使用kb_python包时发生报错如何解决
from IPython.core.display import display, HTML
import warnings
warnings.filterwarnings('ignore')
import dynamo as dyn
import kb_python as kb
import bamnostic as ba
filename="C:/Users/ALIENWARE/Downloads/pol.csv"
dyn.get_all_dependencies_version()
dyn.configuration.set_figure_params("dynamo", background="white")
!kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 intron_t2c.txt --workflow lamanno -n 4
Homo_sapiens.GRCh38.dna.toplevel.fa
Homo_sapiens.GRCh38.106.gtf
运行结果:
[2022-04-18 17:53:37,078] WARNING [main] Support for split indices (`-n`) will be deprecated in the next major release. Please read the release notes on GitHub for more information.
[2022-04-18 17:53:37,078] INFO [ref_lamanno] Preparing Homo_sapiens.GRCh38.dna.toplevel.fa, Homo_sapiens.GRCh38.106.gtf
[2022-04-18 17:55:02,195] INFO [ref_lamanno] Splitting genome Homo_sapiens.GRCh38.dna.toplevel.fa into cDNA at E:\发电机\pythonProject\朱庇特\tmp\tmp2l0gyueo
[2022-04-18 17:55:02,195] ERROR [main] An exception occurred
Traceback (most recent call last):
File "E:\anaconda\lib\site-packages\kb_python-0.27.2-py3.9.egg\kb_python\main.py", line 1301, in main
COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
File "E:\anaconda\lib\site-packages\kb_python-0.27.2-py3.9.egg\kb_python\main.py", line 254, in parse_ref
ref_lamanno(
File "E:\anaconda\lib\site-packages\ngs_tools-1.5.14-py3.9.egg\ngs_tools\logging.py", line 62, in inner
return func(*args, **kwargs)
File "E:\anaconda\lib\site-packages\kb_python-0.27.2-py3.9.egg\kb_python\ref.py", line 662, in ref_lamanno
cdna_temp_path = ngs.fasta.split_genomic_fasta_to_cdna(
File "E:\anaconda\lib\site-packages\ngs_tools-1.5.14-py3.9.egg\ngs_tools\fasta\__init__.py", line 35, in split_genomic_fasta_to_cdna
with Fasta(fasta_path, 'r') as f_in, Fasta(out_path, 'w') as f_out:
File "E:\anaconda\lib\site-packages\ngs_tools-1.5.14-py3.9.egg\ngs_tools\fasta\Fasta.py", line 20, in __init__
super(Fasta, self).__init__(path, mode)
File "E:\anaconda\lib\site-packages\ngs_tools-1.5.14-py3.9.egg\ngs_tools\utils.py", line 500, in __init__
self._open()
File "E:\anaconda\lib\site-packages\ngs_tools-1.5.14-py3.9.egg\ngs_tools\utils.py", line 531, in _open
raise IOError(
OSError: Remote URLs may not be opened in `w` mode
w改成r
有用的话采纳一下吧,谢谢