algo/: Count number of sequences independently of input format

Use OnlineBioReader rather than a Fasta reader

algo/core/bioreader.cpp

@@ -237,3 +237,57 @@ OnlineBioReader *OnlineBioReaderFactory::create(const string &filename,
                                                 int nb_sequences_max, int only_nth_sequence) {
   return new OnlineFasta(filename, extract_field, extract_separator, nb_sequences_max, only_nth_sequence);
 }
+
+// http://stackoverflow.com/a/5840160/4475279
+unsigned long long filesize(const char* filename)
+{
+    std::ifstream in(filename, std::ifstream::ate | std::ifstream::binary);
+    return in.tellg();
+}
+
+unsigned long long nb_sequences_in_file(string f, bool approx)
+{
+  if (approx)
+    return approx_nb_sequences_in_file(f);
+
+  OnlineBioReader *sequences = OnlineBioReaderFactory::create(f, 1, " ");
+  unsigned long long nb_sequences = 0 ;
+
+  while (sequences->hasNext())
+    {
+      sequences->next();
+      nb_sequences++ ;
+    }
+
+  cout << "  ==> " << nb_sequences << " sequences" << endl;
+
+  delete sequences ;
+  return nb_sequences ;
+}
+
+
+unsigned long long approx_nb_sequences_in_file(string f)
+{
+  OnlineBioReader *sequences = OnlineBioReaderFactory::create(f, 1, " ");
+  int nb_sequences = 0 ;
+
+  while (nb_sequences < SAMPLE_APPROX_NB_SEQUENCES && sequences->hasNext())
+    {
+      sequences->next();
+      nb_sequences++ ;
+    }
+
+  cout << "  ==> " ;
+
+  if (sequences->hasNext())
+    {
+      cout << "approx. " ;
+      float ratio = (float) filesize(f.c_str()) / (float) sequences->getPos();
+      nb_sequences = (unsigned long long) (ratio * nb_sequences);
+    }
+
+  cout << nb_sequences << " sequences" << endl;
+
+  delete sequences ;
+  return nb_sequences ;
+}

algo/core/bioreader.hpp

@@ -28,6 +28,8 @@
 #include <vector>
 #include <list>
 
+#define SAMPLE_APPROX_NB_SEQUENCES 200
+
 using namespace std;
 
 typedef string seqtype ;
@@ -223,6 +225,21 @@ ostream &operator<<(ostream &out, const Sequence &seq);
 const BioReader BIOREADER_UNKNOWN = BioReader(true, "_");
 const BioReader BIOREADER_AMBIGUOUS = BioReader(true, "?");
 
+unsigned long long filesize(const char* filename);
+
+/**
+ * Count the number of sequences in a Fasta file.
+ * @complexity Linear in the file size
+ * @return the number of sequences
+ */
+unsigned long long nb_sequences_in_file(string f, bool approx = false);
+
+/**
+ * Give an approximate count of the number of sequences in the file
+ * @complexity linear in SAMPLE_APPROX_NB_SEQUENCES
+ * @return the approximate number of sequences
+ */
+unsigned long long approx_nb_sequences_in_file(string f);
 
 class OnlineBioReaderFactory {
 public:

algo/core/fasta.cpp

@@ -32,13 +32,6 @@
 #include "../lib/gzstream.h"
 
 
-// http://stackoverflow.com/a/5840160/4475279
-unsigned long long filesize(const char* filename)
-{
-    std::ifstream in(filename, std::ifstream::ate | std::ifstream::binary);
-    return in.tellg();
-}
-
 // OnlineFasta
 
 OnlineFasta::OnlineFasta(int extract_field, string extract_separator,
@@ -175,52 +168,4 @@ void OnlineFasta::unexpectedEOF() {
   throw invalid_argument("Unexpected EOF while reading FASTA/FASTQ file");
 }
 
-unsigned long long nb_sequences_in_fasta(string f, bool approx)
-{
-  if (approx)
-    return approx_nb_sequences_in_fasta(f);
-
-  OnlineFasta *sequences = new OnlineFasta(f, 1, " ");
-  unsigned long long nb_sequences = 0 ;
-
-  while (sequences->hasNext())
-    {
-      sequences->next();
-      nb_sequences++ ;
-    }
-
-  cout << "  ==> " << nb_sequences << " sequences" << endl;
-
-  delete sequences ;
-  return nb_sequences ;
-}
-
-
-#define SAMPLE_APPROX_NB_SEQUENCES 200
-
-unsigned long long approx_nb_sequences_in_fasta(string f)
-{
-  OnlineFasta *sequences = new OnlineFasta(f, 1, " ");
-  int nb_sequences = 0 ;
-
-  while (nb_sequences < SAMPLE_APPROX_NB_SEQUENCES && sequences->hasNext())
-    {
-      sequences->next();
-      nb_sequences++ ;
-    }
-
-  cout << "  ==> " ;
-
-  if (sequences->hasNext())
-    {
-      cout << "approx. " ;
-      float ratio = (float) filesize(f.c_str()) / (float) sequences->getPos();
-      nb_sequences = (unsigned long long) (ratio * nb_sequences);
-    }
-
-  cout << nb_sequences << " sequences" << endl;
-
-  delete sequences ;
-  return nb_sequences ;
-}
 

algo/core/fasta.h

@@ -10,9 +10,6 @@ using namespace std;
 
 #include "bioreader.hpp"
 
-unsigned long long filesize(const char* filename);
-
-
 /**
  * Read a FASTA/FASTQ file.
  * Space complexity: constant. Only one sequence is stored at most in memory.
@@ -78,13 +75,4 @@ protected:
    */
   string getInterestingLine(int state = FASTX_UNINIT);
 };
-
-/**
- * Count the number of sequences in a Fasta file
- * @return the number of sequences
- */
-unsigned long long nb_sequences_in_fasta(string f, bool approx = false);
-unsigned long long approx_nb_sequences_in_fasta(string f);
-
-
 #endif

algo/tests/unit-tests/testTools.cpp

@@ -50,12 +50,12 @@ void testOnlineBioReaderMaxNth() {
 
 
 void testFastaNbSequences() {
-  TAP_TEST(nb_sequences_in_fasta("../../germline/homo-sapiens/IGHV.fa") == 349, TEST_FASTA_NB_SEQUENCES, "ccc");
+  TAP_TEST(nb_sequences_in_file("../../germline/homo-sapiens/IGHV.fa") == 349, TEST_FASTA_NB_SEQUENCES, "ccc");
 
-  int a1 = approx_nb_sequences_in_fasta("../../germline/homo-sapiens/IGHV.fa");
+  int a1 = approx_nb_sequences_in_file("../../germline/homo-sapiens/IGHV.fa");
   TAP_TEST(a1 >= 345 && a1 <= 355, TEST_FASTA_NB_SEQUENCES, "");
 
-  int a2 = nb_sequences_in_fasta("../../data/Stanford_S22.fasta", true);
+  int a2 = nb_sequences_in_file("../../data/Stanford_S22.fasta", true);
   TAP_TEST(a2 >= 13100 && a2 <= 13200, TEST_FASTA_NB_SEQUENCES, "");
 }
 

algo/vidjil.cpp

@@ -916,7 +916,7 @@ int main (int argc, char **argv)
     cout << endl ;
 
     // Number of reads for e-value computation
-    unsigned long long nb_reads_for_evalue = (expected_value > NO_LIMIT_VALUE) ? nb_sequences_in_fasta(f_reads, true) : 1 ;
+    unsigned long long nb_reads_for_evalue = (expected_value > NO_LIMIT_VALUE) ? nb_sequences_in_file(f_reads, true) : 1 ;
 
     
   //////////////////////////////////
@@ -925,7 +925,7 @@ int main (int argc, char **argv)
     int only_nth_read = 1 ;
     if (max_reads_processed_sample != NO_LIMIT_VALUE)
       {
-        only_nth_read = nb_sequences_in_fasta(f_reads) / max_reads_processed_sample;
+        only_nth_read = nb_sequences_in_file(f_reads) / max_reads_processed_sample;
         if (only_nth_read == 0)
           only_nth_read = 1 ;