Merge pull request #61 from martinghunt/random_reads_use_float

Random reads use float

pyfastaq/runners/to_random_subset.py

@@ -9,11 +9,13 @@ def run(description):
                       'from a mates file.  Ouptut is interleaved if mates file given',
         usage = 'fastaq to_random_subset [options] <infile> <outfile> <percent>')
     parser.add_argument('--mate_file', help='Name of mates file')
+    parser.add_argument('--seed', help='Seed for random number generator. If not given, python\'s default is used', metavar='INT')
     parser.add_argument('infile', help='Name of input file')
     parser.add_argument('outfile', help='Name of output file')
-    parser.add_argument('percent', type=int, help='Per cent probability of keeping any given read (pair) in [0,100]', metavar='INT')
+    parser.add_argument('percent', type=float, help='Per cent probability of keeping any given read (pair) in [0,100]', metavar='FLOAT')
     options = parser.parse_args()
 
+    random.seed(a=options.seed)
     seq_reader = sequences.file_reader(options.infile)
     fout = utils.open_file_write(options.outfile)
 
@@ -27,7 +29,7 @@ def run(description):
             except StopIteration:
                 print('Error! Didn\'t get mate for read', seq.id, file=sys.stderr)
                 sys.exit(1)
-        if random.randint(0, 100) <= options.percent:
+        if 100 * random.random() <= options.percent:
             print(seq, file=fout)
             if options.mate_file:
                 print(mate_seq, file=fout)

setup.py

@@ -4,7 +4,7 @@
 
 setup(
     name='pyfastaq',
-    version='3.12.1',
+    version='3.13.0',
     description='Script to manipulate FASTA and FASTQ files, plus API for developers',
     packages = find_packages(),
     author='Martin Hunt',