Workshop on command line tools - day 2

I Workshop on command-line tools

(day 2)

Center for Applied GenomicsChildren's Hospital of Philadelphia

February 12-13, 2015

awk - a powerful way to check conditions and show specific columnsExample: show only CNV that use less than 3 targets (exons)tail -n +2 DATA.xcnv | awk '$8 <= 3'

awk - different ways to do the same thingtail -n +2 DATA.xcnv | awk '$8 <= 3'

# same effect 1

tail -n +2 DATA.xcnv | awk '$8 <= 3 {print}'

# same effect 2

tail -n +2 DATA.xcnv | awk 'if ($8 <= 3) {print}'

# same effect 3

tail -n +2 DATA.xcnv | awk 'if ($8 <= 3) {print $0}'

# different effect

tail -n +2 DATA.xcnv | awk 'if ($8 <= 3) {print $1}'

awk - more options on if statement# Applying XHMM "gold" thresholds (KB >= 1,

# NUM_TARG >= 3, Q_SOME >= 65, Q_NON_DIPLOID >= 65)

tail -n +2 DATA.xcnv | \

awk '$4 >= 1 && $8 >= 3 && $10 >= 65 && $11 >= 65' \

> DATA.gold.xcnv

# Using only awk

awk 'NR > 1 && $4 >= 1 && $8 >= 3 &&

$10 >= 65 && $11 >= 65' DATA.xcnv > DATA.gold2.xcnv

diff - compare files line by line

# Comparediff DATA.gold.xcnv DATA.gold2.xcnv

# Tip: install tkdiff to use a# graphic version of diff

Exercises1. Using adhd.map, show 10 SNPs with rsID starting with 'rs' on

chrom. 2, between positions 1Mb and 2Mb2. Check which chromosome has more SNPs3. Check which snp IDs are duplicated

Suggestions# 1.

grep '\brs' adhd.map | \

awk '$1 == 2 && int($4) >= 1000000 && int($4) <= 2000000' | \

less

# 2.

cut -f1 adhd.map | sort | uniq -c | sort -k1n | tail -1

# 3.

cut -f2 adhd.map | sort | uniq -c | awk '$1 > 1'

More awk - inserting external variablesawk -v Mb=1000000 -v chrom=2 \

'$1 == chrom && int($4) >= Mb && int($4) <= 2*Mb' \

adhd.map | less

# Printing specific columns

awk -v Mb=1000000 -v chrom=2 \

'$1 == chrom && int($4) >= Mb && int($4) <= 2*Mb

{print $1" "$2" "$4}' \

adhd.map | less

Using awk to check number of variantsin ped files# Options using only awk, but takes (much) more time

awk 'NR == 1 {print (NF-6)/2}' adhd.ped

awk 'NR < 2 {print (NF-6)/2}' adhd.ped # Slow, too

# Better alternative

head -n 1 adhd.ped | awk '{print (NF-6)/2}'

# Now, the map file

wc -l adhd.map

time - time command execution

time head -n 1 adhd.ped | awk '{print (NF-6)/2}'real 0m0.485suser 0m0.391ssys 0m0.064s

time awk 'NR < 2 {print (NF-6)/2}' adhd.ped

# Forget… just press Ctrl+Creal 1m0.611suser 0m51.261ssys 0m0.826s

top - display and update sorted information about processes / display Linux taks

top

z : colork : kill processu : choose specific userc : show complete commands running1 : show usage of singles CPUsq : quit

screen - screen manager with terminal emulation (i)

screenscreen -S <session_name>Ctrl+a, then c: create windowCtrl+a, then n: go to next windowCtrl+a, then p: go to previous windowCtrl+a, then 0: go to window number 0Ctrl+a, then z: leave your session, but keep running

screen - screen manager with terminal emulation (ii)

Ctrl+a, then [ : activate copy mode (to scroll screen) q : quit copy modeexit : close current windowscreen -r : resume the only session detachedscreen -r <session_name> : resume specific session detachedscreen -rD <session_name> : reattach session

split - split a file into piecessplit -l <lines_of_each_piece> <input> <prefix>

# Examplesplit -l 100000 adhd.map map_

wc -l map_*

in-line Perl/sed to find and replace (i)head DATA.gold.xcnv | cut -f3 | perl -pe 's/chr/CHR/g'

head DATA.gold.xcnv | cut -f3 | perl -pe 's/chr//g'

# Other possibilities

head DATA.gold.xcnv | cut -f3 | perl -pe 's|chr||g'

head DATA.gold.xcnv | cut -f3 | perl -pe 's!chr!!g'

head DATA.gold.xcnv | cut -f3 | sed 's/chr//g'

# Creating a BED file

head DATA.gold.xcnv | cut -f3 | perl -pe 's/[:-]/\t/g'

in-line Perl/sed to find and replace (ii)# "s" means substitute

# "g" means global (replace all matches, not only first)

# See the difference...

head DATA.gold.xcnv | cut -f3 | sed 's/9/nine/g'

head DATA.gold.xcnv | cut -f3 | sed 's/9/nine/'

# Adding more replacements

head DATA.gold.xcnv | cut -f3 | sed 's/1/one/g; s/2/two/g'

copy from terminal to clipboard/paste from clipboard to terminal

# This is like Ctrl+V in your terminal

pbpaste

# This is like Ctrl+C from your terminal

head DATA.xcnv | pbcopy

# Then, Ctrl+V in other text editor

# On Linux, you can install "xclip"http://sourceforge.net/projects/xclip/

datamash - command-line calculations

tail -n +2 DATA.xcnv | \ head | \ cut -f6,10,11 | \ datamash mean 1 sum 2 min 3 # mean of 1st column # sum of 2nd column # minimum of 3rd column

http://www.gnu.org/software/datamash/

touch - change file access and modification times

ls -lh DATA.gold.xcnvtouch DATA.gold.xcnvls -lh DATA.gold.xcnv

Introduction to "for" looptail -n +2 DATA.xcnv | cut -f1 | sort | uniq | head > samples.txt

for sample in `cat samples.txt`; do touch $sample.txt; done

ls -lh Sample*

for sample in `cat samples.txt`; do

mv $sample.txt $sample.csv;

done

ls -lh Sample*

Variables (i)

i=1name=Leandrocount=`wc -l adhd.map`echo $iecho $nameecho $count

Variables (ii)

# Examplesbwa=/home/users/llima/tools/bwahg19=/references/hg19.fasta

# Do not run$bwa index $hg19

System variablesecho $HOMEecho $USERecho $PWD

# directory where bash looks for your programsecho $PATH

Exercise

1. Create a program that shows input parameters/arguments

2. Create a program (say, "fields", or "colnames") that prints the column names of a <tab>-delimited file (example: DATA.xcnv)

3. Send this program to your PATH

Running a bash script (i)cat > arguments.shecho Your program is $0echo Your first argument is $1echo Your second argument is $2

echo You entered $# parameters.# Ctrl+C to exit "cat"

Running a bash script (ii)bash arguments.shbash arguments.sh A B C D E

ls -lh arguments.sh

-rw-r--r--

# First characterb Block special file.c Character special file.d Directory.l Symbolic link.s Socket link.p FIFO.- Regular file.

chmod - set permissions (i)

Next charactersuser, group, others | read, write, executels -lh arguments.sh-rw-r--r--

# Everybody can read# Only user can write/modify

chmod - set permissions (ii)

# Add writing permission to groupchmod g+w arguments.sh ls -lh arguments.sh# Remove writing permission from groupchmod g-w arguments.shls -lh arguments.sh# Add execution permission to allchmod a+x arguments.shls -lh arguments.sh

chmod - set permissions (iii)

# Add writing permission to group./arguments.sh ./arguments.sh A B C D E# change the namemv arguments.sh arguments# Send to your PATH (showing on Mac)sudo cp arguments /usr/local/bin/# Go to other directory# Type argu<Tab>, and "which arguments"

Run your program again