Does anyone know how to get rid of '\r'?
I have to run 89 files in the supercomputer, I have done so far the two next scripts
The first one is .sh to run it on shell
$ID=$(sed "${PBS_ARRAYID}q;d" ID_index.txt)
$echo "Processing $ID"
$python $PBS_O_WORKDIR/script.py $ID
where the ID_index text implies the index from 1 to 89 datafiles
Then I have the next script in python
#!/usr/bin/python
import pandas as pd
import numpy as np
import sys
ID_1 = sys.argv[1]
vcf_info = sample_id + '.snp.INFO'
ID_1 = sys.argv[1]
ID_1_info = ID_1 + 'sample_cases.lgen'
ID_2 = sys.argv[2]
ID_2_info = ID_2 + 'sample_controls.lgen'
# Reading files
df_1 = pd.read_table(ID_1_info, delim_whitespace=True , header=None)
df_2 = pd.read_table(ID_2_info, delim_whitespace=True , header=None)
.
.
.
Because the output link to read the datafiles returns a space, this is the error:
df_1 = pd.read_table(ID_1_info, delim_whitespace=True , header=None) File "pandas/io/parsers.py", line 685, in parser_f return _read(filepath_or_buffer, kwds) File "pandas/io/parsers.py", line 457, in _read parser = TextFileReader(fp_or_buf, **kwds) File "pandas/io/parsers.py", line 895, . . . pandas._libs.parsers.TextReader._setup_parser_source FileNotFoundError: [Errno 2] File b'1\r_sample_cases.lgen' does not exist: b'1\r_sample_cases.lgen'
The original name of the data to read is 1_sample_cases.lgen
How can I remove '\r' or at least replace them that the result looks like the name of the data file? I did read a lot of answers about this, but none helped.
Hopefully someone can help me. Thank you,
Ale.
