PyTFBS 1.0.0__tar.gz → 1.0.2__tar.gz

pytfbs-1.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: PyTFBS
+Version: 1.0.2
+Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
+Author-email: Tinghua Huang <thua45@126.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/thua45/pytfbs
+Project-URL: Documentation, https://github.com/thua45/pytfbs#readme
+Project-URL: Repository, https://github.com/thua45/pytfbs
+Project-URL: Issues, https://github.com/thua45/pytfbs/issues
+Keywords: PyTFBS,Transcription Factor,Binding Site
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: numpy==1.26; sys_platform == "darwin"
+Requires-Dist: numpy>=2.0; sys_platform == "win32"
+Requires-Dist: numpy>=2.0; sys_platform == "linux"
+Provides-Extra: dev
+Requires-Dist: matplotlib; extra == "dev"
+Provides-Extra: test
+Requires-Dist: matplotlib; extra == "test"
+Dynamic: license-file
+
+# PyTFBS
+
+A Python package for dpredicting transcription factor binding sites.
+
+## Installation
+
+```bash
+pip install torch numpy PyTFBS
+```
+
+## Usage
+
+```python
+from PyTFBS import motif, predict
+
+# download PyTFBS data, only need to run once!!!
+motif.download_data()
+
+# list available models
+motif.list_models(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+
+# get avaiable motifs
+motifs = motif.get_motifs(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+print(motifs)
+
+# get models based on motif name
+models = motif.get_models('RFX2_HUMAN.H11MO.0.A')
+print(models)
+
+# predict one model
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 'out_file.txt')
+
+# speed up using mutil-threading (for Windows OS only)
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, 'out_file.txt')
+
+# run prediction with user motif data
+# the my_motif_dir should be organized as [[motif], [trace], [par]]
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', data_dir='my_motif_dir')
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, data_dir='my_motif_dir')
+```

pytfbs-1.0.2/PyTFBS/motif.py

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+# from importlib import resources
+import urllib.request
+import zipfile
+import os
+from pathlib import Path
+
+PyTFBS_data_dir = './PyTFBS_data'
+
+def download_with_progress(url, filename=None):
+	"""
+	带进度显示的下载函数
+	"""
+	def progress_callback(block_num, block_size, total_size):
+		"""
+		进度回调函数
+		
+		Args:
+			block_num: 当前已下载的块数量
+			block_size: 每个块的大小（字节）
+			total_size: 文件总大小（字节）
+		"""
+		downloaded = block_num * block_size
+		percent = downloaded / total_size * 100 if total_size > 0 else 0
+		
+		# 限制显示频率，避免刷新太快
+		if block_num % 100 == 0 or downloaded >= total_size:
+			print(f"\rProgress: {percent:.1f}% ({downloaded}/{total_size} bytes)", end='', flush=True)
+	
+	# 如果没有指定文件名，从URL中提取
+	if filename is None:
+		filename = os.path.basename(url)
+	
+	print(f"start download: {url}")
+	print(f"save as: {filename}")
+	
+	try:
+		urllib.request.urlretrieve(url, filename, progress_callback)
+		print("donwload sucessful")
+	except Exception as e:
+		print(f"donwload failed: {e}")
+		exit(1)
+
+# 使用示例
+# download_with_progress("https://example.com/largefile.zip", "downloaded_file.zip")
+
+def extractall_individual_files(zip_path, extract_path):
+	"""
+	使用 extract() 方法逐个解压文件，确保覆盖
+	"""
+	os.makedirs(extract_path, exist_ok=True)
+	
+	with zipfile.ZipFile(zip_path, 'r') as zip_ref:
+		# 获取所有成员信息
+		members = zip_ref.infolist()
+		
+		print(f"extracting {len(members)} file...")
+		
+		for i, member in enumerate(members, 1):
+			try:
+				# 直接使用 extract() 方法，它会处理覆盖
+				zip_ref.extract(member, extract_path)
+				
+				if i % 10 == 0 or i == len(members):
+					print(f"progress: {i}/{len(members)}")
+					
+			except Exception as e:
+				print(f"extracting failed {member.filename}: {e}")
+				exit(1)
+	
+	print("extracting finished")
+
+# 使用示例
+# extractall_individual_files("example.zip", "extracted_files")
+
+def download_and_extract_zip(url, extract_to):
+	"""
+	下载ZIP文件并解压到指定目录
+	
+	Args:
+		url: ZIP文件的URL
+		extract_to: 解压目标目录
+	"""
+	# 创建目标目录
+	Path(extract_to).mkdir(parents=True, exist_ok=True)
+	
+	# 临时ZIP文件路径
+	zip_path = os.path.join(extract_to, "temp.zip")
+	
+	try:
+		# 下载文件
+		# print(f"downloading: {url}")
+		# urllib.request.urlretrieve(url, zip_path)
+		download_with_progress(url, zip_path)
+		# print("donwload finished")
+		
+		# 解压文件
+		# print(f"extracting: {extract_to}")
+		# with zipfile.ZipFile(zip_path, 'r') as zip_ref:
+		# 	zip_ref.extractall(extract_to, overwrite=True)
+		extractall_individual_files(zip_path, extract_to)
+		# print("extract finished")
+		
+	except Exception as e:
+		print(f"错误: {e}")
+		return False
+	finally:
+		# 清理临时ZIP文件
+		if os.path.exists(zip_path):
+			os.remove(zip_path)
+			print("clearing temp files")
+	
+	return True
+
+def download_data(data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	if not (os.path.exists(data_dir) and os.path.isdir(data_dir)):
+		print(data_dir, 'not exist, creating...')
+		folder_path = Path(data_dir)
+		folder_path.mkdir(exist_ok=True)
+	url = "http://www.thua45.cn/PyTFBS/PyTFBS_data.zip"
+	extract_dir = data_dir
+	# extract_dir = "./downloaded_content"
+	success = download_and_extract_zip(url, extract_dir)
+	if success:
+		print("models installed successful")
+
+def list_models(motif_name=None, species=None, accuracy=None, sensitivity=None, data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	index_file = data_dir + '/motif_index.txt'
+	if not os.path.exists(index_file):
+		print('motif_index.txt not exist, you may need to run download_data() first')
+		exit(1)
+	header = ''
+	result = []
+	for line in open(index_file, 'r'):
+		if line[0] == "#":
+			header = line.rstrip()
+			continue
+		lblocks = line.rstrip().split('\t')
+		if motif_name != None and lblocks[0] != motif_name:
+			continue
+		if species != None and lblocks[1] != species:
+			continue
+		if accuracy != None and float(lblocks[3]) < accuracy:
+			continue
+		if sensitivity != None and float(lblocks[4]) < sensitivity:
+			continue
+		result.append(lblocks)
+	print(header)
+	for rline in result:
+		print('\t'.join(rline))
+
+def get_motifs(motif_name=None, species=None, accuracy=None, sensitivity=None, data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	index_file = data_dir + '/motif_index.txt'
+	if not os.path.exists(index_file):
+		print('motif_index.txt not exist, you may need to run download_data() first')
+		exit(1)
+	header = ''
+	result = []
+	for line in open(index_file, 'r'):
+		if line[0] == "#":
+			header = line.rstrip()
+			continue
+		lblocks = line.rstrip().split('\t')
+		if motif_name != None and lblocks[0] != motif_name:
+			continue
+		if species != None and lblocks[1] != species:
+			continue
+		if accuracy != None and float(lblocks[3]) < accuracy:
+			continue
+		if sensitivity != None and float(lblocks[4]) < sensitivity:
+			continue
+		result.append(lblocks[0])
+	return result
+
+def get_models(motif_name, data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	index_file = data_dir + '/motif_index.txt'
+	if not os.path.exists(index_file):
+		print('motif_index.txt not exist, you may need to run download_data() first')
+		exit(1)
+	models = []
+	for line in open(index_file, 'r'):
+		if line[0] == "#":
+			header = line.rstrip()
+			continue
+		lblocks = line.rstrip().split('\t')
+		if lblocks[0] != motif_name:
+			continue
+		models.append(lblocks[2])
+	return {'motif_name': motif_name, 'models': models}

pytfbs-1.0.2/PyTFBS/predict.py

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+#!/usr/bin/env python
+import os
+from importlib import resources
+from collections import defaultdict
+from importlib import resources
+import math
+import torch
+import torch.nn as nn
+from torch.nn import functional as F
+
+PyTFBS_data_dir = './PyTFBS_data'
+
+def has_non_acgtn_upper(sequence):
+	"""只检查大写ACGT字符"""
+	valid_chars = {'A', 'C', 'G', 'T', 'N'}
+	return any(char.upper() not in valid_chars for char in sequence)
+
+def sequence_to_numbers(sequence, mapping=None):
+	# 将ACGT序列转换为数字列表
+	if mapping is None:
+		mapping = {'A': 0, 'C': 1, 'G': 2, 'T': 3, 'N': 4}
+	return [mapping.get(base.upper(), -1) for base in sequence]
+
+def to_base(line_str):
+	seq_base = 'ACGT'
+	line_blocks = line_str.split('\t')
+	line_data = [float(bi) for bi in line_blocks]
+	max_index = line_data.index(max(line_data))
+	# print(max_index)
+	base = seq_base[max_index]
+	return base
+
+def read_motif(fasta_file):
+	motifs_all = {}
+	#fasta = {}
+	#motifs = []
+	#motif_names = []
+	fp = open(fasta_file, 'r')
+	header = ''
+	seq = ''
+	motif = []
+	for line in fp:
+		line_str = line.rstrip()
+		if line_str[0] == '>':
+			if header != '':
+				#fasta[header] = seq
+				#motifs.append(motif)
+				#motif_names.append(header)
+				motifs_all[header] = (motif, seq)
+			header = line_str[1:len(line_str)]
+			seq = ''
+			motif = []
+		else:
+			seq += to_base(line_str)
+			motif.append(to_mdata_n_frq(line_str))
+	else:
+		if header != '':
+			# fasta[header] = seq
+			# motifs.append(motif)
+			# motif_names.append(header)
+			motifs_all[header] = (motif, seq)
+	fp.close()
+	return motifs_all
+
+def cal_base_freq(fasta_seqs):
+	base_sum = [0.25, 0.25, 0.25, 0.25, 0.25]
+	for seq_name in fasta_seqs.keys():
+		for base in fasta_seqs[seq_name]:
+			if base == 'A' or base == 'a':
+				base_sum[0] += 1
+			elif base == 'C' or base == 'c':
+				base_sum[1] += 1
+			elif base == 'G' or base == 'g':
+				base_sum[2] += 1
+			elif base == 'T' or base == 't':
+				base_sum[3] += 1
+			elif base == 'N' or base == 'n':
+				base_sum[4] += 1
+	bsum = sum(base_sum)
+	base_freq1 = [bs / bsum for bs in base_sum]
+	return base_freq1
+
+def read_motif_single(fasta_file):
+	motif_name = ''
+	motif = []
+	for line in open(fasta_file, 'r'):
+		line_str = line.rstrip()
+		if line_str == '':
+			continue
+		if line_str[0] == '>':
+			motif_name = line_str[1:len(line_str)]
+		else:
+			motif.append(to_mdata_n_frq(line_str))
+	return motif_name, motif
+
+def cal_base_freq(fasta_seqs):
+	base_sum = [0.25, 0.25, 0.25, 0.25, 0.25]
+	for seq_name in fasta_seqs.keys():
+		for base in fasta_seqs[seq_name]:
+			if base == 'A' or base == 'a':
+				base_sum[0] += 1
+			elif base == 'C' or base == 'c':
+				base_sum[1] += 1
+			elif base == 'G' or base == 'g':
+				base_sum[2] += 1
+			elif base == 'T' or base == 't':
+				base_sum[3] += 1
+			elif base == 'N' or base == 'n':
+				base_sum[4] += 1
+	bsum = sum(base_sum)
+	base_freq1 = [bs / bsum for bs in base_sum]
+	return base_freq1
+
+def read_fasta(file):
+	fasta = {}
+	header = ''
+	seq = ''
+	seq_id = 0
+	for line in open(file, 'r'):
+		line_str = line.rstrip()
+		if line_str[0] == '>':
+			if header != '':
+				seq_id += 1
+				fasta[header] = seq
+			header = line_str[1:len(line_str)]
+			seq = ''
+		else:
+			seq += line_str
+	else:
+		if header != '':
+			seq_id += 1
+			fasta[header] = seq
+	seq_freq = cal_base_freq(fasta)
+	return fasta, seq_freq
+
+def to_mdata_n(line_str):
+	seq_base = 'ACGT'
+	line_blocks = line_str.split('\t')
+	line_data = [float(bi) + 0.25 for bi in line_blocks]
+	line_data.append(0.25)
+	return line_data
+
+def to_mdata_n_frq(line_str):
+	seq_base = 'ACGT'
+	line_blocks = line_str.split('\t')
+	line_data = [float(bi) + 0.25 for bi in line_blocks]
+	line_data.append(0.25)
+	sum_base = sum(line_data)
+	line_data_frq = [da / sum_base for da in line_data]
+	return line_data_frq
+
+'''
+def forward(x, params):
+	# global parameters
+	w1, b1, w2, b2, w3, b3 = params
+	x = x @ w1.t() + b1
+	x = torch.tanh(x)
+	x = x @ w2.t() + b2
+	x = torch.tanh(x)
+	x = x @ w3.t() + b3
+	x = torch.tanh(x)
+	return x
+'''
+
+def forward(x, params):
+	# global parameters
+	w1, b1, w2, b2, w3, b3 = params
+	x = x @ w1.t() + b1
+	x = F.relu(x)
+	x = x @ w2.t() + b2
+	x = F.relu(x)
+	x = x @ w3.t() + b3
+	x = F.relu(x)
+	return x
+
+def predict_llrs(seq, motif, header, motif_name):
+	global parameters
+	base_freq, j_mean = parameters['jpar']
+	# print('base_freq, j_mean: ', base_freq, j_mean)
+	model_pars = parameters['model']
+	dseq = sequence_to_numbers(seq)
+	seq_len = len(seq)
+	motif_len = len(motif)
+	j_best = -10.0
+	best_pos = 0
+	best_llrs = []
+	llr_matrix = []
+	j_tmps = []
+	for si in range(seq_len - motif_len + 1):
+		llr_sum = 0.0
+		llrs = []
+		for mi in range(motif_len):
+			base = dseq[si + mi]
+			if base == 4:
+				llr = 0.0
+			else:
+				llr = math.log(motif[mi][base] / base_freq[base]);
+			llr_sum += llr
+			# print(motif[mi][base], base_freq[base])
+			llrs.append(llr)
+		# llrs_norm = [llr - j_mean for llr in llrs]
+		llrs_norm = llrs
+		# print('llrs_norm: ', llrs_norm)
+		j_tmp = llr_sum / motif_len
+		if j_tmp > 0.0:
+			llr_matrix.append(llrs_norm)
+			j_tmps.append(j_tmp)
+	data = torch.tensor(llr_matrix)
+	data = data.view(-1, motif_len)
+	logits = forward(data, model_pars)
+	predict = torch.sigmoid(logits * 4.0)
+	# print('predict.shape:', predict.shape)
+	col_index = 1
+	#indices = torch.nonzero(predict[:, col_index] >= 0.5, as_tuple=False)
+	indices = torch.nonzero((predict[:, 1] > 0.75) & (predict[:, 0] < 0.25), as_tuple=False)
+	for value in indices:
+		match_seq = seq[value.item(): value.item() + motif_len]
+		print(header, motif_name, value.item(), match_seq, j_tmps[value.item()], predict[value, 0].item(), predict[value, 1].item())
+
+def predict_seq():
+	motifs_all = read_motif('motif_data.txt')
+	# fasta, seq_freq = read_fasta('GCF_000001405.40_GRCh38.p14_promoter_1.1k.txt')
+	fasta, seq_freq = read_fasta('GCF_000001405.40_GRCh38.p14_promoter_1.1k_rdm1000.txt')
+	# print(len(fasta))
+	for seq_name in fasta.keys():
+		seq = fasta[seq_name].upper()
+		if has_non_acgtn_upper(seq):
+			continue
+		for motif_name in motifs_all.keys():
+			if motif_name != 'ANDR_HUMAN.H11MO.0.A':
+				continue
+			motif = motifs_all[motif_name][0]
+			predict_llrs(seq, motif, seq_name, motif_name)
+
+def seq2onehot(seq_in, motif_len, motif, base_freq):
+	datas = []
+	poss = []
+	j_tmps = []
+	seq_len = len(seq_in)
+	for si in range(seq_len - motif_len + 1):
+		seq = seq_in[si: si + motif_len]
+		j_tmp = jindex(seq, motif, base_freq)
+		# print(j_tmp)
+		if j_tmp <= 0.0:
+			continue
+		poss.append(si)
+		j_tmps.append(j_tmp)
+		seq_onehot = []
+		dseq = sequence_to_numbers(seq.upper())
+		for si in dseq:
+			sonehot = [0.0, 0.0, 0.0, 0.0, 0.0]
+			sonehot[si] = 1.0
+			seq_onehot += sonehot
+		datas.append(seq_onehot)
+	return datas, poss, j_tmps
+
+def jindex(seq, motif, base_freq):
+	dseq = sequence_to_numbers(seq)
+	motif_len = len(motif)
+	llr_sum = 0.0
+	for mi in range(motif_len):
+		base = dseq[mi]
+		if base == 4:
+			llr = 0.0
+		else:
+			llr = math.log(motif[mi][base] / base_freq[base]);
+		llr_sum += llr
+	j_tmp = llr_sum / motif_len
+	return j_tmp
+
+def predict_tfbs(file, motif_name, motif, data_dim, model, base_freq, out_file):
+	fasta, seq_freq = read_fasta(file)
+	# print(len(fasta))
+	motif_len = int(data_dim[0] / 5)
+	fp = open(out_file, 'w')
+	for seq_name in fasta.keys():
+		seq = fasta[seq_name].upper()
+		if has_non_acgtn_upper(seq):
+			continue
+		data_onehot, poss, j_tmps = seq2onehot(seq, motif_len, motif, base_freq)
+		data = torch.tensor(data_onehot)
+		data = data.view(-1, data_dim[0])
+		logits = model(data).flatten().tolist()
+		#indices = torch.nonzero(logits > 0.5, as_tuple=False).squeeze().tolist()
+		#indices = torch.nonzero(logits[:, 1] > logits[:, 0], as_tuple=False)
+		#indices = [i for i, value in enumerate(logits) if value > 0.5]
+		for vi in range(len(logits)):
+			if logits[vi] > 0.5:
+				value = vi
+				match_seq = seq[poss[value]: poss[value] + motif_len]
+				fp.write('\t'.join([seq_name, str(poss[value]), match_seq, str(j_tmps[value]), str(logits[value])]) + '\n')
+	fp.close()
+
+def load_module(file):
+	saved_data = torch.load(file)
+	base_freq = saved_data['base_freq']
+	data_dim = saved_data['data_dim']
+	w1 = saved_data['w1']
+	b1 = saved_data['b1']
+	w2 = saved_data['w2']
+	b2 = saved_data['b2']
+	w3 = saved_data['w3']
+	b3 = saved_data['b3']
+	parameters = {'jpar': [base_freq, data_dim], 'model': [w1, b1, w2, b2, w3, b3]}
+	return parameters
+
+def read_motif_cmp(file):
+	motif_cmp = {}
+	for line in open(file, 'r'):
+		if line[0: 3] != 'Cmp':
+			continue
+		lblocks = line.rstrip().split(' ')
+		motif_cmp[lblocks[1]] = lblocks[2]
+	return motif_cmp
+
+def loade_model_pars(model_file, data_dim):
+	# 加载模型参数
+	# 首先需要创建相同结构的模型
+	global x_dimention
+	global optimizer
+	model_pars = torch.load(model_file)
+	#seq_freq = model_pars['base_freq']
+	#data_dim = model_pars['data_dim']
+	#del model_pars['base_freq']
+	#del model_pars['data_dim']
+	x_dimention = data_dim[0]
+	y_dimention = data_dim[1]
+	# 1. 定义模型
+	model = nn.Sequential(
+		nn.Linear(x_dimention, 64),
+		nn.ReLU(),
+		nn.Linear(64, 32),
+		nn.ReLU(), 
+		nn.Linear(32, 1),
+		nn.Sigmoid()
+	)
+	model.load_state_dict(model_pars)
+	#new_model.eval()
+	return model
+
+def script(motif_id, model_id, seq_file, out_file, data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	if not (os.path.exists(data_dir) and os.path.isdir(data_dir)):
+		print("PyTFBS_data folder can not found!")
+		exit(1)
+	motif_file = data_dir + '/motif/' + motif_id + '.pwm'
+	model_file = data_dir + '/par/' + model_id + '_par.pth'
+	if not os.path.exists(motif_file):
+		print(motif_file, 'not exist!')
+		exit(1)
+	if not os.path.exists(model_file):
+		print(model_file, 'not exist!')
+		exit(1)
+	if not os.path.exists(seq_file):
+		print(seq_file, 'not exist!')
+		exit(1)
+	motif_name, motif = read_motif_single(motif_file)
+	data_dim = [len(motif) * 5, 1]
+	model = loade_model_pars(model_file, data_dim)
+	# run predict
+	fasta, seq_freq = read_fasta(seq_file)
+	# seq_freq = [0.22698189046475983, 0.2685381453335145, 0.2744548727333858, 0.22957776564437835, 0.00044732582396156444]
+	motif_len = len(motif)
+	fp = open(out_file, 'w')
+	seq_n = len(fasta)
+	finished_n = 0
+	for seq_name in fasta.keys():
+		seq = fasta[seq_name].upper()
+		if has_non_acgtn_upper(seq):
+			continue
+		data_onehot, poss, j_tmps = seq2onehot(seq, motif_len, motif, seq_freq)
+		data = torch.tensor(data_onehot)
+		data = data.view(-1, data_dim[0])
+		logits = model(data).flatten().tolist()
+		#indices = torch.nonzero(logits > 0.5, as_tuple=False).squeeze().tolist()
+		#indices = torch.nonzero(logits[:, 1] > logits[:, 0], as_tuple=False)
+		#indices = [i for i, value in enumerate(logits) if value > 0.5]
+		for vi in range(len(logits)):
+			if logits[vi] > 0.5:
+				value = vi
+				match_seq = seq[poss[value]: poss[value] + motif_len]
+				fp.write('\t'.join([seq_name, str(poss[value]), match_seq, str(j_tmps[value]), str(logits[value])]) + '\n')
+		finished_n += 1
+		if finished_n % 100 == 0 or finished_n == seq_n:
+			print(str(finished_n) + '/' + str(seq_n))
+	fp.close()
+
+def win_bin(motif_id, model_id, seq_file, thread_n, out_file, data_dir=None):
+	if data_dir == None:
+		data_dir = PyTFBS_data_dir
+	if not (os.path.exists(data_dir) and os.path.isdir(data_dir)):
+		print("PyTFBS_data folder can not found!")
+		exit(1)
+	motif_file = data_dir + '/motif/' + motif_id + '.pwm'
+	model_file = data_dir + '/trace/' + model_id + '_trace.pth'
+	PyTFBS_exe = data_dir + '/PyTFBS_bin/PyTFBS.exe'
+	if not os.path.exists(motif_file):
+		print(motif_file, 'not exist!')
+		exit(1)
+	if not os.path.exists(model_file):
+		print(model_file, 'not exist!')
+		exit(1)
+	if not os.path.exists(seq_file):
+		print(seq_file, 'not exist!')
+		exit(1)
+	cmd = '\"' + PyTFBS_exe + '\" -m ' + motif_file + ' -z ' + model_file + ' -i ' + seq_file + ' -t ' + str(thread_n) + ' -o ' + out_file + ''
+	cmd = cmd.replace('/', '\\')
+	print(cmd)
+	os.system(cmd)
+
+if __name__ == '__main__':
+	script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'GCF_000001405.40_GRCh38.p14_promoter_1.1k.txt', 'out_file.txt')

pytfbs-1.0.2/PyTFBS.egg-info/PKG-INFO

@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: PyTFBS
+Version: 1.0.2
+Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
+Author-email: Tinghua Huang <thua45@126.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/thua45/pytfbs
+Project-URL: Documentation, https://github.com/thua45/pytfbs#readme
+Project-URL: Repository, https://github.com/thua45/pytfbs
+Project-URL: Issues, https://github.com/thua45/pytfbs/issues
+Keywords: PyTFBS,Transcription Factor,Binding Site
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: numpy==1.26; sys_platform == "darwin"
+Requires-Dist: numpy>=2.0; sys_platform == "win32"
+Requires-Dist: numpy>=2.0; sys_platform == "linux"
+Provides-Extra: dev
+Requires-Dist: matplotlib; extra == "dev"
+Provides-Extra: test
+Requires-Dist: matplotlib; extra == "test"
+Dynamic: license-file
+
+# PyTFBS
+
+A Python package for dpredicting transcription factor binding sites.
+
+## Installation
+
+```bash
+pip install torch numpy PyTFBS
+```
+
+## Usage
+
+```python
+from PyTFBS import motif, predict
+
+# download PyTFBS data, only need to run once!!!
+motif.download_data()
+
+# list available models
+motif.list_models(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+
+# get avaiable motifs
+motifs = motif.get_motifs(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+print(motifs)
+
+# get models based on motif name
+models = motif.get_models('RFX2_HUMAN.H11MO.0.A')
+print(models)
+
+# predict one model
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 'out_file.txt')
+
+# speed up using mutil-threading (for Windows OS only)
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, 'out_file.txt')
+
+# run prediction with user motif data
+# the my_motif_dir should be organized as [[motif], [trace], [par]]
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', data_dir='my_motif_dir')
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, data_dir='my_motif_dir')
+```

pytfbs-1.0.2/PyTFBS.egg-info/SOURCES.txt

@@ -0,0 +1,12 @@
+LICENSE
+README.md
+pyproject.toml
+PyTFBS/__init__.py
+PyTFBS/motif.py
+PyTFBS/predict.py
+PyTFBS.egg-info/PKG-INFO
+PyTFBS.egg-info/SOURCES.txt
+PyTFBS.egg-info/dependency_links.txt
+PyTFBS.egg-info/entry_points.txt
+PyTFBS.egg-info/requires.txt
+PyTFBS.egg-info/top_level.txt

{pytfbs-1.0.0/src → pytfbs-1.0.2}/PyTFBS.egg-info/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
 PyTFBS = PyTFBS.cli:main
+PyTFBS-cleanup = PyTFBS.uninstall:cleanup

pytfbs-1.0.2/PyTFBS.egg-info/requires.txt

@@ -0,0 +1,16 @@
+torch
+
+[:sys_platform == "darwin"]
+numpy==1.26
+
+[:sys_platform == "linux"]
+numpy>=2.0
+
+[:sys_platform == "win32"]
+numpy>=2.0
+
+[dev]
+matplotlib
+
+[test]
+matplotlib

pytfbs-1.0.2/README.md

@@ -0,0 +1,40 @@
+# PyTFBS
+
+A Python package for dpredicting transcription factor binding sites.
+
+## Installation
+
+```bash
+pip install torch numpy PyTFBS
+```
+
+## Usage
+
+```python
+from PyTFBS import motif, predict
+
+# download PyTFBS data, only need to run once!!!
+motif.download_data()
+
+# list available models
+motif.list_models(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+
+# get avaiable motifs
+motifs = motif.get_motifs(species='Homo sapiens', accuracy=0.9, sensitivity=0.9)
+print(motifs)
+
+# get models based on motif name
+models = motif.get_models('RFX2_HUMAN.H11MO.0.A')
+print(models)
+
+# predict one model
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 'out_file.txt')
+
+# speed up using mutil-threading (for Windows OS only)
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, 'out_file.txt')
+
+# run prediction with user motif data
+# the my_motif_dir should be organized as [[motif], [trace], [par]]
+predict.script('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', data_dir='my_motif_dir')
+predict.win_bin('CEBPB_HUMAN.H11MO.0.A', 'CEBPB_HUMAN.H11MO.0.A_1231', 'input_seq_file.fasta', 64, data_dir='my_motif_dir')
+```

{pytfbs-1.0.0 → pytfbs-1.0.2}/pyproject.toml

@@ -4,28 +4,27 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "PyTFBS"
-version = "1.0.0"
+version = "1.0.2"
+license = "MIT"  # SPDX expression
 description = "PyTFBS: A Python Package for Transcription Factor Binding Site Prediction"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 authors = [
     {name = "Tinghua Huang", email = "thua45@126.com"}
 ]
-license = {text = "Acdemic"}
 keywords = ["PyTFBS", "Transcription Factor", "Binding Site"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "requests>=2.25.0",
-    "numpy>=1.21.0",
+    "torch",
+    "numpy==1.26; sys_platform == 'darwin'",
+    "numpy>=2.0; sys_platform == 'win32'",
+    "numpy>=2.0; sys_platform == 'linux'",
 ]
 
 [project.urls]
@@ -36,18 +35,17 @@ Issues = "https://github.com/thua45/pytfbs/issues"
 
 [project.optional-dependencies]
 dev = [
-    "pytest>=6.0",
+    "matplotlib",
 ]
 test = [
-    "pytest>=6.0",
+    "matplotlib",
 ]
 
 [project.scripts]
 PyTFBS = "PyTFBS.cli:main"
+PyTFBS-cleanup = "PyTFBS.uninstall:cleanup"
 
 [tool.setuptools]
-packages = {find = {where = ["src"]}}
-package-dir = {"" = "src"}
+packages = ["PyTFBS"]
+package-data = {"*" = ["*.txt", "*.md", "*.rst", "data/*"]}
 
-[tool.setuptools.package-data]
-mypackage = ["*.txt", "*.json", "data/*", "templates/*"]

pytfbs-1.0.0/PKG-INFO

@@ -1,48 +0,0 @@
-Metadata-Version: 2.4
-Name: PyTFBS
-Version: 1.0.0
-Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
-Author-email: Tinghua Huang <thua45@126.com>
-License: Acdemic
-Project-URL: Homepage, https://github.com/thua45/pytfbs
-Project-URL: Documentation, https://github.com/thua45/pytfbs#readme
-Project-URL: Repository, https://github.com/thua45/pytfbs
-Project-URL: Issues, https://github.com/thua45/pytfbs/issues
-Keywords: PyTFBS,Transcription Factor,Binding Site
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: requests>=2.25.0
-Requires-Dist: numpy>=1.21.0
-Provides-Extra: dev
-Requires-Dist: pytest>=6.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest>=6.0; extra == "test"
-Dynamic: license-file
-
-# My Package
-
-A Python package for dpredicting transcription factor binding sites.
-
-## Installation
-
-```bash
-pip install PyTFBS
-```
-
-## Usage
-
-```python
-import PyTFBS
-
-result = PyTFBS.predict()
-print(result)
-```

pytfbs-1.0.0/README.md

@@ -1,18 +0,0 @@
-# My Package
-
-A Python package for dpredicting transcription factor binding sites.
-
-## Installation
-
-```bash
-pip install PyTFBS
-```
-
-## Usage
-
-```python
-import PyTFBS
-
-result = PyTFBS.predict()
-print(result)
-```

pytfbs-1.0.0/src/PyTFBS.egg-info/PKG-INFO

@@ -1,48 +0,0 @@
-Metadata-Version: 2.4
-Name: PyTFBS
-Version: 1.0.0
-Summary: PyTFBS: A Python Package for Transcription Factor Binding Site Prediction
-Author-email: Tinghua Huang <thua45@126.com>
-License: Acdemic
-Project-URL: Homepage, https://github.com/thua45/pytfbs
-Project-URL: Documentation, https://github.com/thua45/pytfbs#readme
-Project-URL: Repository, https://github.com/thua45/pytfbs
-Project-URL: Issues, https://github.com/thua45/pytfbs/issues
-Keywords: PyTFBS,Transcription Factor,Binding Site
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: requests>=2.25.0
-Requires-Dist: numpy>=1.21.0
-Provides-Extra: dev
-Requires-Dist: pytest>=6.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest>=6.0; extra == "test"
-Dynamic: license-file
-
-# My Package
-
-A Python package for dpredicting transcription factor binding sites.
-
-## Installation
-
-```bash
-pip install PyTFBS
-```
-
-## Usage
-
-```python
-import PyTFBS
-
-result = PyTFBS.predict()
-print(result)
-```

pytfbs-1.0.0/src/PyTFBS.egg-info/SOURCES.txt

@@ -1,11 +0,0 @@
-LICENSE
-README.md
-pyproject.toml
-src/PyTFBS/__init__.py
-src/PyTFBS/tango.py
-src/PyTFBS.egg-info/PKG-INFO
-src/PyTFBS.egg-info/SOURCES.txt
-src/PyTFBS.egg-info/dependency_links.txt
-src/PyTFBS.egg-info/entry_points.txt
-src/PyTFBS.egg-info/requires.txt
-src/PyTFBS.egg-info/top_level.txt

pytfbs-1.0.0/src/PyTFBS.egg-info/requires.txt

@@ -1,8 +0,0 @@
-requests>=2.25.0
-numpy>=1.21.0
-
-[dev]
-pytest>=6.0
-
-[test]
-pytest>=6.0