removing synth.py

15_seqmagique/seqmagique_rich.py

@@ -2,11 +2,8 @@
 """ Mimic seqmagick, print stats on FASTA sequences """
 
 import argparse
-import os
-import sys
 import numpy as np
 from typing import List, NamedTuple, TextIO
-from rich import box
 from rich.console import Console
 from rich.progress import track
 from rich.table import Table, Column
@@ -58,11 +55,13 @@ def main() -> None:
                   Column(header='Num. Seqs', justify='right'),
                   header_style="bold black")
 
-    for file in track([process(fh) for fh in args.file]):
+    for fh in track(args.file):
+        file = process(fh)
         table.add_row(file.filename, str(file.min_len), str(file.max_len),
                       str(file.avg_len), str(file.num_seqs))
 
-    Console().print(table)
+    console = Console()
+    console.print(table)
 
 
 # --------------------------------------------------

15_seqmagique/solution1.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-""" Mimic seqmagick, print stats on FASTA sequences """
+""" Mimic seqmagick """
 
 import argparse
 from typing import List, NamedTuple, TextIO
@@ -28,7 +28,7 @@ def get_args() -> Args:
     """Get command-line arguments"""
 
     parser = argparse.ArgumentParser(
-        description='Argparse Python script',
+        description='Mimic seqmagick',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
     parser.add_argument('file',

16_fastx_grep/solution.py

@@ -6,7 +6,7 @@
 import re
 import sys
 from Bio import SeqIO
-from typing import List, Match, NamedTuple, TextIO, Optional
+from typing import List, NamedTuple, TextIO
 
 
 class Args(NamedTuple):
@@ -17,7 +17,6 @@ class Args(NamedTuple):
     output_format: str
     outfile: TextIO
     insensitive: bool
-    verbose: bool
 
 
 # --------------------------------------------------
@@ -65,19 +64,13 @@ def get_args() -> Args:
                         help='Case-insensitive search',
                         action='store_true')
 
-    parser.add_argument('-v',
-                        '--verbose',
-                        help='Be chatty',
-                        action='store_true')
-
     args = parser.parse_args()
 
     return Args(pattern=args.pattern,
                 files=args.file,
                 input_format=args.format,
                 output_format=args.outfmt,
                 outfile=args.outfile,
-                verbose=args.verbose,
                 insensitive=args.insensitive)
 
 
@@ -86,18 +79,9 @@ def main() -> None:
     """ Make a jazz noise here """
 
     args = get_args()
+    regex = re.compile(args.pattern, re.IGNORECASE if args.insensitive else 0)
 
-    def progress(msg: str) -> None:
-        if args.verbose:
-            print(msg, file=sys.stderr)
-
-    def search(text: str) -> Optional[Match[str]]:
-        flag = re.IGNORECASE if args.insensitive else 0
-        return re.search(args.pattern, text, flag)
-
-    num_checked, num_took = 0, 0
-    for i, fh in enumerate(args.files, start=1):
-        progress(f'{i:3}: {fh.name}')
+    for fh in args.files:
         input_format = args.input_format or guess_format(fh.name)
 
         if not input_format:
@@ -106,14 +90,9 @@ def search(text: str) -> Optional[Match[str]]:
         output_format = args.output_format or input_format
 
         for rec in SeqIO.parse(fh, input_format):
-            num_checked += 1
-            if any(map(search, [rec.id, rec.description])):
-                num_took += 1
+            if any(map(regex.search, [rec.id, rec.description])):
                 SeqIO.write(rec, args.outfile, output_format)
 
-    outfile = 'STDOUT' if args.outfile == sys.stdout else args.outfile.name
-    progress(f'Checked {num_checked:,}, wrote {num_took:,} to "{outfile}".')
-
 
 # --------------------------------------------------
 def guess_format(filename: str) -> str:

16_fastx_grep/tests/fastx_grep_test.py

@@ -52,7 +52,28 @@ def test_cannot_guess() -> None:
     pattern = random_string()
     rv, out = getstatusoutput(f'{RUN} {pattern} {BAD_EXT}')
     assert rv != 0
-    assert out == f'Please specify file format for "{BAD_EXT}"'
+    assert re.search(f'Please specify file format for "{BAD_EXT}"', out)
+
+
+# --------------------------------------------------
+def test_out_file() -> None:
+    """ out_file """
+
+    out_file = random_string()
+    if os.path.isfile(out_file):
+        os.remove(out_file)
+
+    try:
+        flag = '-o' if random.choice([0, 1]) else '--outfile'
+        rv, out = getstatusoutput(f'{RUN} {flag} {out_file} LSU {LSU}')
+        assert rv == 0
+        assert os.path.isfile(out_file)
+        expected = open(LSU + '.upper.out').read().rstrip()
+        assert open(out_file).read().rstrip() == expected
+
+    finally:
+        if os.path.isfile(out_file):
+            os.remove(out_file)
 
 
 # --------------------------------------------------
@@ -62,11 +83,23 @@ def run(pattern: str,
         opts: List[str] = []) -> None:
     """ Runs on command-line input """
 
+    assert os.path.isfile(expected_file)
     expected = open(expected_file).read().rstrip()
-    cmd = f"{RUN} {' '.join(opts)} {pattern} {input_file}"
-    rv, out = getstatusoutput(cmd)
-    assert rv == 0
-    assert out == expected
+
+    out_file = random_string()
+    if os.path.isfile(out_file):
+        os.remove(out_file)
+
+    try:
+        cmd = f"{RUN} {' '.join(opts)} {pattern} -o {out_file} {input_file}"
+        rv, out = getstatusoutput(cmd)
+
+        assert os.path.isfile(out_file)
+        assert rv == 0
+        assert open(out_file).read().rstrip() == expected
+    finally:
+        if os.path.isfile(out_file):
+            os.remove(out_file)
 
 
 # --------------------------------------------------
@@ -105,53 +138,6 @@ def test_lsu_lowercase_insensitive() -> None:
     run('lsu', LSU, LSU + '.i.lower.out', ['--insensitive'])
 
 
-# --------------------------------------------------
-def test_outfile() -> None:
-    """ outfile """
-
-    outfile = random_string()
-    if os.path.isfile(outfile):
-        os.remove(outfile)
-
-    try:
-        flag = '-o' if random.choice([0, 1]) else '--outfile'
-        rv, out = getstatusoutput(f'{RUN} {flag} {outfile} LSU {LSU}')
-        assert rv == 0
-        assert out == ''
-        assert os.path.isfile(outfile)
-        expected = open(LSU + '.upper.out').read().rstrip()
-        assert open(outfile).read().rstrip() == expected
-
-    finally:
-        if os.path.isfile(outfile):
-            os.remove(outfile)
-
-
-# --------------------------------------------------
-def test_outfile_verbose() -> None:
-    """ outfile + verbose """
-
-    outfile = random_string()
-    if os.path.isfile(outfile):
-        os.remove(outfile)
-
-    try:
-        flag = '-v' if random.choice([0, 1]) else '--verbose'
-        rv, out = getstatusoutput(f'{RUN} {flag} -o {outfile} LSU {LSU}')
-        assert rv == 0
-        assert out.splitlines() == [
-            '  1: ./tests/inputs/lsu.fq',
-            f'Checked 4, wrote 2 to "{outfile}".'
-        ]
-        assert os.path.isfile(outfile)
-        expected = open(LSU + '.upper.out').read().rstrip()
-        assert open(outfile).read().rstrip() == expected
-
-    finally:
-        if os.path.isfile(outfile):
-            os.remove(outfile)
-
-
 # --------------------------------------------------
 def test_outfmt_fastq_to_fasta() -> None:
     """ outfmt """

17_synth/.gitignore

@@ -1 +1,2 @@
 out.fa
+synth.py