Merge branch 'update_tests' into 'main'

feat: added test_cli.py

See merge request !34

readsequencer/cli.py

@@ -4,35 +4,34 @@ from readsequencer.read_sequencer import ReadSequencer
 
 LOG = logging.getLogger(__name__)
 
-parser = argparse.ArgumentParser(
-    prog="read_sequencer",
-    description="Simulates sequencing of DNA sequences specified by an FASTA file.",
-)
 
-parser.add_argument("output", help="path to FASTA file")
-parser.add_argument("-i", "--input", default=None, help="path to FASTA file")
-parser.add_argument(
-    "-r", "--read-length", default=100, help="read length for sequencing", type=int
-)
-parser.add_argument(
-    "-n",
-    "--n_random",
-    default=100,
-    type=int,
-    help="n random sequences. Just used if input fasta file is not specified.",
-)
-parser.add_argument(
-    "-s",
-    "--chunk-size",
-    default=10000,
-    type=int,
-    help="chunk_size for batch processing",
-)
-
-args = parser.parse_args()
+def main():
+    parser = argparse.ArgumentParser(
+        prog="read_sequencer",
+        description="Simulates sequencing of DNA sequences specified by an FASTA file.",
+    )
 
+    parser.add_argument("output", help="path to FASTA file")
+    parser.add_argument("-i", "--input", default=None, help="path to FASTA file")
+    parser.add_argument(
+        "-r", "--read-length", default=100, help="read length for sequencing", type=int
+    )
+    parser.add_argument(
+        "-n",
+        "--n_random",
+        default=100,
+        type=int,
+        help="n random sequences. Just used if input fasta file is not specified.",
+    )
+    parser.add_argument(
+        "-s",
+        "--chunk-size",
+        default=10000,
+        type=int,
+        help="chunk_size for batch processing",
+    )
 
-def main():
+    args = parser.parse_args()
     LOG.info("Read sequencer started.")
     if args.input is not None:
         read_sequencer = ReadSequencer(

requirements-dev.txt

@@ -3,4 +3,5 @@ coverage
 flake8
 flake8-docstrings
 mypy
-pylint
+pylint
\ No newline at end of file
+cli_test_helpers
\ No newline at end of file

tests/fasta_testfile/test.fasta

->1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 481 bp
-tgagcactcggtgccaagggcggggatacacagatggttggctgatacaaccgggactta
-aattccctagactagatctgtgttggaacgcctctctacg
->2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 495 bp
-ctgaatcaggtgtaggttctttttacgtcgtttaaggagctacacggtatcttgttttca
-gttaaggtgccacacccccgggtggatcatccgtcagctt
->3|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 193 bp
-acttcagtactggaaggatctaggaaccattaatgcgagtgtggtgacgccagacgaccc
-ccggtgttctgccaccttctttggataggagaaccgtcac
->4|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 625 bp
-acgtctggagcgtgggttgacccctgtacatggttctttccggatccttaacgtgccgat
-acaactcaaaggtaactgtgcttaccacttccgaagctac
->5|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 845 bp
-agagcgtacggcgcgcatcgtataccctacgagggcggcgtgtggaggaacgctgggctg
-acactgtagaagattagatacacttgtccctaaaattaac
->6|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 703 bp
-tgcagtcgatgtgctattcgttttaggcagtctacgcgcttagtaactcccacggccata
-gacttatctcagacatggaccatgtcgatatcggacgccg
->7|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 243 bp
-actctttagaatgggtttcactaatagtacgtgcatacaatttcgtcagaaagggcgctt
-gctaagggacacggatcaatgatgaccagacttatggtgt
->8|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 863 bp
-attggcccggtccaggacagagccttatattgctactggtatgagaaccgttctgacgta
-aacttgatggctttacgcctgcacgggcttcatacacaca
->9|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 494 bp
-aagcgaaactcctagaacttcccatcaggcaatcgtgtcccacgaagcacggatactacg
-ggcactagttgaatggggggtttttttcgtaggtcgtaat
->10|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 86 bp
-atcctagcgccaaagatttactgttatggggtcgacgaacactagccgataatgccgtcc
-tgggatctctagcctagtattatgcgTCTTCGGAGCAGGG
->11|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 360 bp
-cgcctgagggtcctaaatctgacgtatgatcgaagagattggaaggtcccggcgggtcac
-cccacgttgcgatcatggccaaggccatggtttgctcaaa
->12|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 140 bp
-gaattcctggggatttactcacccccgaggcggacaagatttccagctggatcaccgagg
-gttacttaatcccttcgatgctttcaaaggccctaatcag
->13|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 832 bp
-aatactctcgttgaagcgtcggacagtaaagtgagagatttcggcccacggtagtcggac
-attctcagtggggagcgaagagttgcgcttagagccgacg
->14|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 296 bp
-atcggggtgcgaaatcccctgagctggttgactacatacgtaaccacgttccgtgcgtca
-tctaagcgtatcggctcatactggtggtaactagacttgg
->15|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 515 bp
-accttcaatttgttcgcccgggacaagtagaaattactgtaaactaaacttaacctattc
-cttgttaaagtccgcaccaagtgtactgtaagaatggtcg
->16|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 820 bp
-ccggctcaatcctgtagaaccgcgtacaacacacccaagctataccgcacacggcgcctt
-agcaaccactgcttatctgcgtattatacctttacaatca
->17|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 791 bp
-attgttagggcctgtccggaaaagatcaacggaagatattcaccagcacctatgctgact
-cacgtagttcccgacgttcagtcccctccaacgtggaagg
->18|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 328 bp
-accgattacaggcagtcggccttgtccgctcgtatatccagggatgttccaccgaaagtg
-ggagtgtggcacttattggtaaaaggcatttttacgaacg
->19|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
-ggagtggaaaattctgtagtccgttggcggcgaccgcaaaccagaataatatggtcacgt
-taggccctcgggccccttcatatgtacggagtcattgaat
->20|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 440 bp
-atcttaaacagcccaatcggctcgccgaccaatttcccgcttcacagtacgcggaagaat
-ctgcagatagaagtcagccctctcacgtcaataggaatgc
->21|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 840 bp
-cataactcgtgagtggccctgtacaagtcattgcatcacaatccttgcaatttgctcctt
-tggccaagcgtacaagaccccggacccatacgctcccggc
->22|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 234 bp
-caccgcgaaagtgactcagttttcccggtcttatcacggtcgttgtcgtccagattccgg
-ttgttaactgcgggagctataacacttattccttactgcg
->23|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 917 bp
-atcaagtgattacctggtaacccgccgctcttgcagtgttcaccctttgtgtcgtcttag
-tgtttgtacacgttaaggaaaagcgttagcttaaccatta
->24|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 676 bp
-cacacggcatcgcaaagcgagctatccagagatgatacatgtggttgaaggtgattgcgt
-caacatgggggttgctcagtttggttggtcaatcaacggt
->25|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 870 bp
-ctgatcaccaatagcttgcgcttaacacacgcgccttacaattatatgacgcccttgcca
-atgacagatagagccattaatcgtggaaaccaggcattta
->26|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 751 bp
-gggtgcgttatggggactaaagactgttactaccggtactccgccttatagagccgtcac
-gtattaatcagctatcaacagatactatcgtcacagccct
->27|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 574 bp
-gtactgcaccttgcactgctatctacaatgccgagggtcgccctagtgctttgcatgttt
-ggcctctacctacgagtctacgcgggcgtttttaagcaag
->28|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 169 bp
-agctccctaaacaacacccgcgtaaaaccttcagttatggtgccgactaaccctgtggat
-gtcttagcgctctcgttccgatgggtgctgatactagtaa
->29|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 408 bp
-tgcagtgatgcatcgataagaccgcatagttacctccttacaggtgacgctaggctaatt
-gggagtgctggcacttgtgccctacagtcaagcgctcacg
->30|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 52 bp
-caaagcgattcgggttaacgcacttaagagttcgacgtaggttagtcccctcCTTTTAGG
-TGTCTAACTAGAGAGGCGCCCTATTGGGCTCAGGATGACG
->31|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 581 bp
-tgctctgacgtgtaagcgccttcgataacgtctttgcagcgccccacaaagtaaggaccg
-gtctaacagggcttccgaatcaatagactgatagtaatgg
->32|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 249 bp
-gcggaactacctctctaagaccgcacaacaagtgtagtagatgaagatcacgcagagtgc
-tcggcactgcatttttatacgtcgaatcagaaacgaggtt
->33|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 297 bp
-gccctcgcgccagcttacttttagaaaacatcgaccggtaagagatacctgggtgagctg
-ggcttcacgacatgttcttaaatcaatactctaaatctgc
->34|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 573 bp
-gcctaggggtcttgaccacagggagtacgagcattgatcattggagcaggtggctaatat
-tgatagtggttagaccaccggcgcatcatcgtacgagcgc
->35|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 559 bp
-gaaaaagtcgccccattcagttacaatcgtcttcagaagccagctcggttggggctatct
-gcggggtaatgcaacagggggctaccagacggtaaaccag
->36|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 187 bp
-ctaagtccttatctatgatgcatctttcgttactgcgacaatatccgagacgagcagagt
-tacacgccgaggtgtaaacgaatacgattgctatatgcaa
->37|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 549 bp
-ttcatatggggatttggaatcgggtttgtgcggaatatgcccacgagactgcttatgtca
-acgagacgacccattgtcacgttgtaaggccaccaataac
->38|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 916 bp
-gtggcctaccataaatcaatttgggttaacgctctttgatctacgcactatgttgattca
-cttaccccttgtcaccgggcagaagagagccagtttaggt
->39|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 848 bp
-accccggtcgctttggccggtcgtagccctaatcaattctgttcgtatcactaaagtaac
-ggtttgaaatcctttgcaaacttgatctgggtatatgaac
->40|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 289 bp
-agagcaaaagaaagtctgctccgcgtgacacacttgctcgttgtagtaactgcacgcgcc
-gtctactcgacagggaccccccgtcggttcctctctatag
->41|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 642 bp
-ctggggaatgaccgtaccgatctaattccccgtcgaaaaacttatgacgcgcagttgtcc
-ttatgcttgagacatgaatccttgccccatattggcgatc
->42|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 993 bp
-gcaagaagccaaaaaccttgcaggaggtcatttaagtttacccgcgcataagcagagacg
-gacctctctgagatctcgcaccgcgcgcccggccggcact
->43|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 473 bp
-ggttgtccaggcgcgagcaagtagctgactcgctaatcttaacgagtattgcttaggact
-tccaaatactccaagacgtcaatacgctttatctttgtga
->44|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 272 bp
-gtagaacttgttccccatggacaatgctagttccgttaatgccaggtattcatgtgccaa
-gcgcctgcctggggaatacgagcctctctacaaacttacg
->45|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 860 bp
-aaaagcatcactctaacgacgctaccgtctgaatagatcaagattgctatcggttcgacc
-ttgatcgcatgtgaacccgcccaaaaacccgtctcgacaa
->46|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 884 bp
-aagcctctacaggctctgcggtttggctttacttaacggtgagtcaggaaaacattactg
-ctacgttcaccgtgttcagagatagagagtacattaggga
->47|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 888 bp
-gcgccttgaagaggcgaggtctaaaggcaaaaatttagatccgccctatgagacggccga
-cgcggagaattccctaaccactattgtcctctgcatcgat
->48|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 588 bp
-catcaagatgggttacgtaggaccgagattcagtctctgggttagagccgacagcggggc
-cgctacatagtacacggcgaggaatgcggggttgggctga
->49|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 626 bp
-taacctcagtctcgttcccccctcggtagttcggacccttattcgcttatctcacattca
-tcactgtagaccaaggaccgggcatacttgcggatatcta
->50|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 214 bp
-taactgtcggtcactgctcatcccgactagttcggctcactagacttactcgcggaagcg
-agaagtaggacgtcgtgtaatactccaacgtcgttacgca

tests/test_cli.py

+import readsequencer.cli
+import pytest
+from cli_test_helpers import ArgvContext, shell
+import os
+import glob
+def test_entrypoint():
+    """
+    Is entrypoint script installed? (setup.py)
+    """
+    result = shell('readsequencer --help')
+    assert result.exit_code == 0
+
+def test_usage_no_args():
+    """
+    Does CLI abort w/o arguments, displaying usage instructions?
+    """
+    with ArgvContext('readsequencer'), pytest.raises(SystemExit):
+        readsequencer.cli.main()
+
+    result = shell('readsequencer')
+
+    assert 'usage:' in result.stderr

tests/test_read_sequencer.py

 import pytest
-
+import os
+import glob
 from readsequencer.read_sequencer import ReadSequencer
 
-
-sequencer = ReadSequencer()
-
-
-def test_chunksize():
+def test_init_default():
+    sequencer = ReadSequencer()
+    assert sequencer.fasta is None
+    assert sequencer.read_length == 150
+    assert sequencer.output is None
     assert sequencer.chunk_size == 10000
+    assert sequencer.bases == ("A", "T", "C", "G")
 
 
-def test_run_Input():
-    assert sequencer.fasta == None
+def test_run_random():
+    sequencer = ReadSequencer(
+        output="./tests/fasta_testfile/results.fasta")
+    sequencer.define_random_sequences(n_seq=100)
+    assert sequencer.output == "./tests/fasta_testfile/results.fasta"
     assert sequencer.read_length == 150
-    assert sequencer.output == None
     assert sequencer.chunk_size == 10000
+    assert sequencer.fasta is None
+    sequencer.run_sequencing()
+    os.remove("./tests/fasta_testfile/results.fasta")
+
+def test_run_random_chunks():
+    # setup class
+    sequencer = ReadSequencer(
+        output="./tests/fasta_testfile/results.fasta",
+        read_length=150,
+        chunk_size=10)
+    sequencer.define_random_sequences(n_seq=50)
+    # run sequencing
+    sequencer.run_sequencing()
+    # check results
+    assert sequencer.output == "./tests/fasta_testfile/results.fasta"
+    assert sequencer.read_length == 150
+    assert sequencer.n_sequences == 50
+    # clean up
+    result_files = glob.glob("./tests/fasta_testfile/results*")
+    assert len(result_files) == 5
+    for file in result_files:
+        os.remove(file)
+
 
+def test_run_sequencing():
+    sequencer = ReadSequencer(
+        fasta="./tests/fasta_testfile/50_seqs_50_1000_bp.fasta",
+        output="./tests/fasta_testfile/results.fasta",
+        read_length=50,
+        chunk_size=10000)
+    sequencer.get_n_sequences()
+    sequencer.run_sequencing()
+    assert sequencer.output == "./tests/fasta_testfile/results.fasta"
+    assert sequencer.read_length == 50
+    assert sequencer.n_sequences == 50
+    result_file = glob.glob("./tests/fasta_testfile/results*")
+    assert len(result_file) == 1
+    for file in result_file:
+        os.remove(file)
 
-def test_run_Random():
-    assert ReadSequencer(
-        output="./tests/fasta_testfile/results.fasta"
-    ).output == "./tests/fasta_testfile/results.fasta"
-    assert ReadSequencer(read_length=1000).read_length == 1000
-    assert ReadSequencer(chunk_size=10000).chunk_size == 10000
-    assert ReadSequencer(
+def test_run_sequencing_chunks():
+    # setup class
+    sequencer = ReadSequencer(
+        fasta="./tests/fasta_testfile/50_seqs_50_1000_bp.fasta",
         output="./tests/fasta_testfile/results.fasta",
-        read_length=1000,
-        chunk_size=10000).fasta == None
+        read_length=150,
+        chunk_size=10)
+    # run sequencing
+    sequencer.get_n_sequences()
+    sequencer.run_sequencing()
+    # check results
+    assert sequencer.output == "./tests/fasta_testfile/results.fasta"
+    assert sequencer.read_length == 150
+    assert sequencer.n_sequences == 50
+    # clean up
+    result_files = glob.glob("./tests/fasta_testfile/results*")
+    assert len(result_files) == 5
+    for file in result_files:
+        os.remove(file)
+
+
+