Merge pull request #30 from gbouras13/dev

v0.1.3

HISTORY.md

@@ -1,5 +1,11 @@
 # History
 
+0.1.3 (2024-03-19)
+------------------
+
+* Adds compability with Apple Silicon (M1/M2/M3) GPUs
+* Fixes memory issue for `phold plot` with many contigs
+
 0.1.2 (2024-03-06)
 ------------------
 

README.md

@@ -60,12 +60,21 @@ mamba create -n pholdENV -c conda-forge -c bioconda phold
 
 To utilise `phold` with GPU, a GPU compatible version of `pytorch` must be installed. By default conda/mamba will install a CPU-only version. 
 
-Therefore, if you have an NVIDIA GPU, please try:
+If you have an NVIDIA GPU, please try:
 
 ```bash
 mamba create -n pholdENV -c conda-forge -c bioconda phold pytorch=*=cuda*
 ```
 
+If you have a Mac running an Apple Silicon chip (M1/M2/M3), `phold` should be able to use the GPU. Please try:
+
+```bash
+mamba create -n pholdENV python==3.11  
+conda activate pholdENV
+mamba install pytorch::pytorch torchvision torchaudio -c pytorch 
+mamba install -c conda-forge -c bioconda phold 
+```
+
 If you are having trouble with `pytorch` see [this link](https://pytorch.org) for more instructions. If you have an older version of CUDA installed, then you might find [this link useful](https://pytorch.org/get-started/previous-versions/).
 
 Once `phold` is installed, to download and install the database run:

docs/install.md

@@ -38,6 +38,17 @@ cd phold
 pip install -e .
 ```
 
+## Mac (M1/M2/M3)
+
+If you have a Mac that runs Apple Silicon (M1/M2/M3), please try:
+
+```bash
+mamba create -n pholdENV python==3.11  
+conda activate pholdENV
+mamba install pytorch::pytorch torchvision torchaudio -c pytorch 
+mamba install -c conda-forge -c bioconda phold 
+```
+
 ## Torch 
 
 To utilise `phold` with GPU, a GPU compatible version of `pytorch` must be installed. 
@@ -46,7 +57,7 @@ If it is not automatically installed via the installation methods above, please
 
 If you have an older version of the CUDA driver installed on your NVIDIA GPU, then you might find [this link useful](https://pytorch.org/get-started/previous-versions/).
 
-Phold has been tested on NVIDIA GPUs (A100, RTX4090) and AMD GPUs (Radeon). 
+Phold has been tested on NVIDIA (A100, RTX4090), AMD (MI250) and Mac (M1 Pro) GPUs. 
 
 Installation on AMD GPUs requires a version of `torch` compatible with rocm e.g.
 
@@ -92,11 +103,9 @@ conda config --add channels conda-forge
 
 We would recommend installing `phold` into a fresh environment. Assuming you installed miniforge, to create an environment called `pholdENV` with `phold` installed (assuming you have an NVIDIA GPU):
 
-
 ```bash
 mamba create -n pholdENV -c conda-forge -c bioconda phold pytorch=*=cuda*
 ```
-
 If you don't have a GPU:
 
 ```bash

pyproject.toml

@@ -5,7 +5,7 @@ requires = ["setuptools>=61.0", "wheel>=0.37.1"]
 [project]
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 name = "phold"
-version = "0.1.2" # change VERSION too
+version = "0.1.3" # change VERSION too
 description = "Phage Annotations using Protein Structures"
 readme = "README.md"
 requires-python = ">=3.8, <3.12"

src/phold/features/create_foldseek_db.py

@@ -210,7 +210,7 @@ def generate_foldseek_db_from_pdbs(
 
     if num_pdbs == 0:
         logger.error(
-            f"No pdbs with matching CDS ids were found at all. Check the {pdb_dir}"
+            f"No pdbs with matching CDS ids were found at all. Check the {pdb_dir} directory"
         )
 
     # generate the db

src/phold/features/predict_3Di.py

@@ -96,20 +96,24 @@ def get_T5_model(
 
     global device
 
-    if torch.cuda.is_available():
-        if cpu is True:
-            device = torch.device("cpu")
-            dev_name = "cpu"
-        else:
-            device = torch.device("cuda:0")
-            dev_name = "cuda:0"
-    else:
+    if cpu is True:
         device = torch.device("cpu")
         dev_name = "cpu"
-        if cpu is not True:
-            logger.warning("No available GPU was found, but --cpu was not specified")
-            logger.warning("ProstT5 will be run with CPU only")
-
+    else:
+        # check for NVIDIA/cuda
+        if torch.cuda.is_available():
+            device = torch.device("cuda:0")
+            dev_name = "cuda:0"
+        # check for apple silicon/metal
+        elif torch.backends.mps.is_available():
+            device = torch.device("mps")
+            dev_name = "mps"
+        else:
+            device = torch.device("cpu")
+            dev_name = "cpu"
+            if cpu is not True:
+                logger.warning("No available GPU was found, but --cpu was not specified")
+                logger.warning("ProstT5 will be run with CPU only")
 
     # logger device only if the function is called
     logger.info("Using device: {}".format(dev_name))

src/phold/plot/plot.py

@@ -5,6 +5,7 @@
 from pycirclize import Circos
 from pycirclize.parser import Genbank
 from matplotlib.lines import Line2D
+import matplotlib.pyplot as plt
 from matplotlib.patches import Patch
 import numpy as np
 from Bio import SeqUtils
@@ -625,3 +626,5 @@ def create_circos_plot(
 
     # Save the image as an SVG
     fig.savefig(svg_plot_file, format="svg", dpi=dpi)
+
+    plt.close(fig)

src/phold/utils/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

tests/conftest.py

@@ -6,4 +6,5 @@
 def pytest_addoption(parser):
     parser.addoption("--gpu_available", action="store_true")
     parser.addoption("--run_remote", action="store_true")
+    parser.addoption("--threads", action="store", default=1)
 

tests/test_data/NC_043029_aa.fasta

@@ -0,0 +1,30 @@
+>NC_043029_CDS_0001
+MAVDRARFRMAVEGGAGGFSPLSPGEKGQRAAAEIGPGSNTGQKGQQDAIIDYLTIVVPLSALEEVNCKKLDLLLFRIFGFRGEVVAGAIREKNWNFYEQSAVLIDRENEVVGRVGIGGKKSTVCLSLTGMGCKWIRDWARVYKQCSMLDAKITRVDCAHDDYEGERLDVHALREVAAQGGFTEGGCPPRHRFISDEGHNTGCTLYVGGKGHKELCVYEKGKAEGLPSSRWVRAEVRLYGKHMEIPLDVLLNPGAYLRGSYSALQDLIKGVCTRLRTIRKHVEVSAEAMVLWMERQVGPALSVLRGAFGDSWSDFCEARIVRDGHPGRFRGIAKGDALHRFVREELCPSAA*
+>NC_043029_CDS_0002
+MPICRVKSAAVEERHNSKTNTINRSQTVGLDLGNGFELPFRVGLGSRPPYTPGEYDIDPQSFALSQYGDLVLKRYVDLVPLQAKAAAAPAKP*
+>NC_043029_CDS_0003
+MAVLIPACREADLDTAAGTCTAVIWIPQPALLPELPIEDAQAIGAKIALLWAVAYVFRLIRKKIEQS*
+>NC_043029_CDS_0004
+MHKMFNALKGKGAALAAVGTAALASAPAFASGGGGVDVGPVVTSINGALGPVGQIGAAVLLVLVGIKVYKWVRRAM*
+>NC_043029_CDS_0005
+MGAPRDVTATGGQGRLPPPGLLTPWIGQGAWDGRVDLAVRMARGLRDHLRGLQLMRWVARVFASAFIRRVAVLLVAALVGWCFSGRAHAAACASYTDQCTEGAAKQGALAWGGAQSKCVAVAGPNGRAGGNVSSKKSEGAGRGYFTVKAECLLNGNVVTYVEPAPPAEQGQWFYTQSCDAQPSYTGTGPWGSGGSAKNGSLGCRNGCDGIWQTNADASKTWTPLGNTCPDDEKKTCETYGDGYYWNSLLKVCEPPEGKCQGGGRPNSLGQCAPEPCPEGMAQQADGTCKKKDNECPAGQVRSPDGKCLPGDGQCAKGEVRGQDGTCKKDADNDGNPDPVNEDSFSGGDDCSAPPSCSGSPIMCGQARIQWRIDCNTRKNRNIAGGTCASMPICTGEKCDAMEYSALLMQWRSACALEKMAQGNGNGGGDNGDTKAIRDALTGTGGAVTTAPDRPSSDVWAPRSGTPVKPDTGGYGWGRTCPQPPSFEVFGNVIQINTAPLCNWLILGGYFVMGLAALASLRIIASRDA*
+>NC_043029_CDS_0006
+MPMLISTLLTALAALFRSKWGPWVAEAMVWLGLSWATNEFLVQPWIDQMEQAMRAGTPGGEFGALVIAYAGLMKFDVACTMIASAVTAKFAVGAAKTFLTKRA*
+>NC_043029_CDS_0007
+MPIELFTGQPGNGKTALMMERLVAEAKAASRPIFAAGIDGLDPGLATVLDDPRHWNNKDADGNYIVPDGSLIFVDEAWKWFGHLHDATRQQTPRHVLELAEHRHRGLDFVWTTQQPNQLYPFVRGLIGSHAHVVRRFGTKMLDVYRWGELNEEIKSLAKRDMAQRTTRLLPSQVFGQYKSAEVHTIKARIPFKVMLLPVLAIAAIVFAYLAYTSLRPSSFAGGEGKEGTQSASADAAPSPFRPAGAKEDAPRWPTAAAYAKDHLPRISTMPWTAPVFDERQARSDPQLVCMSSLEGLDAQGVRQEASCRCLTEQGTAYELSQPECRTLARNGPVYNPYRERSEERSTQRIEDLERSRPGVATTSAGGVAQHVERSMGTFPESPSYRSDSYMTTAPGPNKL*
+>NC_043029_CDS_0008
+MTSSARELLKWLAVILMTGDHVAKVIYGGYVPGLSEAGRVAFPLFALVMAYNLAQPGADVGKSVRRLALWGAIAQPVHALAFGYWLPLNILLTFGVCAAAVYAACQRNWIVLAFAAVVLPAFVDYQWAGVAFVLLAWLGFRTGRLLLTLVAFAPLCAFNGNLWALVAIPAALGLSHTAWSVPRGRWTFYGYYVAHLACLGLLAPILRP*
+>NC_043029_CDS_0009
+MERERPEYLQPIPRRRWEFPWLGMWAVLLLGGAGAGIWLHLKTGDAWNTRFMAAAETSDAAAPIEPSQADTDASRQVMIAEIRARRELAEIAAKRARAGRSDTPAHTDELRCINGIAFRRIPGGWENVPGAPCP*
+>NC_043029_CDS_0010
+MRDRKLTGPWAGFSFKGGRLVTPEGRELEPQDLAWLSLTAAQAQEWRRMMESSRAIDKPRNPLSFNAASVVNLSDALAQRRKKRSPGAMAGPDAEPPAAVLPVPGPKRRQRV*
+>NC_043029_CDS_0011
+MRSIDLLLDKAREKCERPSDRALAEKLRVTASAVSKWRKGGVITEMHATALAAIAGLDGEIVVRVMEEQAETPAQRRVWRSVLDRLSAAAAVLMLVVFAAPGAARAKAIDSQGSSGSDQPHSVYYVRIILGWLARLLPLPRHLLWHGA*
+>NC_043029_CDS_0012
+MIDPFIAFVLLAAIVAVSIGSAKLVSWCLDRRGESARRSAREAAIVAEACAELAATGWTAEDEASFQAIRGQQLVFLKHLQEVRHG*
+>NC_043029_CDS_0013
+MVKVLLFSAVLFGAVAILKDELYFAVVSALLGLLAYGFQAAEDRSNGR*
+>NC_043029_CDS_0014
+MAVDQFREFLRDPFVVSVLGGVLLTGLYWSLVLALRAKGAGNGR*
+>NC_043029_CDS_0015
+MAAECLVITKADWDQLMQLFAGMFLLLAFCAVFSPFDLHSWEYRVRRYLRRRRIARIRESV

tests/test_integration.py

@@ -10,6 +10,10 @@
 # to run with remote and with gpu
 pytest --run_remote  --gpu_available .
 
+# to run with 8 threads 
+
+pytest --run_remote  --gpu_available --threads 8 .
+
 """
 
 # import
@@ -46,18 +50,18 @@
 remote_fasta_dir: Path = f"{output_dir}/combined_truncated_phold_remote_fasta"
 proteins_predict_dir: Path = f"{output_dir}/combined_truncated_phold_proteins_predict"
 proteins_compare_dir: Path = f"{output_dir}/combined_truncated_phold_proteins_compare"
+proteins_compare_pdb_dir: Path = f"{output_dir}/NC_043029_phold_proteins_compare_pdb"
 plots_dir: Path = f"{output_dir}/plot_output"
 
 
 logger.add(lambda _: sys.exit(1), level="ERROR")
-threads = 1
+# threads = 1
 
 
 def remove_directory(dir_path):
     if os.path.exists(dir_path):
         shutil.rmtree(dir_path)
 
-
 @pytest.fixture(scope="session")
 def gpu_available(pytestconfig):
     return pytestconfig.getoption("gpu_available")
@@ -66,6 +70,11 @@ def gpu_available(pytestconfig):
 def run_remote(pytestconfig):
     return pytestconfig.getoption("run_remote")
 
+@pytest.fixture(scope="session")
+def threads(pytestconfig):
+    return pytestconfig.getoption("threads")
+
+
 
 def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
     """executes shell command and returns stdout if completes exit code 0
@@ -90,15 +99,15 @@ def test_install():
     exec_command(cmd)
 
 
-def test_run_genbank(gpu_available):
+def test_run_genbank(gpu_available, threads):
     """test phold run with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
     cmd = f"phold run -i {input_gbk} -o {run_gbk_dir} -t {threads} -d {database_dir} -f"
     if gpu_available is False:
         cmd = f"{cmd} --cpu"
     exec_command(cmd)
 
-def test_run_fasta(gpu_available):
+def test_run_fasta(gpu_available, threads):
     """test phold run with genbank input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"
     cmd = f"phold run -i {input_fasta} -o {run_fasta_dir} -t {threads} -d {database_dir} -f"
@@ -107,7 +116,7 @@ def test_run_fasta(gpu_available):
     exec_command(cmd)
 
 
-def test_predict_genbank(gpu_available):
+def test_predict_genbank(gpu_available, threads):
     """test phold predict with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
     cmd = f"phold predict -i {input_gbk} -o {predict_gbk_dir} -t {threads}  -d {database_dir} -f"
@@ -116,21 +125,27 @@ def test_predict_genbank(gpu_available):
     exec_command(cmd)
 
 
-def test_compare_genbank():
+def test_compare_genbank(threads):
     """test phold compare with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
     cmd = f"phold compare -i {input_gbk} -o {compare_gbk_dir} --predictions_dir {predict_gbk_dir} -t {threads} -d {database_dir} -f"
     exec_command(cmd)
 
 
-def test_compare_pdb():
+def test_compare_pdb(threads):
     """test phold compare with pdbs input"""
     input_gbk: Path = f"{test_data}/NC_043029.gbk"
     cmd = f"phold compare -i {input_gbk} -o {compare_pdb_dir} -t {threads} -d {database_dir} --pdb --pdb_dir {pdb_dir} -f"
     exec_command(cmd)
 
+def test_proteins_compare_pdb(threads):
+    """test phold proteins-compare with pdbs input"""
+    input_faa: Path = f"{test_data}/NC_043029_aa.fasta"
+    cmd = f"phold proteins-compare -i {input_faa} -o {proteins_compare_pdb_dir} -t {threads} -d {database_dir} --pdb --pdb_dir {pdb_dir} -f"
+    exec_command(cmd)
+
 
-def test_predict_fasta(gpu_available):
+def test_predict_fasta(gpu_available, threads):
     """test phold predict with fasta input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"
     cmd = f"phold predict -i {input_fasta} -o {predict_fasta_dir} -t {threads} -d {database_dir} -f"
@@ -139,14 +154,14 @@ def test_predict_fasta(gpu_available):
     exec_command(cmd)
 
 
-def test_compare_fasta():
+def test_compare_fasta(threads):
     """test phold compare with fasta input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"
     cmd = f"phold compare -i {input_fasta} -o {compare_fasta_dir} --predictions_dir {predict_fasta_dir} -t {threads} -d {database_dir} -f"
     exec_command(cmd)
 
 
-def test_proteins_predict(gpu_available):
+def test_proteins_predict(gpu_available, threads):
     """test phold proteins-predict"""
     input_fasta: Path = f"{test_data}/phanotate.faa"
     cmd = f"phold proteins-predict -i {input_fasta} -o {proteins_predict_dir} -t {threads} -d {database_dir} -f"
@@ -155,7 +170,7 @@ def test_proteins_predict(gpu_available):
     exec_command(cmd)
 
 
-def test_proteins_compare():
+def test_proteins_compare(threads):
     """test phold proteins-compare"""
     input_fasta: Path = f"{test_data}/phanotate.faa"
     cmd = f"phold proteins-compare -i {input_fasta} --predictions_dir {proteins_predict_dir} -o {proteins_compare_dir} -t {threads} -d {database_dir} -f"
@@ -170,14 +185,14 @@ def test_plot():
 
 
 
-def test_remote_genbank(run_remote):
+def test_remote_genbank(run_remote, threads):
     """test phold remote with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
     if run_remote is True:
         cmd = f"phold remote -i {input_gbk} -o {remote_gbk_dir} -t {threads} -d {database_dir} -f"
         exec_command(cmd)
 
-def test_remote_fasta(run_remote):
+def test_remote_fasta(run_remote, threads):
     """test phold remote with fasta input"""
     input_fasta: Path = (
         f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"