File size: 9,181 Bytes
89c0b51 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 |
# Copyright 2024 ByteDance and/or its affiliates.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import logging
import os
import tarfile
import time
from typing import List, Tuple
import requests
from requests.auth import HTTPBasicAuth
from tqdm import tqdm
TQDM_BAR_FORMAT = "{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} estimate remaining: {remaining}]"
logger = logging.getLogger(__name__)
username = "example_user"
password = "example_password"
def run_mmseqs2_service(
x,
prefix,
use_env=True,
use_filter=True,
use_templates=False,
filter=None,
use_pairing=False,
pairing_strategy="greedy",
host_url="https://api.colabfold.com",
user_agent: str = "",
email: str = "",
) -> Tuple[List[str], List[str]]:
submission_endpoint = "ticket/pair" if use_pairing else "ticket/msa"
headers = {}
if user_agent != "":
headers["User-Agent"] = user_agent
else:
logger.warning(
"No user agent specified. Please set a user agent (e.g., 'toolname/version contact@email') to help us debug in case of problems. This warning will become an error in the future."
)
def submit(seqs, mode, N=101):
n, query = N, ""
for seq in seqs:
query += f"{seq}\n"
n += 1
while True:
error_count = 0
try:
# https://requests.readthedocs.io/en/latest/user/advanced/#advanced
# "good practice to set connect timeouts to slightly larger than a multiple of 3"
res = requests.post(
f"{host_url}/{submission_endpoint}",
data={"q": query, "mode": mode, "email": email},
timeout=6.02,
headers=headers,
auth=HTTPBasicAuth(username, password),
)
except requests.exceptions.Timeout:
logger.warning("Timeout while submitting to MSA server. Retrying...")
continue
except Exception as e:
error_count += 1
logger.warning(
f"Error while fetching result from MSA server. Retrying... ({error_count}/5)"
)
logger.warning(f"Error: {e}")
time.sleep(5)
if error_count > 5:
raise
continue
break
try:
out = res.json()
except ValueError:
logger.error(f"Server didn't reply with json: {res.text}")
out = {"status": "ERROR"}
return out
def status(ID):
while True:
error_count = 0
try:
res = requests.get(
f"{host_url}/ticket/{ID}",
timeout=6.02,
headers=headers,
auth=HTTPBasicAuth(username, password),
)
except requests.exceptions.Timeout:
logger.warning(
"Timeout while fetching status from MSA server. Retrying..."
)
continue
except Exception as e:
error_count += 1
logger.warning(
f"Error while fetching result from MSA server. Retrying... ({error_count}/5)"
)
logger.warning(f"Error: {e}")
time.sleep(5)
if error_count > 5:
raise
continue
break
try:
out = res.json()
except ValueError:
logger.error(f"Server didn't reply with json: {res.text}")
out = {"status": "ERROR"}
return out
def download(ID, path):
error_count = 0
while True:
try:
res = requests.get(
f"{host_url}/result/download/{ID}",
timeout=6.02,
headers=headers,
auth=HTTPBasicAuth(username, password),
)
except requests.exceptions.Timeout:
logger.warning(
"Timeout while fetching result from MSA server. Retrying..."
)
continue
except Exception as e:
error_count += 1
logger.warning(
f"Error while fetching result from MSA server. Retrying... ({error_count}/5)"
)
logger.warning(f"Error: {e}")
time.sleep(5)
if error_count > 5:
raise
continue
break
with open(path, "wb") as out:
out.write(res.content)
# process input x
seqs = [x] if isinstance(x, str) else x
# compatibility to old option
if filter is not None:
use_filter = filter
# setup mode
if use_filter:
mode = "env" if use_env else "all"
else:
mode = "env-nofilter" if use_env else "nofilter"
if use_pairing:
use_templates = False
use_env = False
mode = ""
# greedy is default, complete was the previous behavior
if pairing_strategy == "greedy":
mode = "pairgreedy"
elif pairing_strategy == "complete":
mode = "paircomplete"
# define path
path = prefix
if not os.path.isdir(path):
os.mkdir(path)
# call mmseqs2 api
tar_gz_file = f"{path}/out.tar.gz"
N, REDO = 101, True
# deduplicate and keep track of order
seqs_unique = []
# TODO this might be slow for large sets
[seqs_unique.append(x) for x in seqs if x not in seqs_unique]
Ms = [N + seqs_unique.index(seq) for seq in seqs]
# lets do it!
logger.error("Msa server is running.")
if not os.path.isfile(tar_gz_file):
TIME_ESTIMATE = 100
with tqdm(total=TIME_ESTIMATE, bar_format=TQDM_BAR_FORMAT) as pbar:
while REDO:
pbar.set_description("SUBMIT")
# Resubmit job until it goes through
out = submit(seqs_unique, mode, N)
while out["status"] in ["UNKNOWN", "RATELIMIT"]:
sleep_time = 60
logger.error(f"Sleeping for {sleep_time}s. Reason: {out['status']}")
# resubmit
time.sleep(sleep_time)
out = submit(seqs_unique, mode, N)
if out["status"] == "ERROR":
raise Exception(
f"MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later."
)
if out["status"] == "MAINTENANCE":
raise Exception(
f"MMseqs2 API is undergoing maintenance. Please try again in a few minutes."
)
# wait for job to finish
ID, TIME = out["id"], 0
pbar.set_description(out["status"])
while out["status"] in ["UNKNOWN", "RUNNING", "PENDING"]:
t = 60
logger.error(f"Sleeping for {t}s. Reason: {out['status']}")
time.sleep(t)
out = status(ID)
pbar.set_description(out["status"])
if out["status"] == "RUNNING":
TIME += t
pbar.n = min(99, int(100 * TIME / (30.0 * 60)))
pbar.refresh()
if out["status"] == "COMPLETE":
pbar.n = 100
pbar.refresh()
REDO = False
if out["status"] == "ERROR":
REDO = False
raise Exception(
f"MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later."
)
# Download results
download(ID, tar_gz_file)
with tarfile.open(tar_gz_file) as tar_gz:
tar_gz.extractall(os.path.dirname(tar_gz_file))
files = os.listdir(os.path.dirname(tar_gz_file))
if (
"0.a3m" not in files
or "pdb70_220313_db.m8" not in files
or "uniref_tax.m8" not in files
):
raise FileNotFoundError(
f"Files 0.a3m, pdb70_220313_db.m8, and uniref_tax.m8 not found in the directory."
)
else:
print("Files downloaded and extracted successfully.")
|