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drlabl · Feb 4, 2021 · 30afd42 · 30afd42
1 parent 3e85e4b
commit 30afd42
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Showing 11 changed files with 51 additions and 6 deletions.
diff --git a/01_dna/tests/dna_test.py b/01_dna/tests/dna_test.py
@@ -2,7 +2,7 @@
 
 import os
 import platform
-from subprocess import getstatusoutput, getoutput
+from subprocess import getstatusoutput
 
 PRG = './dna.py'
 RUN = f'python {PRG}' if platform.system() == 'Windows' else PRG
@@ -20,13 +20,23 @@ def test_exists() -> None:
 
 # --------------------------------------------------
 def test_usage() -> None:
-    """ Prints usage with no args or for help """
+    """ Prints usage """
 
-    for arg in ['', '-h', '--help']:
-        out = getoutput(f'{RUN} {arg}')
+    for arg in ['-h', '--help']:
+        rv, out = getstatusoutput(f'{RUN} {arg}')
+        assert rv == 0
         assert out.lower().startswith('usage:')
 
 
+# --------------------------------------------------
+def test_dies_no_args() -> None:
+    """ Dies with no arguments """
+
+    rv, out = getstatusoutput(RUN)
+    assert rv != 0
+    assert out.lower().startswith('usage:')
+
+
 # --------------------------------------------------
 def test_arg() -> None:
     """ Uses command-line arg """

diff --git a/05_gc/solution1_list.py b/05_gc/solution1_list.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO, List, Tuple
 from Bio import SeqIO
 
@@ -22,6 +23,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution2_unit.py b/05_gc/solution2_unit.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO, List
 from Bio import SeqIO
 
@@ -28,6 +29,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution3_max_var.py b/05_gc/solution3_max_var.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 
@@ -28,6 +29,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution4_list_comp.py b/05_gc/solution4_list_comp.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 
@@ -28,6 +29,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution5_filter.py b/05_gc/solution5_filter.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 
@@ -28,6 +29,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution6_map.py b/05_gc/solution6_map.py
@@ -2,6 +2,7 @@
 """ Compute GC content """
 
 import argparse
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 
@@ -28,6 +29,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution7_re.py b/05_gc/solution7_re.py
@@ -3,6 +3,7 @@
 
 import argparse
 import re
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 
@@ -29,6 +30,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/solution8_list_comp_map.py b/05_gc/solution8_list_comp_map.py
@@ -3,6 +3,7 @@
 
 import argparse
 import re
+import sys
 from typing import NamedTuple, TextIO
 from Bio import SeqIO
 from Bio.Seq import Seq
@@ -31,6 +32,8 @@ def get_args() -> Args:
     parser.add_argument('file',
                         metavar='FILE',
                         type=argparse.FileType('rt'),
+                        nargs='?',
+                        default=sys.stdin,
                         help='Input sequence file')
 
     args = parser.parse_args()

diff --git a/05_gc/tests/cgc_test.py b/05_gc/tests/cgc_test.py
@@ -59,6 +59,15 @@ def test_good_input2() -> None:
     assert out == 'Rosalind_5723 52.806415'
 
 
+# --------------------------------------------------
+def test_stdin() -> None:
+    """ Works on STDIN """
+
+    rv, out = getstatusoutput(f'cat {SAMPLE1} | {RUN}')
+    assert rv == 0
+    assert out == 'Rosalind_0808 60.919540'
+
+
 # --------------------------------------------------
 def random_string() -> str:
     """ Generate a random string """

diff --git a/18_fastx_sampler/sampler_dir_reader.py b/18_fastx_sampler/sampler_dir_reader.py
@@ -5,6 +5,7 @@
 import os
 import random
 import gzip
+from pathlib import Path
 from Bio import SeqIO
 from typing import List, NamedTuple, Optional
 
@@ -27,7 +28,8 @@ def get_args() -> Args:
         description='Probabalistically subset FASTA files',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
-    parser.add_argument('dir',
+    parser.add_argument('-d',
+                        '--dir',
                         metavar='DIR',
                         type=str,
                         nargs='+',
@@ -80,7 +82,7 @@ def get_args() -> Args:
     files = []
     for dirname in args.dir:
         if os.path.isdir(dirname):
-            filenames.extend(list(Path(dirname).rglob('*')))
+            files.extend(list(Path(dirname).rglob('*')))
 
     if not files:
         parser.error('Found no files')