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'))
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'))