new stuff

16_fastx_grep/foo

@@ -0,0 +1,8 @@
+@ITSLSUmock2p.ITS_M01380:138:000000000-C9GKM:1:1101:14440:2042 2:N:0
+CAAGTTACTTCCTCTAAATGACCAAGCCTAGTGTAGAACCATGTCGTCAGTGTCAGTCTGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAATGTAATACTACTAGTAATTATTAATATTATAATTTTGTCTATTAGCATCTTATTATAGATAGAAGATATTATTCATATTTCACTATCTTATACTGATATCAGCTTTATCAGATCACACTCTAGTGAAGATTGTTCTTAACTGAAATTTCCTTCTTCATACAGACACATTAATCTTACCTA
++
+EFGGGGGGGGGCGGGGGFCFFFGGGGGFGGGGGGGGGGGFGGGGGGGFGFFFCFGGFFGGGGGGGGGFGGGGFGGGDG<FD@4@CFFGGGGCFFAFEFEG+,9,,,,99,,,5,,49,4,8,4,444,4,4,,,,,,,,,,,,,,8,,,,63,,,,,,,,376,3,,,,,,,8,,,,,,,,,+++++++++++++3++25+++0+*+0+*0+***))*0))1/+++**************.****.*******0*********/(,(/).)))1)).).).
+@ITSLSUmock2p.ITS_M01384:138:000000000-C9GKM:1:1101:14440:2043 2:N:0
+ACCCGTCAATTTCTTTAAGTTTTAGCCTTGCGACCGTACTCCCCAGGCGGTGCACTTAGTGGTTTTCCGGCGACCCGGGCGGCGTCAGAGCCCCCCAAGTCTCGTGCACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCCTCAGCGTCAGTACCGGCCCAGCCACCCGTCTTCACCTTCGGCGTTCCTGTAGATATCTACGCATTTCACCGCTACACCTACAGTTCCGGTGGCGCCTACCGGCCTCAAGAAACGCAGTATGCCCAGCTATT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGFGGGGGGGGGGGG9FGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGCGFGFGGGGGGGGGGGGGGGGGDGGGDEEFGGGGGGGGGGGGFFGGG9EGFGGFCGGCGGGCCGEGGGEGFGGGG6B6*=EGGGGGGG8ECCEGGGGCFGDEEGGG?FGFGGC39:>EGGGGGGF7=9:A@FBF>DGCGFF=75C=DBCF74DFFFF*/91B>9>?9?>>:B?>F>FBB:??200:699>?AA2)34F?2))54

16_fastx_grep/mk-outs.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+set -u
+
+PRG="./fastx_grep.py"
+EMPTY="./tests/inputs/empty.fa"
+LSU="./tests/inputs/lsu.fq"
+LSU_FA="./tests/inputs/lsu.fa"
+
+rm -f ./tests/inputs/*.out
+
+"$PRG" -o "$EMPTY.out" XXX "$EMPTY" 
+
+"$PRG" -o "$LSU.upper.out" LSU "$LSU"
+"$PRG" -o "$LSU.lower.out" lsu "$LSU"
+
+"$PRG" -o "$LSU.i.upper.out" -i LSU "$LSU"
+"$PRG" -o "$LSU.i.lower.out" -i lsu "$LSU"
+
+"$PRG" -O fasta -o "$LSU.fa.out" LSU "$LSU"
+"$PRG" -O fasta-2line  -o "$LSU.2fa.out" LSU "$LSU"
+
+echo "Done."

16_fastx_grep/solution.py

@@ -6,11 +6,22 @@
 import re
 import sys
 from Bio import SeqIO
+from typing import List, NamedTuple, TextIO
+
+
+class Args(NamedTuple):
+    """ Command-line arguments """
+    pattern: str
+    files: List[TextIO]
+    input_format: str
+    output_format: str
+    outfile: TextIO
+    verbose: bool
 
 
 # --------------------------------------------------
-def get_args():
-    """Get command-line arguments"""
+def get_args() -> Args:
+    """ Get command-line arguments """
 
     parser = argparse.ArgumentParser(
         description='Grep through FASTX files',
@@ -24,7 +35,7 @@ def get_args():
     parser.add_argument('file',
                         metavar='FILE',
                         nargs='+',
-                        type=argparse.FileType('r'),
+                        type=argparse.FileType('rt'),
                         help='Input file(s)')
 
     parser.add_argument('-f',
@@ -35,7 +46,7 @@ def get_args():
                         default='')
 
     parser.add_argument('-O',
-                        '--out_format',
+                        '--outfmt',
                         help='Output file format',
                         metavar='str',
                         choices=['fasta', 'fastq', 'fasta-2line'],
@@ -44,33 +55,69 @@ def get_args():
     parser.add_argument('-o',
                         '--outfile',
                         help='Output file',
+                        type=argparse.FileType('wt'),
                         metavar='FILE',
-                        default=None)
+                        default=sys.stdout)
+
+    parser.add_argument('-v',
+                        '--verbose',
+                        help='Be chatty',
+                        action='store_true')
 
     args = parser.parse_args()
 
-    if not args.format:
-        args.format = guess_format(args.file[0].name)
+    return Args(pattern=args.pattern,
+                files=args.file,
+                input_format=args.format,
+                output_format=args.outfmt,
+                outfile=args.outfile,
+                verbose=args.verbose)
+
+
+# --------------------------------------------------
+def main() -> None:
+    """ Make a jazz noise here """
+
+    args = get_args()
+
+    def progress(msg):
+        if args.verbose:
+            print(msg, file=sys.stderr)
 
-    if not args.format:
-        parser.error('Cannot guess --format, please specify')
+    regex = re.compile(args.pattern)
+    num_checked, num_took = 0, 0
+    for i, fh in enumerate(args.files, start=1):
+        progress(f'{i:3}: {fh.name}')
+        input_format = args.input_format or guess_format(fh.name)
+
+        if not input_format:
+            sys.exit(f'Please specify file format for "{fh.name}"')
 
-    return args
+        output_format = args.output_format or input_format
+
+        for rec in SeqIO.parse(fh, input_format):
+            num_checked += 1
+            if any(map(regex.search, [rec.id, rec.description])):
+                num_took += 1
+                SeqIO.write(rec, args.outfile, output_format)
+
+    outfile = 'STDOUT' if args.outfile == sys.stdout else args.outfile.name
+    progress(f'Done, checked {num_checked}, wrote {num_took} to "{outfile}".')
 
 
 # --------------------------------------------------
-def guess_format(file):
-    """Guess format from extension"""
+def guess_format(filename: str) -> str:
+    """ Guess format from extension """
 
-    ext = re.sub('^.', '', os.path.splitext(file)[1])
+    ext = re.sub('^.', '', os.path.splitext(filename)[1])
 
     return 'fasta' if re.match(
         'f(ast|n)?a$', ext) else 'fastq' if re.match('f(ast)?q$', ext) else ''
 
 
 # --------------------------------------------------
-def test_guess_format():
-    """Test guess_format"""
+def test_guess_format() -> None:
+    """ Test guess_format """
 
     assert guess_format('/foo/bar.fa') == 'fasta'
     assert guess_format('/foo/bar.fna') == 'fasta'
@@ -80,25 +127,6 @@ def test_guess_format():
     assert guess_format('/foo/bar.fx') == ''
 
 
-# --------------------------------------------------
-def main():
-    """Make a jazz noise here"""
-
-    args = get_args()
-    regex = re.compile(args.pattern)
-    out_fh = args.outfile or sys.stdout
-    checked, took = 0, 0
-
-    for fh in args.file:
-        for rec in SeqIO.parse(fh, args.format):
-            checked += 1
-            if any(map(regex.search, [rec.id, rec.description])):
-                took += 1
-                SeqIO.write(rec, out_fh, args.out_format or args.format)
-
-    print(f'Done, checked {checked}, took {took}.', file=sys.stderr)
-
-
 # --------------------------------------------------
 if __name__ == '__main__':
     main()

16_fastx_grep/tests/fastx_grep_test.py

@@ -6,22 +6,25 @@
 import string
 import re
 from subprocess import getstatusoutput
+from typing import List
 
 PRG = './fastx_grep.py'
 RUN = f'python {PRG}' if platform.system() == 'Windows' else PRG
 EMPTY = './tests/inputs/empty.fa'
 LSU = './tests/inputs/lsu.fq'
+LSU_FA = './tests/inputs/lsu.fa'
+BAD_EXT = './tests/inputs/lsu.fx'
 
 
 # --------------------------------------------------
-def test_exists():
+def test_exists() -> None:
     """exists"""
 
     assert os.path.isfile(PRG)
 
 
 # --------------------------------------------------
-def test_usage():
+def test_usage() -> None:
     """usage"""
 
     for flag in ['-h', '--help']:
@@ -42,27 +45,128 @@ def test_bad_file() -> None:
     assert re.search(f"No such file or directory: '{bad}'", out)
 
 
-# # --------------------------------------------------
-# def run(input_file: str, expected_file: str) -> None:
-#     """ Runs on command-line input """
+# --------------------------------------------------
+def test_cannot_guess() -> None:
+    """ Dies on unguessable extension """
+
+    pattern = random_string()
+    bad = random_string()
+    rv, out = getstatusoutput(f'{RUN} {pattern} {BAD_EXT}')
+    assert rv != 0
+    assert out == f'Please specify file format for "{BAD_EXT}"'
+
+
+# --------------------------------------------------
+def run(pattern: str,
+        input_file: str,
+        expected_file: str,
+        opts: List[str] = []) -> None:
+    """ Runs on command-line input """
+
+    expected = open(expected_file).read().rstrip()
+    cmd = f"{RUN} {' '.join(opts)} {pattern} {input_file}"
+    rv, out = getstatusoutput(cmd)
+    assert rv == 0
+    assert out == expected
+
+
+# --------------------------------------------------
+def test_empty_file() -> None:
+    """ Handles empty file """
+
+    pattern = random_string()
+    run(pattern, EMPTY, EMPTY + '.out')
+
+
+# --------------------------------------------------
+def test_lsu_uppercase() -> None:
+    """ LSU """
+
+    run('LSU', LSU, LSU + '.upper.out')
+
+
+# --------------------------------------------------
+def test_lsu_lowercase() -> None:
+    """ lsu """
+
+    run('lsu', LSU, LSU + '.lower.out')
+
 
-#     expected = open(expected_file).read().rstrip()
-#     rv, out = getstatusoutput(f'{RUN} {input_file}')
-#     assert rv == 0
-#     assert out == expected
+# --------------------------------------------------
+def test_lsu_uppercase_insensitive() -> None:
+    """ -i LSU """
+
+    run('LSU', LSU, LSU + '.i.upper.out', ['-i'])
+
+
+# --------------------------------------------------
+def test_lsu_lowercase_insensitive() -> None:
+    """ -i lsu """
+
+    run('lsu', LSU, LSU + '.i.lower.out', ['--insensitive'])
 
 
-# # --------------------------------------------------
-# def test_empty_file() -> None:
-#     """ Handles empty file """
+# --------------------------------------------------
+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)
 
-#     run(*EMPTY)
 
-# # --------------------------------------------------
-# def test_input1() -> None:
-#     """ Runs on command-line input """
+# --------------------------------------------------
+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'Done, 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 """
+
+    flag = '-O' if random.choice([0, 1]) else '--outfmt'
+    run('LSU', LSU, LSU + '.fa.out', [f'{flag} fasta'])
+
+
+# --------------------------------------------------
+def test_outfmt_fastq_to_fasta2line() -> None:
+    """ outfmt """
 
-#     run(*TEST1)
+    flag = '-O' if random.choice([0, 1]) else '--outfmt'
+    run('LSU', LSU, LSU + '.2fa.out', [f'{flag} fasta-2line'])
 
 
 # --------------------------------------------------

16_fastx_grep/tests/inputs/lsu.fa

@@ -0,0 +1,13 @@
+>ITSLSUmock2p.ITS_M01380:138:000000000-C9GKM:1:1101:14440:2042 2:N:0
+CAAGTTACTTCCTCTAAATGACCAAGCCTAGTGTAGAACCATGTCGTCAGTGTCAGTCTG
+AGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAATGTAATACTACTAGTAATT
+ATTAATATTATAATTTTGTCTATTAGCATCTTATTATAGATAGAAGATATTATTCATATT
+TCACTATCTTATACTGATATCAGCTTTATCAGATCACACTCTAGTGAAGATTGTTCTTAA
+CTGAAATTTCCTTCTTCATACAGACACATTAATCTTACCTA
+>ITSLSUmock2p.ITS_M01384:138:000000000-C9GKM:1:1101:14440:2043 2:N:0
+ACCCGTCAATTTCTTTAAGTTTTAGCCTTGCGACCGTACTCCCCAGGCGGTGCACTTAGT
+GGTTTTCCGGCGACCCGGGCGGCGTCAGAGCCCCCCAAGTCTCGTGCACATCGTTTACGG
+CGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCCTCAGCGTCAG
+TACCGGCCCAGCCACCCGTCTTCACCTTCGGCGTTCCTGTAGATATCTACGCATTTCACC
+GCTACACCTACAGTTCCGGTGGCGCCTACCGGCCTCAAGAAACGCAGTATGCCCAGCTAT
+T

16_fastx_grep/tests/inputs/lsu.fq

@@ -1,5 +1,16 @@
+@M00773:480:000000000-BLYPT:1:2106:12063:1841 1:N:0:AGGCGACCTTA
+TTTCTGTGCCAGCAGCCGCGGTAAGACAGAGGTGGCGAGCGTTGTTCGGATTTACTGGGCGTAAAGCGCGGGTAGGCGGTTCGGCCAGTCAGATGTGAAATCCCACCGCTTAACGGTGGAACGGCGTCTGATACTACCGGACTTGAGTGCAGGAGAGGAGGGTGGAATTTCCGGTGTAGCGGTGAAATGCGTAGAGATCGGAAGGAACACCAGTGGCGAAGGCGGCCCTCTGGACTGCAACTGACGCTGAGACGCGAAAGCGTGGGGAGCACACAGGATTAGATACCCTGGTAGTCAACGC
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGEGGGGGGGEGGGGGGDGDGGGGGGGGGGGFDGGGGGGGGFFFFDFG7FFGGGGGGGGG7EGGGGGDGGEGGGGGG=EFGDGGFGGDEGGGGFFC5;EEDFEFGEGFCFGEECC8?5CEE*:5*;?FGGFGCCFGAFFGGGDGGFFGCDECGGGGE;EE8EC=390;575>8<+9FGGFC<8CGFF:9+9,<D5)
 @ITSLSUmock2p.ITS_M01380:138:000000000-C9GKM:1:1101:14440:2042 2:N:0
 CAAGTTACTTCCTCTAAATGACCAAGCCTAGTGTAGAACCATGTCGTCAGTGTCAGTCTGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAATGTAATACTACTAGTAATTATTAATATTATAATTTTGTCTATTAGCATCTTATTATAGATAGAAGATATTATTCATATTTCACTATCTTATACTGATATCAGCTTTATCAGATCACACTCTAGTGAAGATTGTTCTTAACTGAAATTTCCTTCTTCATACAGACACATTAATCTTACCTA
 +
 EFGGGGGGGGGCGGGGGFCFFFGGGGGFGGGGGGGGGGGFGGGGGGGFGFFFCFGGFFGGGGGGGGGFGGGGFGGGDG<FD@4@CFFGGGGCFFAFEFEG+,9,,,,99,,,5,,49,4,8,4,444,4,4,,,,,,,,,,,,,,8,,,,63,,,,,,,,376,3,,,,,,,8,,,,,,,,,+++++++++++++3++25+++0+*+0+*0+***))*0))1/+++**************.****.*******0*********/(,(/).)))1)).).).
-
+@M00773:480:000000000-BLYPT:1:2106:12063:1841 2:N:0:AGGCGACCTTA
+ACCCGCCAATTTCTTTGAGTTTCAACCTTGCGGCCGTACTCCCCAGGCGGGGCACTTACTCCGTTAGGTGCGGCACGGGAGGGGTCGATACCTCCCACACTTAGTGCCCATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGTCTCAGCGTCAGTTGCAGTCCAGAGGGCCGCCTTCGCCACTGGTGTTCCTTCCGAGCCCTACGCATTTCACCGCTACACCGGAAATTCCACCCTCCTCTCCTGCACTCAAGTCTGGCAGTAGCAGACGCCGTT
++
+CCCCCDGGGGGGGGGGGGG<CECGGGFGGGGGGGGGGGGGF@FGGGGGGFDGGGGCDFGGGGGGCGGGGFDGCFFGGCGEDGEF:FGGGGCGCFGGFFGG@EGGGGGGDGFGGCF7D>FGGG><FCEGCFEFGEE@<:CFGGGGGCGGCGFGEC<<EGG:C:E5FE*:?E8C?ECEGG88C;E9AFFFGF@:EF*;88*/A5EFG8*/ACC**:*7<00C:ED))(-7>)0)9DEDFFF>8=*0.6C75C>DD?:@*)9(41:??FFF(9:2<FF70?):A).3)(,46))5)..,3(,41
+@ITSLSUmock2p.ITS_M01384:138:000000000-C9GKM:1:1101:14440:2043 2:N:0
+ACCCGTCAATTTCTTTAAGTTTTAGCCTTGCGACCGTACTCCCCAGGCGGTGCACTTAGTGGTTTTCCGGCGACCCGGGCGGCGTCAGAGCCCCCCAAGTCTCGTGCACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCCTCAGCGTCAGTACCGGCCCAGCCACCCGTCTTCACCTTCGGCGTTCCTGTAGATATCTACGCATTTCACCGCTACACCTACAGTTCCGGTGGCGCCTACCGGCCTCAAGAAACGCAGTATGCCCAGCTATT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGFGGGGGGGGGGGG9FGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGCGFGFGGGGGGGGGGGGGGGGGDGGGDEEFGGGGGGGGGGGGFFGGG9EGFGGFCGGCGGGCCGEGGGEGFGGGG6B6*=EGGGGGGG8ECCEGGGGCFGDEEGGG?FGFGGC39:>EGGGGGGF7=9:A@FBF>DGCGFF=75C=DBCF74DFFFF*/91B>9>?9?>>:B?>F>FBB:??200:699>?AA2)34F?2))54

16_fastx_grep/tests/inputs/lsu.fq.2fa.out

@@ -0,0 +1,4 @@
+>ITSLSUmock2p.ITS_M01380:138:000000000-C9GKM:1:1101:14440:2042 2:N:0
+CAAGTTACTTCCTCTAAATGACCAAGCCTAGTGTAGAACCATGTCGTCAGTGTCAGTCTGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAATGTAATACTACTAGTAATTATTAATATTATAATTTTGTCTATTAGCATCTTATTATAGATAGAAGATATTATTCATATTTCACTATCTTATACTGATATCAGCTTTATCAGATCACACTCTAGTGAAGATTGTTCTTAACTGAAATTTCCTTCTTCATACAGACACATTAATCTTACCTA
+>ITSLSUmock2p.ITS_M01384:138:000000000-C9GKM:1:1101:14440:2043 2:N:0
+ACCCGTCAATTTCTTTAAGTTTTAGCCTTGCGACCGTACTCCCCAGGCGGTGCACTTAGTGGTTTTCCGGCGACCCGGGCGGCGTCAGAGCCCCCCAAGTCTCGTGCACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGTGCCTCAGCGTCAGTACCGGCCCAGCCACCCGTCTTCACCTTCGGCGTTCCTGTAGATATCTACGCATTTCACCGCTACACCTACAGTTCCGGTGGCGCCTACCGGCCTCAAGAAACGCAGTATGCCCAGCTATT