added fast phylip parser - issue #135

xflouris · May 12, 2017 · 5991008 · 5991008
1 parent 31b25f6
commit 5991008
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Showing 7 changed files with 102 additions and 375 deletions.
diff --git a/examples/newick-phylip-unrooted/newick-phylip-unrooted.c b/examples/newick-phylip-unrooted/newick-phylip-unrooted.c
@@ -93,7 +93,6 @@ int main(int argc, char * argv[])
 {
   unsigned int i;
   unsigned int tip_nodes_count, inner_nodes_count, nodes_count, branch_count;
-  unsigned int sequence_count;
   unsigned int matrix_count, ops_count;
   unsigned int * matrix_indices;
   double * branch_lengths;
@@ -104,7 +103,7 @@ int main(int argc, char * argv[])
   /* we accept only two arguments - the newick tree (unrooted binary) and the
      alignment in the form of FASTA reads */
   if (argc != 3)
-    fatal(" syntax: %s [newick] [fasta]", argv[0]);
+    fatal(" syntax: %s [newick] [phylip]", argv[0]);
 
   /* parse the unrooted binary tree in newick format, and store the number
      of tip nodes in tip_nodes_count */
@@ -162,12 +161,18 @@ int main(int argc, char * argv[])
   }
 
   /* read PHYLIP alignment */
-  pll_msa_t * msa = pll_phylip_parse_msa(argv[2], &sequence_count);
+  pll_phylip_t * fd = pll_phylip_open(argv[2], pll_map_phylip);
+  if (!fd)
+    fatal(pll_errmsg);
+
+  pll_msa_t * msa = pll_phylip_parse_interleaved(fd);
   if (!msa)
     fatal(pll_errmsg);
 
+  pll_phylip_close(fd);
+
   /* compress site patterns */
-  if (sequence_count != tip_nodes_count)
+  if ((unsigned int)(msa->count) != tip_nodes_count)
     fatal("Number of sequences does not match number of leaves in tree");
 
 #ifdef COMPRESS

diff --git a/examples/parsimony/npr-pars.c b/examples/parsimony/npr-pars.c
@@ -66,7 +66,6 @@ int main(int argc, char * argv[])
 {
   unsigned int i,j,n;
   unsigned int tip_nodes_count, inner_nodes_count, nodes_count, branch_count;
-  unsigned int sequence_count;
   unsigned int ops_count;
   pll_parsimony_t * pars;
   pll_pars_buildop_t * operations;
@@ -129,11 +128,17 @@ int main(int argc, char * argv[])
   }
 
   /* read PHYLIP alignment */
-  pll_msa_t * msa = pll_phylip_parse_msa(argv[2], &sequence_count);
+  pll_phylip_t * fd = pll_phylip_open(argv[2], pll_map_phylip);
+  if (!fd)
+    fatal(pll_errmsg);
+
+  pll_msa_t * msa = pll_phylip_parse_interleaved(fd);
   if (!msa)
     fatal(pll_errmsg);
 
-  if (sequence_count != tip_nodes_count)
+  pll_phylip_close(fd);
+
+  if ((unsigned int)(msa->count) != tip_nodes_count)
     fatal("Number of sequences does not match number of leaves in tree");
 
   /* create the PLL parsimony instance

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -31,13 +31,12 @@ core_pmatrix.c \
 core_likelihood.c \
 parse_utree.y \
 parse_rtree.y \
-parse_phylip.y \
 lex_utree.l \
 lex_rtree.l \
-lex_phylip.l \
 fast_parsimony.c \
 stepwise.c \
-random.c
+random.c \
+phylip.c
 
 libpll_la_CFLAGS = $(AM_CFLAGS)
 

diff --git a/src/lex_phylip.l b/src/lex_phylip.l
diff --git a/src/maps.c b/src/maps.c
@@ -101,16 +101,45 @@ const unsigned int pll_map_aa[256] =
 
 
 /*
-  map for fasta parsing
+  maps for fasta and phylip parsing
 
   legal symbols: ?*- 0123456789 abcdefghijklmnopqrstuvxyz (also upper case)
   fatal symbols: period (.), ascii 0-8, ascii 14-31
   silently stripped: tab (9), newline (10 and 13), vt (11), formfeed (12)
   stripped: !"#$&'()+,/:;<=>@^_`æøåÆØÅ§¨´
 
   includes both amino acid and nucleotide sequences, adapt to nt only
+
+  TODO: Would be more suitable to create separate maps for parsing nt data,
+  aa data, binary, etc
 */
 
+const unsigned int pll_map_phylip[256] =
+  {
+    /*
+    0=stripped, 1=legal, 2=fatal, 3=silently stripped
+    @   A   B   C   D   E   F   G   H   I   J   K   L   M   N   O
+    P   Q   R   S   T   U   V   W   X   Y   Z   [   \   ]   ^   _
+    */
+
+/*  0   1   2   3   4   5   6   7   8   9   A   B   C   D   E   F        */
+    2,  2,  2,  2,  2,  2,  2,  2,  2,  3,  3,  3,  3,  3,  2,  2,  /* 0 */
+    2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  /* 1 */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  2,  0,  /* 2 */
+    1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  0,  0,  0,  0,  1,  /* 3 */
+    0,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  /* 4 */
+    1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  0,  0,  0,  0,  /* 5 */
+    0,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  1,  1,  1,  1,  0,  /* 6 */
+    1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  0,  0,  0,  0,  /* 7 */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* 8 */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* 9 */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* A */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* B */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* C */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* D */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  /* E */
+    0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0   /* F */
+  };
 const unsigned int pll_map_fasta[256] =
   {
     /*