Miscellaneous code

small bioinformatics helpful codes

Unix/Bash Commands:

Find Commands

1. find meth/ -name "201247470004_R03C01_Grn.idat" -print

Permissions

1. find Liver_MM/ -type d -exec chmod 775 {} ; #directories
2. find Liver_MM/ -type f -exec chmod 664 {} ; #files
3. setfacl -m u:username:r raw_files #set permissions for a user in group

File Transfers:

1. Command for rsync from HTC to PSC. Adding / at the end of Anish_Projects, transfers the contents under this folder, but not the folder itself. rsync -avh --progress -e "ssh -p 2222" Anish_Projects/ abc46@pghbio.bridges.psc.edu:/pghbio/dbmi/Genomics_Core/achakka/File_Transfers/HTC/
2. Macbook to PSC: rsync -avh --progress -e "ssh -p 2222" T1T2T3candidatesequencelist7_12.fa abc46@pghbio.bridges.psc.edu:/pghbio/dbmi/Genomics_Core/achakka/Misc/Moore/Data
3. Bridges to Bridges2 rsync -avh --progress achakka/ achakka@data.bridges2.psc.edu:/ocean/projects/bio140004p/achakka

md5sum

1. md5sum --quiet -c file.md5sum
2. find your_folder -type f -exec md5sum ‘{}’ ; > md5sum.txt ##recursively obtain md5sum values in an entire folder

Text/Files manipulation

1. First occurrence: ${parameter/pattern/string}
2. All occurrences: ${parameter//pattern/string}
3. head -2 file.maf > all.txt; tail -n +3 -q *.maf >> all.txt

SLURM

1. sbatch --dependency=afterok:11254323 job2.sh