fixed ranges to correct # of reads

src/read_sequencing.py

@@ -40,7 +40,10 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
     while frag_line != "":
         # To stop when the end of file is reached
         if frag_line.startswith('>'):
+            # Determine if this is the first fragment in the file
+            # Ignore the description line (starting with >) of the first fragment
             if not (len(frag_list) == 0 and frag_str == ""):
+                # Not the first fragment. Append to list.
                 frag_list.append(frag_str)
             frag_str = ""
         else:
@@ -60,7 +63,7 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
     sum_frags = sum(map(len, frag_list))
 
     # Repeat the read process for given number of cycles
-    for j in range(1, num_seq_cyc):
+    for j in range(0, num_seq_cyc):
 
         # Loop through fasta fragments that start with 5'
         for frag in frag_list:
@@ -70,7 +73,7 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
             # TODO resolve this issue
             num_frag_reads = round((len(frag)/sum_frags) * num_reads)
 
-            for i in range(1, num_frag_reads):
+            for i in range(0, num_frag_reads):
 
                 # Obtain random first position for the read on the fragment
                 rand_start = randrange(0, len(frag))