diff --git a/readsequencer/cli.py b/readsequencer/cli.py
index ee221c9961b25181055757da95d323cdeeaa5689..76afc5a934c4a7f3f9a082fd53cc5a27e4078f0c 100644
--- a/readsequencer/cli.py
+++ b/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(
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 1d44627feec16e03be395a6bef6249c9f5be1a58..36ace6490a2b11b3c74737db10abcbfc8067af35 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -3,4 +3,5 @@ coverage
flake8
flake8-docstrings
mypy
-pylint
\ No newline at end of file
+pylint
+cli_test_helpers
\ No newline at end of file
diff --git a/tests/fasta_testfile/test.fasta b/tests/fasta_testfile/test.fasta
deleted file mode 100644
index 6aa3033526931a94577fcf3ac506baaa0a7a0283..0000000000000000000000000000000000000000
--- a/tests/fasta_testfile/test.fasta
+++ /dev/null
@@ -1,150 +0,0 @@
->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
diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000000000000000000000000000000000000..6cb9ae1d6146a9045255f46c32e764b2ce18c516
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,22 @@
+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
diff --git a/tests/test_read_sequencer.py b/tests/test_read_sequencer.py
index a50af538b00e86ce12b004376a45b2ba1c496e3b..7157ccd670226bfe55479379fc8fea87b90ff861 100644
--- a/tests/test_read_sequencer.py
+++ b/tests/test_read_sequencer.py
@@ -1,29 +1,83 @@
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)
+
+
+