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run_pretrained_openfold.py: Change default paths of binary to be conda environment bin

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jnwei
2024-04-23 16:40:17 +07:00
committed by Jennifer
parent f4e54ec7ed
commit cfb4c19cac
2 changed files with 11 additions and 7 deletions
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2
README.md
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@@ -188,7 +188,7 @@ python3 run_pretrained_openfold.py \
where `data` is the same directory as in the previous step. If `jackhmmer`,
`hhblits`, `hhsearch` and `kalign` are available at the default path of
`/usr/bin`, their `binary_path` command-line arguments can be dropped.
your conda environment's `bin` directory, their `binary_path` command-line arguments can be dropped.
If you've already computed alignments for the query, you have the option to
skip the expensive alignment computation here with
`--use_precomputed_alignments`.

16
scripts/utils.py
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@@ -1,9 +1,13 @@
import argparse
import ctypes
from datetime import date
import os
import sys
from pathlib import Path
CONDA_ENV_BINARY_PATH= Path(os.environ['CONDA_PREFIX']) / 'bin'
def add_data_args(parser: argparse.ArgumentParser):
parser.add_argument(
'--uniref90_database_path', type=str, default=None,
@@ -30,22 +34,22 @@ def add_data_args(parser: argparse.ArgumentParser):
'--bfd_database_path', type=str, default=None,
)
parser.add_argument(
'--jackhmmer_binary_path', type=str, default='/usr/bin/jackhmmer'
'--jackhmmer_binary_path', type=Path, default=CONDA_ENV_BINARY_PATH / 'jackhmmer',
)
parser.add_argument(
'--hhblits_binary_path', type=str, default='/usr/bin/hhblits'
'--hhblits_binary_path', type=Path, default=CONDA_ENV_BINARY_PATH / 'hhblits',
)
parser.add_argument(
'--hhsearch_binary_path', type=str, default='/usr/bin/hhsearch'
'--hhsearch_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hhsearch',
)
parser.add_argument(
'--hmmsearch_binary_path', type=str, default='/usr/bin/hmmsearch'
'--hmmsearch_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hmmsearch',
)
parser.add_argument(
'--hmmbuild_binary_path', type=str, default='/usr/bin/hmmbuild'
'--hmmbuild_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hmmbuild',
)
parser.add_argument(
'--kalign_binary_path', type=str, default='/usr/bin/kalign'
'--kalign_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'kalign',
)
parser.add_argument(
'--max_template_date', type=str,