lingyuzeng/analysis_pdb
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update test file

Browse Source
This commit is contained in:
root
2024-01-18 14:43:51 +08:00
parent 5ad2d91ed3
commit eb05ccd960
1 changed files with 16 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
test.py
View File

@@ -1,43 +1,31 @@
from tcr_pmhc_complexes import FastaFile from tcr_pmhc_complexes import FastaFile
from pathlib import Path from pathlib import Path
import glob
def test_fasta_file(file_path): def test_fasta_file(file_path):
fasta_file = FastaFile(file=Path(file_path)) fasta_file = FastaFile(file=Path(file_path))
print(f"文件：{file_path}") print(f"File: {file_path}")
print(f"序列数量：{fasta_file.sequence_num}\n") print(f"Number of Sequences: {fasta_file.sequence_num}\n")
for seq in fasta_file.sequences:
header_info = seq.header_info
print(f"PDB ID: {header_info.pdb_id}")
print(f"Chain IDs: {', '.join(header_info.chain_ids)}")
print(f"Author Chain IDs: {', '.join([f'{cid} ({aid})' for cid, aid in header_info.auth_chain_ids.items()])}")
print(f"Description: {header_info.description}")
print(f"Sequence: {seq.sequence.sequence[:30]}...") # 打印部分序列以简化输出
print(f"Sequence Length: {seq.sequence_length}\n") # 新增行来打印序列长度
def test_fasta_file1(file_path):
fasta_file = FastaFile(file=Path(file_path))
print(f"文件：{file_path}")
print(f"序列数量：{fasta_file.sequence_num}\n")
for seq in fasta_file.sequences: for seq in fasta_file.sequences:
header_info = seq.header_info header_info = seq.header_info
print(f"PDB ID: {header_info.pdb_id if header_info.pdb_id else 'N/A'}") print(f"PDB ID: {header_info.pdb_id if header_info.pdb_id else 'N/A'}")
print(f"Chain IDs: {', '.join(header_info.chain_ids) if header_info.chain_ids else 'N/A'}") print(f"Chain IDs: {', '.join(header_info.chain_ids) if header_info.chain_ids else 'N/A'}")
print(f"Author Chain IDs: {', '.join([f'{cid} ({aid})' for cid, aid in header_info.auth_chain_ids.items()]) if header_info.auth_chain_ids else 'N/A'}") print(f"Author Chain IDs: {', '.join([f'{cid} ({aid})' for cid, aid in header_info.auth_chain_ids.items()]) if header_info.auth_chain_ids else 'N/A'}")
print(f"Is Polymeric: {header_info.is_polymeric}") print(f"Is Polymeric: {header_info.is_polymeric if header_info.is_polymeric else 'Unknown'}")
print(f"Description: {header_info.description}") print(f"Description: {header_info.description}")
print(f"Sequence: {seq.sequence.sequence[:30]}...\n") print(f"Sequence: {seq.sequence.sequence[:30]}...")
print(f"Sequence Length: {len(seq.sequence.sequence)}\n")
# 测试三个 fasta 文件 # Discover all .fasta files within directories matching the pattern
test_fasta_files = [ runner_directories = glob.glob('/mnt/mydrive/analysis_pdb-dev/pdb_test1/runner_*')
'/mnt/mydrive/analysis_pdb-dev/pdb_test1/runner_8gvb/8gvb.fasta', fasta_files = [file for directory in runner_directories for file in Path(directory).glob('*.fasta')]
'/mnt/mydrive/analysis_pdb-dev/pdb_test1/runner_8gom/8gom.fasta',
'/mnt/mydrive/analysis_pdb-dev/pdb_test1/runner_7n6e/7n6e.fasta',
'/mnt/mydrive/analysis_pdb-dev/test.fasta'
]
for file in test_fasta_files: # Add the standard FASTA file to the list of files to be tested
test_fasta_file(file) fasta_files.append(Path('/mnt/mydrive/analysis_pdb-dev/test.fasta'))
# Test each FASTA file
for file_path in fasta_files:
test_fasta_file(file_path)
# test_fasta_file('/mnt/mydrive/analysis_pdb-dev/test.fasta')exit