Skip to content

trouble of ICRA #21

Description

@AmberCC15

Hi,I have encountered an issue while trying to use the single_file and get_sample_map functions from the SGVFinder2 module. When I attempt to run my script, I receive the following error message:Traceback (most recent call last):
File "process_fastq.py", line 1, in
from SGVFinder2 import single_file, get_sample_map
File "/data2/qiuli/meta/cebus/SGVFinder2.py", line 1, in
from SGVFinder2 import single_file, get_sample_map
ImportError: cannot import name 'single_file'

Here is the relevant portion of my script:
from SGVFinder2 import single_file, get_sample_map
from pandas import to_pickle

read1 = '/data2/qiuli/meta/cebus/SRR8101048_1.fastq'
read2 = '/data2/qiuli/meta/cebus/SRR8101048_2.fastq'

DATABASE = '/data2/qiuli/meta/SV/P1db'
jspi_file, jsdel_file = single_file(
fq1=read1,
fq2=read2,
outfol='SRR8101048example_out/',
dbpath=DATABASE
)
sample_map = get_sample_map(jsdel_file, DATABASE + '.dlen')
to_pickle(sample_map, jsdel_file.replace('.jsdel', '.smp'))

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions