartite_decode

git-svn-id: http://biopieces.googlecode.com/svn/trunk@265 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_c/Maasha/src/bipartite_decode.c b/code_c/Maasha/src/bipartite_decode.c
new file mode 100644 (file)
index 0000000..0bc706d
--- /dev/null
+++ b/code_c/Maasha/src/bipartite_decode.c
@@ -0,0 +1,148 @@
+/* Martin Asser Hansen (mail@maasha.dk) Copyright (C) 2008 - All right reserved */
+
+#include "common.h"
+#include "filesys.h"
+
+#define BITS_IN_BYTE      8                                /* number of bits in one byte. */
+#define BLOCK_SPACE_MAX   64                               /* maximum space between two blocks. */
+#define BLOCK_MASK        ( ( BLOCK_SPACE_MAX << 1 ) - 1 ) /* mask for printing block space. */
+ 
+/* Byte array for fast convertion of binary blocks back to DNA. */
+char *bin2dna[256] = {
+    "AAAA", "AAAC", "AAAG", "AAAT", "AACA", "AACC", "AACG", "AACT",
+    "AAGA", "AAGC", "AAGG", "AAGT", "AATA", "AATC", "AATG", "AATT",
+    "ACAA", "ACAC", "ACAG", "ACAT", "ACCA", "ACCC", "ACCG", "ACCT",
+    "ACGA", "ACGC", "ACGG", "ACGT", "ACTA", "ACTC", "ACTG", "ACTT",
+    "AGAA", "AGAC", "AGAG", "AGAT", "AGCA", "AGCC", "AGCG", "AGCT",
+    "AGGA", "AGGC", "AGGG", "AGGT", "AGTA", "AGTC", "AGTG", "AGTT",
+    "ATAA", "ATAC", "ATAG", "ATAT", "ATCA", "ATCC", "ATCG", "ATCT",
+    "ATGA", "ATGC", "ATGG", "ATGT", "ATTA", "ATTC", "ATTG", "ATTT",
+    "CAAA", "CAAC", "CAAG", "CAAT", "CACA", "CACC", "CACG", "CACT",
+    "CAGA", "CAGC", "CAGG", "CAGT", "CATA", "CATC", "CATG", "CATT",
+    "CCAA", "CCAC", "CCAG", "CCAT", "CCCA", "CCCC", "CCCG", "CCCT",
+    "CCGA", "CCGC", "CCGG", "CCGT", "CCTA", "CCTC", "CCTG", "CCTT",
+    "CGAA", "CGAC", "CGAG", "CGAT", "CGCA", "CGCC", "CGCG", "CGCT",
+    "CGGA", "CGGC", "CGGG", "CGGT", "CGTA", "CGTC", "CGTG", "CGTT",
+    "CTAA", "CTAC", "CTAG", "CTAT", "CTCA", "CTCC", "CTCG", "CTCT",
+    "CTGA", "CTGC", "CTGG", "CTGT", "CTTA", "CTTC", "CTTG", "CTTT",
+    "GAAA", "GAAC", "GAAG", "GAAT", "GACA", "GACC", "GACG", "GACT",
+    "GAGA", "GAGC", "GAGG", "GAGT", "GATA", "GATC", "GATG", "GATT",
+    "GCAA", "GCAC", "GCAG", "GCAT", "GCCA", "GCCC", "GCCG", "GCCT",
+    "GCGA", "GCGC", "GCGG", "GCGT", "GCTA", "GCTC", "GCTG", "GCTT",
+    "GGAA", "GGAC", "GGAG", "GGAT", "GGCA", "GGCC", "GGCG", "GGCT",
+    "GGGA", "GGGC", "GGGG", "GGGT", "GGTA", "GGTC", "GGTG", "GGTT",
+    "GTAA", "GTAC", "GTAG", "GTAT", "GTCA", "GTCC", "GTCG", "GTCT",
+    "GTGA", "GTGC", "GTGG", "GTGT", "GTTA", "GTTC", "GTTG", "GTTT",
+    "TAAA", "TAAC", "TAAG", "TAAT", "TACA", "TACC", "TACG", "TACT",
+    "TAGA", "TAGC", "TAGG", "TAGT", "TATA", "TATC", "TATG", "TATT",
+    "TCAA", "TCAC", "TCAG", "TCAT", "TCCA", "TCCC", "TCCG", "TCCT",
+    "TCGA", "TCGC", "TCGG", "TCGT", "TCTA", "TCTC", "TCTG", "TCTT",
+    "TGAA", "TGAC", "TGAG", "TGAT", "TGCA", "TGCC", "TGCG", "TGCT",
+    "TGGA", "TGGC", "TGGG", "TGGT", "TGTA", "TGTC", "TGTG", "TGTT",
+    "TTAA", "TTAC", "TTAG", "TTAT", "TTCA", "TTCC", "TTCG", "TTCT",
+    "TTGA", "TTGC", "TTGG", "TTGT", "TTTA", "TTTC", "TTTG", "TTTT"
+};
+
+
+/* Function declarations. */
+void      run_decode( int argc, char *argv[] );
+void      print_usage();
+void      motif_print( uint motif, uint count );
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIN <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+
+int main( int argc, char *argv[] )
+{
+    if ( argc == 1 ) {
+        print_usage();
+    }
+
+    run_decode( argc, argv );
+
+    return EXIT_SUCCESS;
+}
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> FUNCTIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+
+void print_usage()
+{
+    /* Martin A. Hansen, September 2008 */
+
+    /* Print usage and exit. */
+
+    fprintf( stderr,
+        "Usage: bipartite_decode <bipartite file(s)> > result.tab\n"        
+    );
+
+    exit( EXIT_SUCCESS );
+}
+
+
+void run_decode( int argc, char *argv[] )
+{
+    /* Martin A. Hansen, September 2008 */
+
+    /* For each file in argv decode the file of */
+    /* bipartite motifs and output the motifs */
+    /* and their count. */
+
+    FILE *fp    = NULL;
+    int   i     = 0;
+    uint  motif = 0;
+    uint  count = 0;
+
+    for ( i = 1; i < argc; i++ )
+    {
+        fp = read_open( argv[ i ] );
+
+        while ( fscanf( fp, "%u\t%u\n", &motif, &count ) )
+        {
+            assert( ferror( fp ) == 0 );
+
+            motif_print( motif, count );
+
+            if ( feof( fp ) ) {
+                break;
+            }
+        }
+
+        close_stream( fp );
+    }
+}
+
+
+void motif_print( uint motif, uint count )
+{
+    /* Martin A. Hansen, September 2008 */
+
+    /* Converts a binary encoded bipartite motif */
+    /* into DNA and output the motif, distance and */
+    /* count seperated by tabs: */
+    /* BLOCK1 \t BLOCK2 \t DIST \t COUNT */
+
+    uchar  bin1      = 0;
+    uchar  bin2      = 0;
+    ushort dist      = 0;
+    uint   motif_cpy = motif;
+
+    dist = ( ushort ) motif & BLOCK_MASK;
+
+    motif >>= sizeof( uchar ) * BITS_IN_BYTE;
+
+    bin2 = ( uchar ) motif;
+
+    motif >>= sizeof( uchar ) * BITS_IN_BYTE;
+
+    bin1 = ( uchar ) motif;
+
+    printf( "%u\t%s\t%s\t%d\t%d\n", motif_cpy, bin2dna[ bin1 ], bin2dna[ bin2 ], dist, count );
+}
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+