bash_tricks.sh

# makes all files read only
chmod -w *

# renames files with underscores 
for i in *.fastq; do j=$(echo $i | cut -d_ -f1-3 ); k=$(echo $i | cut -d_ -f5); echo mv $i "$j-$k"; done

# adds pwd to $PATH in .bashrc
echo export PATH=$(pwd):$PATH >> ~/.bashrc

# renames files
for file in *.Trinity.fasta
do
	echo mv $file ${file/.trinity_out_2.2.0.Trinity.fasta/}
done

# loop through a set of directories and do stuff:
for f in $(find . -name 'interleave_MMETSP*.qsub.o*'); do ls $f; done

# cp and rename files based on directory name
for i in $(ls); do echo $i; done
for i in */fastqc_report.html; do echo "$i" ${i/fastqc_report.html}"${i%/*}".html; done
for i in */*.html; do echo "*" http://htmlpreview.github.io/?https://github.com/ljcohen/osmotic/blob/master/evaluation_data/fastqc/$i; done

#to kill only specific jobs in the queue
#msu hpcc
qstat -u ljcohen | grep "472" | cut -d "." -f1 | xargs qdel
#ucd farm
squeue -u ljcohen | grep “104517" | sed -r -e "s/[\t\ ]+/./g" | cut -d"." -f 2 | xargs scancel

# top barcodes in unaligned
zcat /ifs/data/sequence/Illumina/production/150501_D00372_0283_BC6UELANXX_Combo_HSQ_59/Data/Intensities/BaseCalls/Unaligned_lanes1-3_5-6/Undetermined_indices/Sample_lane6/lane6_Undetermined_L006_R1_001.fastq.gz | head -400000 | grep '^@HWI' | cut -d : -f 10 | sort | uniq -c | sort -nr | head -20

# list all files and combine all files with same prefix
for i in $(ls | cut -d "_" -f 1,2)
do
    echo $i*_R1*
    echo $i*_R2*
done

# zip files:
zip mmetsp_dib_annotated_fasta.zip fasta/*.fasta
zip mmetsp_dib_annotated_gff.zip gff/*.gff

# find only empty files:
find ~ -empty -type f | wc -l