Added in strutured tests for the command-line tools in metapredict. F…

…or now only metapredict-predict-idrs has tests but plan to add additional tests in going forward

.gitignore

@@ -8,6 +8,8 @@ __pycache__/
 .DS_Store
 *~
 
+metapredict/tests/test_cli/output/*
+
 # cython-specific stuff
 metapredict/backend/cython/domain_definition.c
 metapredict/backend/cython/domain_definition.html

metapredict/tests/test_cli/__init__.py

@@ -0,0 +1,42 @@
+import subprocess
+import pytest
+import os
+
+## Init file for the CLI tests in metapredict
+##
+##
+##
+
+def run_command(cmd, outfile=None):
+    """
+    This function is a catch-all function that 
+    
+    1. Deletes a putative output file 
+    2. Runs 
+
+Function to run the command-line tool and return the output."""
+
+
+    # if an outpufile was passed, try and delete and then check
+    # it was actually deleted
+    if outfile:
+        try:
+            os.remove(outfile)
+        except Exception:
+            pass
+
+        # check the file is missing. This raises an exception if the file doesn't get removed
+        if os.path.isfile(outfile):
+            raise Exception('When preparing to run the command, the output file was not deleted')
+
+    # run the command using subproccess
+    result = subprocess.run(cmd, shell=True, capture_output=True, text=True)
+
+    # return the output from subprocess, which has the following dot-variables associated
+    # with it:
+    #
+    # .stdout (standard output to screen)
+    # .stderr (standard error to screen)
+    # .returncode (command return code; 0 = no errror)
+    #
+    return result

metapredict/tests/test_cli/input/three_seqs.fasta

@@ -0,0 +1,24 @@
+>Q8N6T3
+MASPRTRKVLKEVRVQDENNVCFECGAFNPQWVSVTYGIWICLECSGRHRGLGVHLSFVRSVTMDKWKDIELEKMKAGGNAKFREFLESQEDYDPCWSLQEKYNSRAAALFRDKVVALAEGREWSLESSPAQNWTPPQPRTLPSMVHRVSGQPQSVTASSDKAFEDWLNDDLGSYQGAQGNRYVGFGNTPPPQKKEDDFLNNAMSSLYSGWSSFTTGASRFASAAKEGATKFGSQASQKASELGHSLNENVLKPAQEKVKEGKIFDDVSSGVSQLASKVQGVGSKGWRDVTTFFSGKAEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTKTRKSPSSDSWTCADTSTERRSSDSWEVWGSASTNRNSNSDGGEGGEGTKKAVPPAVPTDDGWDNQNW
+
+>p53
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
+DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
+SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
+RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
+SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
+PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
+GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+
+>sp|P0DMV8|HS71A_HUMAN Heat shock 70 kDa protein 1A OS=Homo sapiens OX=9606 GN=HSPA1A PE=1 SV=1
+MAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVA
+LNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEIS
+SMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAA
+IAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNH
+FVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRA
+RFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLN
+KSINPDEAVAYGAAVQAAILMGDKSENVQDLLLLDVAPLSLGLETAGGVMTALIKRNSTI
+PTKQTQIFTTYSDNQPGVLIQVYEGERAMTKDNNLLGRFELSGIPPAPRGVPQIEVTFDI
+DANGILNVTATDKSTGKANKITITNDKGRLSKEEIERMVQEAEKYKAEDEVQRERVSAKN
+ALESYAFNMKSAVEDEGLKGKISEADKKKVLDKCQEVISWLDANTLAEKDEFEHKRKELE
+QVCNPIISGLYQGAGGPGPGGFGAQGPKGGSGSGPTIEEVD

metapredict/tests/test_cli/test_metapredict-predict-idrs.py

@@ -0,0 +1,175 @@
+import subprocess
+import pytest
+import protfasta
+import os
+
+from . import run_command
+
+
+
+def test_metapredict_predict_IDRs_1():
+    """
+    Basic test for the simplest version of
+
+    """
+
+
+    precomputed_idrs = {'Q8N6T3 IDR_START=123 IDR_END=406': 'WSLESSPAQNWTPPQPRTLPSMVHRVSGQPQSVTASSDKAFEDWLNDDLGSYQGAQGNRYVGFGNTPPPQKKEDDFLNNAMSSLYSGWSSFTTGASRFASAAKEGATKFGSQASQKASELGHSLNENVLKPAQEKVKEGKIFDDVSSGVSQLASKVQGVGSKGWRDVTTFFSGKAEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTKTRKSPSSDSWTCADTSTERRSSDSWEVWGSASTNRNSNSDGGEGGEGTKKAVPPAVPTDDGWDNQNW',
+                        'p53 IDR_START=0 IDR_END=101': 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQK',
+                        'p53 IDR_START=280 IDR_END=393': 'DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD',
+                        'sp|P0DMV8|HS71A_HUMAN Heat shock 70 kDa protein 1A OS=Homo sapiens OX=9606 GN=HSPA1A PE=1 SV=1 IDR_START=607 IDR_END=641': 'SGLYQGAGGPGPGGFGAQGPKGGSGSGPTIEEVD'}
+
+    # remove output if there already
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+
+    ## check that there was no error
+    # no error
+    assert result.returncode == 0
+
+    ## check nothing was printed to screen
+    # no output
+    assert "" in result.stdout
+
+    ## Now we check the command actually worked. Read in the putative
+    # outfile generated by the command
+    # read 
+    D = protfasta.read_fasta('output/test_1.fasta')
+
+    ## assert this matches precomputed predictions
+    for d in D:
+        assert precomputed_idrs[d] == D[d]
+
+
+
+def test_metapredict_predict_IDRs_2():
+    """
+    Basic test for the simplest version of
+
+    """
+
+
+    # check we can compute for different thresholds 
+    precomputed_idrs = {'Q8N6T3 IDR_START=141 IDR_END=406': 'LPSMVHRVSGQPQSVTASSDKAFEDWLNDDLGSYQGAQGNRYVGFGNTPPPQKKEDDFLNNAMSSLYSGWSSFTTGASRFASAAKEGATKFGSQASQKASELGHSLNENVLKPAQEKVKEGKIFDDVSSGVSQLASKVQGVGSKGWRDVTTFFSGKAEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTKTRKSPSSDSWTCADTSTERRSSDSWEVWGSASTNRNSNSDGGEGGEGTKKAVPPAVPTDDGWDNQNW', 'p53 IDR_START=64 IDR_END=89': 'RMPEAAPPVAPAPAAPTPAAPAPAP', 'p53 IDR_START=295 IDR_END=318': 'HHELPPGSTKRALPNNTSSSPQP', 'p53 IDR_START=358 IDR_END=393': 'PGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD', 'sp|P0DMV8|HS71A_HUMAN Heat shock 70 kDa protein 1A OS=Homo sapiens OX=9606 GN=HSPA1A PE=1 SV=1 IDR_START=615 IDR_END=641': 'GPGPGGFGAQGPKGGSGSGPTIEEVD'}
+
+    # remove output if there already
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --threshold 0.9'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+
+    ## check that there was no error
+    # no error
+    assert result.returncode == 0
+
+    ## check nothing was printed to screen
+    # no output
+    assert "" in result.stdout
+
+    ## Now we check the command actually worked. Read in the putative
+    # outfile generated by the command
+    # read 
+    D = protfasta.read_fasta('output/test_1.fasta')
+
+    ## assert this matches precomputed predictions
+    for d in D:
+        assert precomputed_idrs[d] == D[d]
+
+def test_metapredict_predict_IDRs_legacy():
+    """
+    Basic test for the simplest version of
+
+    """
+
+
+    # check we can compute for different thresholds 
+    precomputed_idrs = {'Q8N6T3 IDR_START=124 IDR_END=406': 'SLESSPAQNWTPPQPRTLPSMVHRVSGQPQSVTASSDKAFEDWLNDDLGSYQGAQGNRYVGFGNTPPPQKKEDDFLNNAMSSLYSGWSSFTTGASRFASAAKEGATKFGSQASQKASELGHSLNENVLKPAQEKVKEGKIFDDVSSGVSQLASKVQGVGSKGWRDVTTFFSGKAEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTKTRKSPSSDSWTCADTSTERRSSDSWEVWGSASTNRNSNSDGGEGGEGTKKAVPPAVPTDDGWDNQNW', 'p53 IDR_START=0 IDR_END=102': 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKT', 'p53 IDR_START=277 IDR_END=393': 'PGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD', 'sp|P0DMV8|HS71A_HUMAN Heat shock 70 kDa protein 1A OS=Homo sapiens OX=9606 GN=HSPA1A PE=1 SV=1 IDR_START=610 IDR_END=641': 'YQGAGGPGPGGFGAQGPKGGSGSGPTIEEVD'}
+
+    # remove output if there already
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --legacy'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+
+    ## check that there was no error
+    # no error
+    assert result.returncode == 0
+
+    ## check nothing was printed to screen
+    # no output
+    assert "" in result.stdout
+
+    ## Now we check the command actually worked. Read in the putative
+    # outfile generated by the command
+    # read 
+    D = protfasta.read_fasta('output/test_1.fasta')
+
+    ## assert this matches precomputed predictions
+    for d in D:
+        assert precomputed_idrs[d] == D[d]
+
+
+def test_metapredict_predict_IDRs_test_invalid_sequence_actions():
+    #
+    # Not super sophisticated, but checks that the different invalid sequence actions
+    # perported to work can at least be passed without causing an issue
+    #
+
+
+    def check_results():
+        precomputed_idrs = {'Q8N6T3 IDR_START=123 IDR_END=406': 'WSLESSPAQNWTPPQPRTLPSMVHRVSGQPQSVTASSDKAFEDWLNDDLGSYQGAQGNRYVGFGNTPPPQKKEDDFLNNAMSSLYSGWSSFTTGASRFASAAKEGATKFGSQASQKASELGHSLNENVLKPAQEKVKEGKIFDDVSSGVSQLASKVQGVGSKGWRDVTTFFSGKAEGPLDSPSEGHSYQNSGLDHFQNSNIDQSFWETFGSAEPTKTRKSPSSDSWTCADTSTERRSSDSWEVWGSASTNRNSNSDGGEGGEGTKKAVPPAVPTDDGWDNQNW',
+                            'p53 IDR_START=0 IDR_END=101': 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQK',
+                            'p53 IDR_START=280 IDR_END=393': 'DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD',
+                            'sp|P0DMV8|HS71A_HUMAN Heat shock 70 kDa protein 1A OS=Homo sapiens OX=9606 GN=HSPA1A PE=1 SV=1 IDR_START=607 IDR_END=641': 'SGLYQGAGGPGPGGFGAQGPKGGSGSGPTIEEVD'}
+        D = protfasta.read_fasta('output/test_1.fasta')
+
+        ## assert this matches precomputed predictions
+        for d in D:
+            assert precomputed_idrs[d] == D[d]
+
+
+
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action ignore'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+    assert result.returncode == 0
+    check_results()
+
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action fail'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+    assert result.returncode == 0
+    check_results()
+
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action remove'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+    assert result.returncode == 0
+    check_results()
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action convert-ignore'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+    assert result.returncode == 0
+    check_results()
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action convert-remove'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+    assert result.returncode == 0
+    check_results()
+
+
+    cmd = 'metapredict-predict-idrs input/three_seqs.fasta -o output/test_1.fasta --invalid-sequence-action FAKE-ACTION'
+    outfile = 'output/test_1.fasta'
+    result = run_command(cmd, outfile)
+
+    # expect this to be 1 because error is raised passing a bad action
+    assert result.returncode == 1
+
+