test -f yourFile
FILE=/folder/yourFile
if [ -f "$FILE" ]; then
echo "$FILE exists."
else
echo "$FILE does not exist."
fiIf need to match wildcard in the file names
if test -n "$(find /dir/to/search -maxdepth 1 -name 'files*' -print -quit)"
then
echo found
else
echo not found
fiSource:
https://linuxize.com/post/bash-check-if-file-exists/
https://stackoverflow.com/questions/6363441/check-if-a-file-exists-with-wildcard-in-shell-script
echo "ABCD-EFGH" | tr '[:upper:]' '[:lower:]'Source:
https://stackoverflow.com/questions/2264428/how-to-convert-a-string-to-lower-case-in-bash
If there are NaN in the output from computeMatrix, the generated heatmap is not sorted and a warning message stating Mean of empty slice will show up.
To overcome this, those null values need to be replaced using 0 in the computeMatrix step by --missingDataAsZero tag.
computeMatrix scale-regions -S xxx.bw -R xxx.bed --missingDataAsZero -m xxx -b xxx -a xxx --numberOfProcessors xx -o xxx.gz
plotHeatmap -m xxx.gz -out xxx.pngSource:
https://groups.google.com/g/deeptools/c/B55e0kT_0Ec?pli=1
https://github.com/deeptools/deepTools/issues/490
sacct -u username --format=JobID,JobName%30
sacct -u username --format=JobID,TIME,JobName%30,Start%12,Elapsed,NCPU,CPUTimeSource:
https://stackoverflow.com/questions/42217102/expand-columns-to-see-full-jobname-in-slurm
list.remove('element')Source:
https://www.programiz.com/python-programming/methods/list/remove
import os.path
# Check if a file exist, return True/False
os.path.exists("test.txt")
# Check if a directory exist, return True/False, for >= python3.4
import pathlib
pathlib.Path("test").exists()
Source:
https://www.guru99.com/python-check-if-file-exists.html
When we want to use Unix command in python we can directly use os.system() to realize it. However, if we only want to return the output as a string, for example, return ls file names into a string, we need to use subprocess.check_out instead.
To note that, the output from subprocess.check_out() is a bytes object instead of a string, thus we need to further decode to transform into a string.
fileList = subprocess.check_output('ls someFolder/*', shell=True).decode('utf-8').strip().split('\n')Source:
https://stackoverflow.com/questions/606191/convert-bytes-to-a-string
Below commands all work.
df -h /yourDisk
df -h
df -kSource:
https://docs.oracle.com/cd/E23823_01/html/817-0403/spmonitor-6.html
Check running servers:
jupyter notebook listStop running servers (both works):
jupyter notebook stop
kill $(pgrep jupyter)Source:
https://github.com/jupyter/notebook/issues/1950
https://stackoverflow.com/questions/10162707/how-to-close-ipython-notebook-properly/32745046#32745046
with open('file1.txt','r') as f1, open('file2.txt','r') as f2:
for line1, line2 in zip(f1, f2):
if line1 != line2:
print(line1,'\n',line2)