set some unit tests

JLSteenwyk · Aug 8, 2024 · 9f54970 · 9f54970
1 parent 68ee877
commit 9f54970
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Showing 7 changed files with 66 additions and 20 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,6 +20,17 @@ jobs:
         # install deps for tests
         pip install pytest
         pip install pytest-cov
+    - name: Install HMMER
+      run: |
+        brew install hmmer
+    - name: Install MCL
+      run: |
+        mkdir installmcl
+        cd installmcl
+        wget https://raw.githubusercontent.com/micans/mcl/main/install-this-mcl.sh -o install-this-mcl
+        chmod u+x install-this-mcl.sh
+        ./install-this-mcl.sh
+        mcl --version
     - name: Run tests
       run: |
         make test.fast
@@ -41,6 +52,17 @@ jobs:
         # install test dependencies
         pip install pytest
         pip install pytest-cov
+    - name: Install HMMER
+      run: |
+        brew install hmmer
+    - name: Install MCL
+      run: |
+        mkdir installmcl
+        cd installmcl
+        wget https://raw.githubusercontent.com/micans/mcl/main/install-this-mcl.sh -o install-this-mcl
+        chmod u+x install-this-mcl.sh
+        ./install-this-mcl.sh
+        mcl --version
     - name: Generate coverage report
       run: |
         make test.coverage

diff --git a/orthohmm/args_processing.py b/orthohmm/args_processing.py
@@ -1,4 +1,5 @@
 from distutils.spawn import find_executable
+import shutil
 import logging
 import multiprocessing
 import os.path
@@ -27,7 +28,7 @@ def process_args(args) -> dict:
 
     if args.phmmer:
         phmmer = args.phmmer
-        if not os.path.isfile(phmmer):
+        if not shutil.which(phmmer):
             logger.warning(f"phmmer can't be found at {phmmer}.")
             sys.exit()
     else:
@@ -50,7 +51,7 @@ def process_args(args) -> dict:
 
     if args.mcl:
         mcl = args.mcl
-        if not os.path.isfile(mcl):
+        if not shutil.which(mcl):
             logger.warning(f"mcl can't be found at {mcl}.")
             sys.exit()
     else:

diff --git a/orthohmm/helpers.py b/orthohmm/helpers.py
@@ -2,8 +2,6 @@
 import multiprocessing
 import os
 import subprocess
-import sys
-import time
 from typing import Tuple
 
 from Bio import SeqIO
@@ -31,6 +29,7 @@ def run_phmmer(
     pool.join()
 
 
+# TODO: write unit test
 def calculate_sequence_lengths(
     fasta_directory: str,
     file: str,
@@ -56,9 +55,10 @@ def calculate_sequence_lengths(
     return sequence_lengths
 
 
+# TODO: write unit test
 def get_best_hits(
     df: pd.DataFrame
-) -> pd.DataFrame:
+) -> Tuple[dict, dict]:
     best_hits = df.loc[df.groupby("query name")["norm_score"].idxmax()]
     return best_hits.set_index("query name")["target name"].to_dict(), \
         best_hits.set_index("query name")["norm_score"].to_dict()
@@ -219,9 +219,10 @@ def determine_network_edges(
 def execute_mcl(
     mcl: str,
     inflation_value: float,
+    cpu: int,
     output_directory: str,
 ) -> None:
-    cmd = f"{mcl} {output_directory}/working_dir/orthohmm_edges.txt --abc -I {inflation_value} -o {output_directory}/working_dir/orthohmm_edges_clustered.txt"
+    cmd = f"{mcl} {output_directory}/working_dir/orthohmm_edges.txt -te {cpu} --abc -I {inflation_value} -o {output_directory}/working_dir/orthohmm_edges_clustered.txt"
     subprocess.run(
         cmd,
         shell=True,

diff --git a/orthohmm/orthohmm.py b/orthohmm/orthohmm.py
@@ -34,7 +34,7 @@ def execute(
     mcl: str,
     inflation_value: float,
     **kwargs,
-):
+) -> None:
     print(textwrap.dedent(
             f"""\
           ____       _   _           _    _ __  __ __  __ 
@@ -62,6 +62,18 @@ def execute(
         "reg", "clu", "ov", "env", "dom", "rep", "inc", "description of target"
     ]
 
+    # # wrap execute() in try, except, and finally
+    # try:
+    #     do_something()
+    # except Exception as e:
+    #     logger.error(e)
+    # finally:  # guaranteed to execute
+    #     # if I have the temp directory, delete it
+    #     do_cleanup()
+
+    # TODO: support specific temporary directory supplied by user
+    # Default /tmp/orthohmm-v489q48710ds
+    # v489q48710ds should be a random string
     # create working directory
     if not os.path.isdir(f"{output_directory}/working_dir"):
         os.mkdir(f"{output_directory}/working_dir")
@@ -120,7 +132,7 @@ def execute(
 
     # Step 4: Conduct mcl clustering
     print("Step 4/6: Conducting clustering")
-    execute_mcl(mcl, inflation_value, output_directory)
+    execute_mcl(mcl, inflation_value, cpu, output_directory)
     print("          Completed!\n")
 
     # Step 5: Write out orthogroup files

diff --git a/tests/expected/orthohmm_single_copy_orthogroups/OG2.fa b/tests/expected/orthohmm_single_copy_orthogroups/OG2.fa
@@ -1,4 +1,4 @@
->ENSMUSP00000058613
+>Mus_musculus.GRCm38.pep.all|ENSMUSP00000058613
 MATRSSRRESRLPFLFALVALLPRGALGGGWTQRLHGGPAPLPQDRGFFVVQGDPRDLRLGTHGDAPGAS
 PAARKPLRTRRSAALQPQPIQVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALARPKSSDVYVSYD
 YGKSFSKISEKLNFGVGNNSEAVISQFYHSPADNKRYIFVDAYAQYLWITFDFCSTIHGFSIPFRAADLL
@@ -31,7 +31,7 @@ DQDLFYAIAVKDLIRKTDRSYKVRSRNSTVEYSLSKLEPGGKYHIIVQLGNMSKDSSIKITTVSLSAPDA
 LKIITENDHVLLFWKSLALKEKQFNETRGYEIHMSDSAVNLTAYLGNTTDNFFKVSNLKMGHNYTFTVQA
 RCLFGSQICGEPAVLLYDELSSGADAAVIQAARSTDVAAVVVPILFLILLSLGVGFAILYTKHRRLQSSF
 SAFANSHYSSRLGSAIFSSGDDLGEDDEDAPMITGFSDDVPMVIA
->ENSCAFP00000017344
+>Canis_familiaris.CanFam3.1.pep.all|ENSCAFP00000017344
 MATRSSRRESRLPFLLALVALLPPGAVCAAGAQTLLGGRAPLPQERGVRVLRGEARGGPRGAAEAPPRRR
 RSAALQPEPLQVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALARPRSSDVYVSYDYGKSFKRISE
 KLNFGEGNSSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLLLHSKASDLLL
@@ -64,7 +64,7 @@ DLIRKSDRSYKIKSRNSTVEYTLNKLEPGGKYHIIVQLGNMSKDSSIKITTVSLSAPDALKIITENDHVL
 LFWKSLALKEKHFNESRGYEIHMFDSAMNISAYLGNTTDNFFKISNLKLGHNYTFTVQARCLFGSQICGE
 PAVLLYDELGSGGGASAFQAARSTDVAAVVVPILFLILLSLGVGFAILYTKHRRLQSSFTAFANSHYSSR
 LGSAIFSSGDDLGEDDEDAPMITGFSDDVPMVIA
->ENSTNIP00000017394
+>Tetraodon_nigroviridis.TETRAODON8.pep.all|ENSTNIP00000017394
 MAMRRPAAPQPPARSALCLLLLLCVSGSRSSNLHLRAGPARPQNRGFFTVDAIADPAGGDGAARAAAGGA
 YPPRRSPRSSGESAMPKVYGQANLNDSHNQMVVHWAGEKSNVIVALARDSTGSTGPKSSSVYVSYDYGAS
 FTQVSDKFRPPADGTGAEDTPVISQFYHSPADNKRYLFVDSGSRVLWSSLDFCRSVRSFRLPFRPSDLLL
@@ -97,7 +97,7 @@ YDSPDEPLMYAIHVRDAVRKTERDYKVTTQNNTVEYLLRGLEPGGRYSVSVRLRNMSKEASFSLSTVPLP
 APEALKILTEDDHVFLFWKSLAVREKGFDEARGYEVHVYDSTTNQTSYLGNTTETYLRVSSLQPGHNYTF
 SVQARCLVGGQLCGEAALLLYDQLTAEGGDAAGSGQRSGDMAAVVVPVLFMLLLGVCGGLVILYLRHRRL
 QNNFTAFANSHYNSRLGSAIFSSGDELGDDDEDAPMISGFSDDVPMVIA
->ENSPTRP00000007532
+>Pan_troglodytes.Pan_tro_3.0.pep.all|ENSPTRP00000007532
 MATRSSRRESRLPFLFTLVALLPPGALCEVWTQRLHGGSAPLPQDRGFLVVQGDPRELRLWERGDARGAS
 RADEKPLRRKRSAALQPEPIKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALARPKSSDVYVSYD
 YGKSFKKISDKLNFGVGNRSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLL
@@ -130,7 +130,7 @@ QDLLYAIAVKDLIRKTDRSYKVKSRNSTVEYTLNKLEPGGKYHIIVQLGNMSKDSSIKITTVSLSAPDAL
 KIITENDHVLLFWKSLALKEKHFNESRGYEIHMFDSAMNITAYLGNTTDNFFKISNLKMGHNYTFTVQAR
 CLFGSQICGEPAILLYDELGSGADASATQAARSTDVAAVVVPILFLILLSLGVGFAILYTKHRRLQSSFT
 AFANSHYSSRLGSAIFSSGDDLGEDDEDAPMITGFSDDVPMVIA
->ENSDARP00000129655
+>Danio_rerio.GRCz11.pep.all|ENSDARP00000129655
 MASGQTRKMLALSRCAIYLLLLLVPAAISSTLRLHHDQRFVLPQDRGFSLVSAHLEPAESRVVRLEREVR
 EASAAHQLRVRRNAAGAPVPNVYGMANLNDSHNQMVVHWAGEKSDVIVALARDSVGATDPKTSSVYVSYD
 YGANFTPVSEKFQLPREQEDKKQVISQFYHSPADNKRYLFTDTTNSYLWNTFDFCKTVQGFSIPFKPTDL
@@ -163,7 +163,7 @@ TYAVHVRDTVRKTESDYKVITQNNTVEYTLKGLEPAGRYSITIRLLNMSKEASYTLSTVPLPAPEALKIL
 EEEDHVFLFWKSLAVKDRTFNESRGYEVYVHDSVTNSTKCLGNTTETFFRINSLLAGHNYTFSVRARCLL
 SNQLCGESAVLLYDELGKAAGQNDAASQSGKSEDMAAIVVPVLFLLLVGVCGGLVVLYLRHRRLQHSFTA
 FANSHYNSRLGSAIFSSGDELGDDDEDAPMISGFSDDVPMVIA
->ENSP00000260197
+>Homo_sapiens.GRCh38.pep.all|ENSP00000260197
 MATRSSRRESRLPFLFTLVALLPPGALCEVWTQRLHGGSAPLPQDRGFLVVQGDPRELRLWARGDARGAS
 RADEKPLRRKRSAALQPEPIKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALARPKSSDVYVSYD
 YGKSFKKISDKLNFGLGNRSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLL
@@ -196,7 +196,7 @@ QDLLYAVAVKDLIRKTDRSYKVKSRNSTVEYTLNKLEPGGKYHIIVQLGNMSKDSSIKITTVSLSAPDAL
 KIITENDHVLLFWKSLALKEKHFNESRGYEIHMFDSAMNITAYLGNTTDNFFKISNLKMGHNYTFTVQAR
 CLFGNQICGEPAILLYDELGSGADASATQAARSTDVAAVVVPILFLILLSLGVGFAILYTKHRRLQSSFT
 AFANSHYSSRLGSAIFSSGDDLGEDDEDAPMITGFSDDVPMVIA
->ENSCINP00000024362
+>Ciona_intestinalis.KH.pep.all|ENSCINP00000024362
 AELHDGNTQLVIHWAGLNSSNIAVLTKNQRSGSVRTSNVYFSYDYGATFSRKISSSSSGSLPQARISDFV
 HAYHNIDRYIFMDRHTPSLFTTTDSGRNFHHVTPLPFTPSTLTINPVKPWIVIGHDETGKNLFKSSDFGS
 SWIRIQTRVEKYEFGFSAATSQFETNPDTLYVRRTNLDGSYTILRSETYFQNDIREQVVISHVTDFLLMN
@@ -218,7 +218,7 @@ PIYILMGGKFSDLSVVAASSLSVSSNVFLHTATTPTTPIPTLPPHECGSTHLPCRTSGMCYPLVWRCDGV
 DDCGDDSDEFDCNTTSSTPTAHHLPCFSDLLQFRCANQLCIFRFYKCDGDNDCGDWSDERGCPNGNMSSV
 PSVAPPTANPMHCVDGYTYCGVGGTRTCILDRFVCDGDNDCGNNADEKNCGQQCGTDQFTCHNGRCIALS
 LHCNGIDDCSDNSDENCTTVDCGPSFYRCAADNHCILRSSVCNGYPDCSDNADEQGCAE
->ENSGALP00000046461
+>Gallus_gallus.GRCg6a.pep.all|ENSGALP00000046461
 MGCSQQVLLHHLLPGEGLSQCFNHLAAHSEHKDPSGGPCPRALTLTLTPQGPLAPGIVSVLFRFECLIPP
 QQDGTPCSGSRCPFPLQVSLNDSHNQMVVHWAGEKSNVIVALARDSLSLLGPKNSDVYISYDYGKSFKKI
 SERFSFGDGNSSAVAIAQFYHSPANNQRYIFVDAFVPYLWITTDFCKSIQGFSIPFRAADLLLHSRNPNL
@@ -251,7 +251,7 @@ KDLVRKTDKIYKVKTRNSTVEYTIKKLEPGGKYHVIVQLGNMSKESSMMINTVPLSAPDALKIITENDHI
 LLFWKSLALKESNFNESRGYEVLMFDSLVNRTAYLGNTTENFFKVSNLKIGHNYSFAVRARCLYGGQMCG
 EPATLLYDELGAGEDSSESKLGRSTDVAAIVVPILFLLLVALGAGFVVLYTRHRRLQSSFTAFANSHYSS
 RLGSAIFSSGDDLGDEDDEAPMITGFSDDVPMVIA
->ENSMODP00000016287
+>Monodelphis_domestica.ASM229v1.pep.all|ENSMODP00000016287
 MATGSSCGEPRLPLLFALVALLPPWALTETRSLQSAGGRAALPQERGFFVLQGGMGQPWLRARRDAAGGA
 SRPAGEPRPPRTRRSAAAHQLEPVKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALLGPKSSDVY
 VSYDYGKTFQKISEKFNFGMGNSSEAVIAQFYHSPADNKRYIFVDAYAQYLWITFDFCSTVQGFSIPFRA

diff --git a/tests/unit/test_args_parsing.py b/tests/unit/test_args_parsing.py
@@ -33,6 +33,16 @@ def test_process_args_output_directory_dne(self, args):
         with pytest.raises(SystemExit):
             process_args(args)
 
+    def test_process_args_phmmer_not_installed(self, args):
+        args.phmmer = "phmmer-that-dne"
+        with pytest.raises(SystemExit):
+            process_args(args)
+
+    def test_process_args_mcl_not_installed(self, args):
+        args.mcl = "mcl-that-dne"
+        with pytest.raises(SystemExit):
+            process_args(args)
+
     def test_process_args_default_single_copy_threshold(self, args):
         args.single_copy_threshold = None
         res = process_args(args)

diff --git a/tests/unit/test_parser.py b/tests/unit/test_parser.py
@@ -10,6 +10,6 @@ def parser():
 
 class TestParser(object):
     def test_required_only(self, parser):
-        input_directory = "./tests/samples/"
-        parsed = parser.parse_args([input_directory])
-        assert parsed.input == input_directory
+        fasta_directory = "./tests/samples/"
+        parsed = parser.parse_args([fasta_directory])
+        assert parsed.fasta_directory == fasta_directory