notes

resources when you’re starting to learn bash and forever after

a learning path could start here: a great command line tutorial for absolute beginners

and then go here for a beginners bash tutorial on tldp.org
my favourite sections are …

and then use these as references as you begin to use bash

and this link because i’m always forgetting how to use …

nohup and redirecting output

nohup program_name 1>log 2>&1 &  

1>log means send stdout to log and
2>&1 means send stderr to the same output as stdout
& means return my prompt
another option to nohup is screen (search this document) or start a process and place it into ‘nohup’ like state using cntrl-z, bg, disown - see below

disowning your processes so you can go home

  1. suppose you start running some command and realize that its not going to finish before you want to go home
  2. ctrl+z to stop (pause) the program and get back to the shell
  3. bg to run it in the background
  4. disown -h so that the process isn’t killed when the terminal closes
  5. Type exit to get out of the shell because now you’re good to go as the operation will run in the background in its own process so its not tied to a shell
  6. undock your laptop, shut it down and go home

tar (tape archive)
name the tar archive first and then specify what goes in in it
tar –cvzf this.tar.gz this

bash debugger http://bashdb.sourceforge.net/
sudo yum install bashdb
http://bashdb.sourceforge.net/bashdb.html#Debugger-Command-Reference

IDE for Bash ? try this plugin for eclipse

an example script http://wiki.centos.org/HowTos/Rotational_backup_with_remote_backup_options

how to parse command line parameters Preferred Method: Using straight bash without getopt[s] Two of the most common ways to pass key value pair arguments are: Straight Bash Space Separated Usage ./myscript.sh -e conf -s /etc -l /usr/lib /etc/hosts

#!/bin/bash
# Use > 1 to consume two arguments per pass in the loop (e.g. each
# argument has a corresponding value to go with it).
# Use > 0 to consume one or more arguments per pass in the loop (e.g.
# some arguments don't have a corresponding value to go with it such
# as in the --default example).
# note: if this is set to > 0 the /etc/hosts part is not recognized ( may be a bug )
while [[ $# > 1 ]]
do
key="$1"

case $key in
    -e|--extension)
    EXTENSION="$2"
    shift # past argument
    ;;
    -s|--searchpath)
    SEARCHPATH="$2"
    shift # past argument
    ;;
    -l|--lib)
    LIBPATH="$2"
    shift # past argument
    ;;
    --default)
    DEFAULT=YES
    ;;
    *)
            # unknown option
    ;;
esac
shift # past argument or value
done
echo FILE EXTENSION  = "${EXTENSION}"
echo SEARCH PATH     = "${SEARCHPATH}"
echo LIBRARY PATH    = "${LIBPATH}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)
if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 $1
fi


#checking command line arguments
#check that the lastname exists and does not start with -
if [[ ! ${LASTNAME} || $(expr match ${LASTNAME} "-") == 1 ]]; then
	cat 1>&2 <<EOF
You have not supplied the last name of the client.
Try typing
	handbackData -h
to get help.
EOF
	exit 1
fi

variable dereferencing ($VAR vs ${VAR} vs “${VAR}”)

when should you use these different forms

if statement

hours of fun
!!! note - numeric comparison operators are -eq, -ne, -lt, -le, -gt or -ge. see http://www.tldp.org/LDP/abs/html/comparison-ops.html !!! note - string comparison operators are ==, !=, <, > !!! note - file test operators are -e, -d, and many more http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_07_01.html !!! note spaces inside square brackets !!! quote arguments as part of good form in case the evaluated form has a space in it … e.g. a=”qwe rty” if [ “$a” < “thisString” ] ….

if [ $# -eq 0 ] # note that $# means number of input args then echo “$0 : You must give/supply one integers” exit 1 fi

if test $1 -gt 0 then echo “$1 number is positive” else echo “$1 number is negative” fi

more hours of fun to evaluate boolean test constructs see http://tldp.org/LDP/abs/html/testconstructs.html this does not do what you think if [ 0 ] || [ 0 ]; then echo TRUE; fi [ ] tests for non-null instead, you want this if (( 0 || 0 )); then echo TRUE; fi especially important when evaluating the outcome of string comparison tests USER=bob #test for presence of variable if [ $USER ]; then echo NON_NULL; fi if [ $(expr match $USER “c”) ]; then echo STARTS_WITH_C; fi #### WRONG #### if (( $(expr match $USER “c”) )); then echo STARTS_WITH_C; fi ## CORRECT ##

testing a boolean

if (( $(expr length $USER) == 0 || $(expr match $USER “-“) )); then echo “username is present and does not start with -“; fi

using boolean test conditions inside [[ will work USER=bob if [[ $USER && $(expr length $USER) == 3 ]]; then echo BLAP; fi if [[ $USER && $(expr match $USER “-“) != 3 ]]; then echo BLAP; fi

what is the difference between [ and [[

while loop to process lines in a file

while read p; do echo $p done <peptides.txt

for loop based on a sequence of strings

GATK_FTP=ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.8/hg19 for f in hapmap_3.3.hg19.sites.vcf.gz \ 1000G_omni2.5.hg19.sites.vcf.gz \ 1000G_phase1.indels.hg19.sites.vcf.gz \ Mills_and_1000G_gold_standard.indels.hg19.vcf.gz ; do \ echo $f; \ curl –remote-name ${GATK_FTP}/${f}; \ done

for loop based on evaluation of a command #!/bin/bash for i in $( ls ); do echo item: $i done

for loop based on a generated sequence #!/bin/bash for i in seq 1 10; do echo $i done

for loop for loop - example 1

if [ $# -eq 0 ] then echo “Error - Number missing form command line argument” echo “Syntax : $0 number” echo “Use to print multiplication table for given number” exit 1 fi n=$1 for i in 1 2 3 4 5 6 7 8 9 10 do echo “$n * $i = expr $i \* $n” done

arrays

#array assignment from a string STRING=”one, two, three” #how to set the internal field separator to comma-space or to tab IFS by default will separate on tab or spaces IFS=’, ‘ # to split on either comma or space IFS=$’\t’ # to split strings on tabs read -r -a array «< “$STRING” #### DONT FORGET QUOTES around $STRING

#To access an individual element: echo “${array[0]}”

#To iterate over the elements: for element in “${array[@]}” do echo “$element” done

#To get both the index and the value: for index in “${!array[@]}” do echo “$index ${array[index]}” done

#The last example is useful because Bash arrays are sparse. In other words, #you can delete an element or add an element and then the indices are not #contiguous. unset “array[1]” array[42]=Earth

#To get the number of elements in an array: echo “${#array[@]}”

#As mentioned above, arrays can be sparse so you shouldn’t use the length to #get the last element. Here’s how you can in Bash 4.2 and later: echo “${array[-1]}”

for loop more examples

PARSESOURCES=

for SOURCE in $SOURCES ; do if ! isin “$SOURCE” $EXCLUDEDSOURCES ; then PARSESOURCES=”${PARSESOURCES}${PARSESOURCES:+ }$SOURCE” fi done

#the term ${PARSESOURCES:+ } introduces a space between each term in the list but only when PARSESOURCES is defined - if this term in the code were replaced with a space, the list would begin with a space - see http://www.gnu.org/software/bash/manual/bashref.html#Shell-Parameter-Expansion

#Another example of parameter expansion URL=file://abc/def/file #the following “${URL#file://}” line means “ strip file:// from the beginning of URL (if it exists) if [ “${URL#file://}” != “$URL” ]; then #if the URL begins with file://

read more about parameter substitution http://tldp.org/LDP/abs/html/parameter-substitution.html#PSUB2

could also use substring matching http://tldp.org/LDP/abs/html/moreadv.html#EX45

for loop example 3 for FILENAME in *.mitab.06-06-2013.txt ; do NEWFILENAME=echo $FILENAME | sed 's/06-06-2013/06062013/' ; mv $FILENAME $NEWFILENAME ; done

then zip them up

for file in ls -1 *.mitab.*; do zip “$file”.zip “$file”; done;

for loop example 4 find all files with a given extension and return a non redundant list of all the directories in which they occur

for file in find . *.py -type f; do echo dirname $file » fileofresults; done; or for file in locate *.py; do echo dirname $file » fileofresults; done;

then do

cat fileofresults sort -u

assigning the output of a command to a variable

`` or “$()” notation

#see command substitution - http://www.gnu.org/software/bash/manual/bashref.html#Command-Substitution ALL_SCORES=cut -f 41 All.mitab.04-07-2015.txt | sort | uniq #or ALL_SCORES=$(cut -f 41 All.mitab.04-07-2015.txt | sort | uniq) #or - quoting matters only for multi-line commands ALL_SCORES=”$(cut -f 41 All.mitab.04-07-2015.txt | sort | uniq)”

assigning a tab character to a variable and passing it as a parameter INPUT_DELIM=$’\t’ cut -d “${INPUT_DELIM}” -f 1 some_tab_delimited_file

how to find lines with some value in a specific column

#use awk to find mitab lines with P in the 41st column head All.mitab… > tmp awk ‘BEGIN {FS=”\t”}{if($41 == “P”) print $1}’ < tmp #or pipe it together head All.mitab… | awk ‘BEGIN {FS=”\t”}{if($41 == “P”) print $1}’ #using a regular expression in awk awk ‘BEGIN{FS=”\t”}{if($14 ~ /bind:304633/) print $0}’ < All.mitab.04-07-2015.txt

#use grep to find 866 in the second column of a space-delimited line #-P are for Perl regex grep -P ‘^\S+\s+this123\b’

printing a specific line from a file using mapfile (built-in bash command) mapfile -s 42 -n 3 < All.mitab.04-07-2015.txt printf ‘%s’ “${MAPFILE[2]}” #or echo “${MAPFILE[2]}”

collating (joining/merging) columns/results from multiple files on a common key

join

given the following files tmp0 0 1 2 3 4 5 6 7

tmp1 0 cat 1 has 2 four 3 legs 4 ok 5 tmp1 7 end

tmp2 0 a 1 flower 2 has 3 none 4 ok 6 tmp2 7 end

join -1 1 -2 1 -t $’\t’ -a 1 -a 2 -o 0,1.2,2.2 -e “NA” <(sort tmp1) <(sort tmp2)

join -1 1 \ #key for file 1 is in column 1 -2 1 \ #key for file 2 is in column 1 -t $’\t’ \ # field separator for input/output is a tab -a 1 \ # include all lines from file 1 (i.e. left join) -a 2 \ # include all lines from file 2 (i.e. right join) -o 0,1.2,2.2 \ # format output like this -e “NA” \ # use this string for missing values <(sort tmp0) \ #sort file 1 input <(sort tmp2) #sort file 2 before input <() = bash process substitution

WARNING - DO NOT USE JOIN To ATTEMPT OUTER JOINS ON MULTIPLE FILES write to bug-coreutils@gnu.org the -e option is only available if you specify the output option so you can’t use it to join columns from multiple files (like you might think you can - hours of fun) - the script below overcomes this shortcoming by first re-writing all of the output files so that they contain all of the keys and NA in cases where the the starting file does not contain an entry for that key

implementing a full-outer join using join in bash

the script below does a full outer join on multiple output files that have a common set of keys but where many of the result files will be missing results for some keys

the result files are from bismark methylation extractor and the files are named sample_name.bismark.cov.gz

the script follows 4 main steps first - make a list of unique keys found in any of the files second - rewrite each file as just two columns (a key and a data result) third - rewrite files with all keys (and add an NA to those samples that are missing data for a given key) fourth - full-outer join to create a matrix on all keys on all samples

###

#!/bin/bash

collate.sh

#

collect columns from multiple output files into a key by sample matrix

based on join

author: Ian Donaldson - i.donaldson@qmul.ac.uk

#

usage

review the params below then

./collate.sh

#

set these parameters

PROJECT_DIR=/data/WHRI-GenomeCentre/idonaldson/bisulfite_dev INPUT_DIR=${PROJECT_DIR}/results_bismark_consol OUTPUT_DIR=${PROJECT_DIR}/results_collate #multiple columns in the input file may be specified to create a compound key column KEY_COL=”1,2” #only one column in the input file may be specified as the input column DATA_COL=4 #samples without a data entry for some key will be assigned an NA value (character or string) NA=”NA” #an extension string can be removed from the name of uncompressed input files to get the sample name #so if the input files are named like “sample_name.bismark.cov.gz”, you could specify “.bismark.cov” EXTENSION=”.bismark.cov” #these working directories can be left as is TMP_DIR=${OUTPUT_DIR}/tmp KEY_FILE=${TMP_DIR}/keys

###

no changes required beyond this point

###

#all output files will be written to a single sub-directory if [ ! -e ${OUTPUT_DIR} ]; then mkdir -p ${OUTPUT_DIR}; fi if [ ! -e ${TMP_DIR} ]; then mkdir -p ${TMP_DIR}; fi

#cp data files to be consolidated to a tmp dir find ${INPUT_DIR} -name .bismark.cov.gz | xargs cp -t ${TMP_DIR}/. gunzip ${TMP_DIR}/

step 1

#rewrite all input data files in two columns (key and data) format #this allows for creation of compound keys by pasting together multiple columns specified by KEY_COL for THIS_FILE in $(ls ${TMP_DIR}); do cut –output-delimiter ‘|’ -f ${KEY_COL} ${TMP_DIR}/${THIS_FILE} > ${TMP_DIR}/key.${THIS_FILE} cut -f ${DATA_COL} ${TMP_DIR}/${THIS_FILE} > ${TMP_DIR}/data.${THIS_FILE} paste ${TMP_DIR}/key.${THIS_FILE} ${TMP_DIR}/data.${THIS_FILE} > ${TMP_DIR}/key_data.${THIS_FILE} rm ${TMP_DIR}/data.${THIS_FILE} rm ${TMP_DIR}/key.${THIS_FILE} rm ${TMP_DIR}/${THIS_FILE} done

step 2

#collect a non-redundant list of keys from all input files #keep the file sorted and unique in place to keep mem requirements low echo “!key.sample” > ${KEY_FILE} for THIS_FILE in $(ls ${TMP_DIR}/key_data.*); do cut -f 1 ${THIS_FILE} » ${KEY_FILE} sort -u -o ${KEY_FILE} ${KEY_FILE} done

step 3

#a. add an entry corresponding to the header (see key.sample in KEY_FILE) #b. rewrite the files again so that all keys are present in each with NA’s for missing data for THIS_FILE in $(ls ${TMP_DIR}/key_data.*); do # a FILE_NAME=$(basename ${THIS_FILE} ${EXTENSION}) COL_NAME=${FILE_NAME:9} echo -e “!key.sample\t${COL_NAME}” » $THIS_FILE # b join -1 1 -2 1 -t $’\t’ -a 1 -a 2 -o 0,2.2 -e “${NA}” ${KEY_FILE} <(sort ${THIS_FILE}) > “${TMP_DIR}/complete_${FILE_NAME}” #wc -l “${TMP_DIR}/complete_${FILE_NAME}” done

step 4

COLLATED=${TMP_DIR}/collated cp ${KEY_FILE} ${COLLATED} TMP_COLLATED=${TMP_DIR}/tmp_collated for THIS_FILE in $(ls ${TMP_DIR}/complete_*); do join -1 1 -2 1 -t $’\t’ ${COLLATED} <(sort ${THIS_FILE}) > ${TMP_COLLATED} mv ${TMP_COLLATED} ${COLLATED} done

exit

other solutions for collating result columns from multiple files awk perl python python pandas/numpy R

Math (arithmetic in bash) http://www.bashguru.com/2010/12/math-in-shell-scripts.html use the $((EXPR)) construct for integer math num=$((num1 + num2)) num=$(($num1 + $num2)) # also works num=$((num1 + 2 + 3)) # … num=$[num1+num2] # old, deprecated arithmetic expression syntax

bash does not support floating point and requires an external tool num=$(awk “BEGIN {print $num1+$num2; exit}”) num=$(python -c “print $num1+$num2”) num=$(perl -e “print $num1+$num2”) num=$(echo $num1 + $num2 | bc) # whitespace for echo is important

Printing http://wiki.bash-hackers.org/commands/builtin/printf

here documents

cat 1>&2 «EOF You have not supplied the email of the client. Try typing handbackData -h to get help. EOF

grep and regex

http://www.cyberciti.biz/faq/grep-regular-expressions/

to select all but lines that contain some regex and write to a new file where the regex has a tab in it:

grep -Pv ‘abc\tefg’ some_file > some_new_file or

grep -v $’abc\tefg’ some_file > some_new_file

grep with color in less

grep –color=always someString inthisFile.txt less -R

can i grep on a specific column?

given 0,170,3,1,27,170,3,1,27,1490 0,304,2,2,40,304,2,2,40,1473 0,191,1,0,0,191,1,0,0,0 …

how to combine (AND/OR) grep expressions given a tmp file with: a b c ab

you can pipe greps together to simulate AND grep a tmp | grep b ab

there is no grep AND operator but you can use an expression like

grep -E “^[^a]*b” tmp b

you can use extended grep with a pipe to simulate OR grep -E “a|b” tmp a b ab

or the equivalent in normal regex grep “a|b” tmp

or specify two expressions grep -e a -e b tmp

string operations and regex

a=1234zipper43231 echo “The string being operated upon is "$a".”

length: length of string

b=expr length $a echo “Length of "$a" is $b.”

index: position of first character in substring

that matches a character in string

echo “Numerical position of first "2" in "$a" is "$b".”

substr: extract substring, starting position & length specified

b=expr substr $a 2 6 echo “Substring of "$a", starting at position 2,\ and 6 chars long is "$b".”

#find the index of a substring b=expr index "bob" "o"

#string operations using parameter substitution http://tldp.org/LDP/abs/html/string-manipulation.html ${var#SubStr} # will drop begin of string upto first occur of SubStr ${var##SubStr} # will drop begin of string upto last occur of SubStr ${var%SubStr} # will drop part of string from last occur of SubStr to the end ${var%%SubStr} # will drop part of string from first occur of SubStr to the en

#replace all returns in a file with tabs tr ‘\n’ ‘\t’ < in_file > out_file

#transposing a tab-delimited file using awk

#first replace spaces with underscores tr ‘ ‘ ‘_’ < original.file > no.space.file

transpose.awk { for (i=1; i<=NF; i++) { a[NR,i] = $i } } NF>p { p = NF } END {
for(j=1; j<=p; j++) { str=a[1,j] for(i=2; i<=NR; i++){ str=str” “a[i,j]; } print str } }

then do awk -f transpose.awk no.space.file > outfile

check the file using how to view tabs and returns and white-space characters in less cat -vet filename | less -S

match

The default behavior of the ‘match’ operations is to

#+ search for the specified match at the BEGINNING of the string. #

Using Regular Expressions …

b=expr match "$a" '[0-9]*' # Numerical count. echo Number of digits at the beginning of "$a" is $b. b=expr match "$a" '\([0-9]*\)' # Note that escaped parentheses

== == #+ trigger substring match.

echo “The digits at the beginning of "$a" are "$b".”

how can I GREP a particular data in a certain column. For example, I like to grep the data for column 6 with the vule of 52. I should have :

0 52 3 3 62 52 3 3 62 1411 0 52 2 2 14 52 2 2 14 1501 0 52 3 4 14 52 3 4 14 1473 0 52 1 3 48 52 1 3 48 1431

Code: awk -F, ‘{ if ($6 == 52) print $0 }’ input.txt

The grep solution looks ugly.

Code: grep “^[^,],[^,],[^,],[^,],[^,]*,52,” input.txt

find all of the protein-protein interactions in a mitab file awk ‘BEGIN {FS=”\t”;}{if ($21 == “psi-mi:"MI:0326"(protein)” && $22 == “psi-mi:"MI:0326"(protein)”) print $0;}’ < matrixdb_CORE.tab

finding the next most likely word given a string of words and a training corpus coursera capstone data science swiftkey project

Very early observations on the Bills game: Offense still struggling but the

grep -oiP ‘but the \w+’ all.txt tr ‘[:upper:]’ ‘[:lower:]’ sort uniq -c grep “^\s*[0-9][0-9][0-9]”

using context

grep -i ‘offense’ all.txt grep -oiP ‘but the \w+’ tr ‘[:upper:]’ ‘[:lower:]’ sort uniq -c grep “^\s*[0-9]”

#so what is the correct answer grep -oiP ‘but the (crowd|referees|defense|players)’ all.txt | tr ‘[:upper:]’ ‘[:lower:]’ | sort | uniq -c | grep “^\s*[0-9][0-9]”

#look ahead and look behind http://unix.stackexchange.com/questions/13466/can-grep-output-only-specified-groupings-that-match

#grep - identifying characters by unicode codes - different types of apostrophes

grep(“\u2019”, crps[[1]]$content[2], value=TRUE) [1] ““I don’t know. Maybe they’re getting too much sun. I think I’m going to cut them way back.” I replied.”

gsub(“\u2019”, “'”, crps[[1]]$content[2]) [1] ““I don’t know. Maybe they’re getting too much sun. I think I’m going to cut them way back.” I replied.”

more about unicode http://www.fileformat.info/info/unicode/index.htm

sed

a simple sed script to substitute text in a script will replace first occurrence on each line of blap with blip sed ‘s/blap/blip/’ infile will replace all occurrences on each line of blap with blip sed ‘s/blap/blip/g’ infile

remember to use double quotes to pass a variable to a sed script BLAP=”blap” sed “s/$BLAP/blip/” infile

sed s/InnateDB:/innatedb:IDB-/ file.3.innatedb

its possible to do in place replacement using

sed -i ‘.bak’ s/foo/bar/g fileIn

replacing the ‘.bak’ with an empty ‘’ for the -i parameter means that no backup of the original will be made

heres a useful script to do inplace substitutions

#!/bin/sh

replace.sh

#

find and replace by a given list of files

usage

replace.sh foo bar file

find_this=”$1” replace_with=”$2” this_file=”$3”

sed -i ‘’ “s/$find_this/$replace_with/” “$this_file”

#convert the fasta file to one line per sequence and remove fasta headers cat tmp | sed -r ‘s/>.*$/9/’ | tr -d ‘\n’ | tr ‘9’ ‘\n’ > tmp2 awk ‘{print length}’ > sizes

write a sed script to replace names in the gtf file with more readable gene names

#first obtain gtf file for susScr3 followed protocol - ObtainingGeneAnnotations to obtain from the UCSC Genome Table Browser utility and saved as susScr3-ensembl.gtf and susScr3-ucsc2ensembl-names.txt in

/data/WHRI-GenomeCentre/data/ref/susScr3/GTF

then make a table of name conversions cut -f 8,9 susScr3-ucsc2ensembl-names.txt | sort -u | head -n -2 > ensembl2name

where the last head -n -2 removes the original table header and the row with na na this table looks like ENSSSCT00000000003.2 GTSE1 ENSSSCT00000000004.2 TTC38

cd /data/WHRI-GenomeCentre/data/ref/susScr3/GTF

cp susScr3-ensembl.gtf susScr3-ensembl.gtf.bk cp susScr3-ensembl.gtf tmp wc -l tmp #510144 tmp wc -l ensembl2name #21394 ensembl2name

while read THIS_LINE; do START=$(date +%s.%N);

read -d "\t" -a THIS_ARRAY <<< ${THIS_LINE};
ENSM_NAME=${THIS_ARRAY[0]};
GENE_NAME=${THIS_ARRAY[1]};
sed "s/${ENSM_NAME}/${GENE_NAME}/" < tmp > tmp2;
mv tmp2 tmp

#END=$(date +%s.%N); DIFF=$(echo "$END - $START" | bc);echo $DIFF; done < ensembl2name.tmp

more on sed http://www.grymoire.com/Unix/Sed.html http://www.grymoire.com/Unix/Quote.html http://www.grymoire.com/Unix/Regular.html

awk http://www.grymoire.com/Unix/Awk.html

a very simple awk script

ls -l | awk ‘ BEGIN { print “File\tOwner”; FS=”\t”; # the default file separator is white-space } { print $8, “\t”, $3} END { print “ - DONE -“ } ‘

other ways of running this are

1)specify an input file (input.1) and an output file (output.1)

ls -l > input.1

awk ‘ BEGIN { print “File\tOwner” } { print $8, “\t”, $3} END { print “ - DONE -“ } ‘ < input.1 > output.1

2) add a line to beginning of above #!/bin/sh then save to a file and run by typing

awk -f filename

3) make the file itself executable by changing the first lien to #!/bin/awk -f

find the length of the longest line in a file using wc or awk wc -L or awk ‘ { if ( length > x ) { x = length } }END{ print x }’ filename

sort

sort on a column

bob 123 alice 1 jeremy 111

sort -k2 #to sort on the second column asciibetically sort -k2 -n #to sort numerically

http://ss64.com/bash/

viewing a tab delimited file as line delimited

head | awk -v OFS='\n' '{$1=$1;print}'

#for mitab files awk ‘BEGIN{FS=”\t”;OFS=”\n”;ORS=”\n\n*********\n\n”;}{$1=$1;print}’

http://unix.stackexchange.com/questions/28484/how-can-i-convert-tab-delimited-data-to-comma-delimited-data

wget

cron jobs to backup data

man crontab

crontab -l #to list current cron jobs

crontab -e #to edit the crontab file

0 22 * * * cp -r /home/ian /storage2/backups/.

this line means at 0 minutes and 22 hours

cp -r /home/ian /storage2/backups/.

apparently any output of a command will be sent to the users registered email

0 22 * * * cp -r /home/ian /storage2/backups/.

21 20 * * * /home/ian/bkscript/bkscript

email

#setting up email $ sudo vi /etc/aliases Scroll down to the person who gets roots email

root: marc

Uncomment the line and change the value to your choice root example@yourdomain.com You can also send it to existing users as below root: username1, username2 Save and close the file, then run the following to implement changes. newaliases

Now send a test Email to check it works properly.

echo “Test Email” | mail -s “This is a test email.” externalemail@domain.com

timing scripts

  1. use the time function for single commands like ‘ls’ mytime=”$(time ( ls ) 2>&1 1>/dev/null )” echo “$mytime”

real 0m0.006s user 0m0.001s sys 0m0.005s

  1. use the date function and the bc function (basic precision calculator)

START=$(date +%s.%N) command END=$(date +%s.%N) DIFF=$(echo “$END - $START” | bc) echo $DIFF

scp, ssh - secure copy and secure shell - loginless setup imagine two machines: host_src (source) and host_dest (destination) and you want to ssh or scp without having to login ( say from a script)

on host_src ssh-keygen -t rsa scp ~/.ssh/id_rsa.pub @host_dest:.

then ssh to host_dest cat id_rsa.pub » ~/.ssh/authorized_keys chmod 700 ~/.ssh/authorized_keys

transferring large data sets see http://moo.nac.uci.edu/~hjm/HOWTO_move_data.html#rsync or http://www.cyberciti.biz/faq/lftp-mirror-example/ for overview consider using lftp -multistreaming protocol like bbcp

browsing with lftp lftp lftp :~> open -u anonymous,ian.oslo@gmail.com ftp.ensembl.org

problems with proxy and lftp it may be necessary to manually set the proxy (or rather in case below unset it

So it looks as if the connecting is being sent to the proxy server. I can see this by running “debug” before performing ls:

adm.talmage@mplinux03p:~$ lftp ftp://jicdiejy:wymhi-bison-83@bsg-ftp.well.ox.ac.uk

lftp jicdiejy@bsg-ftp.well.ox.ac.uk:~> debug

lftp jicdiejy@bsg-ftp.well.ox.ac.uk:~> ls

—- Connecting to proxy ws500b (10.158.0.29) port 8080

`ls’ at 0 [Logging in…]

The proxy server is not socks compliant, so I believe it can only handle HTTP and HTTPS connections. Its probably just flat out refusing this connection.

I’m not sure where lftp will be picking up these proxy settings from, but I got this to work by doing the following to disable the proxy settings first. Unfortunately, this needs to be done each time as I’ve no idea where its configured globally, so resets itself the next time you connected:

lftp jicdiejy@bsg-ftp.well.ox.ac.uk:/> lftp ftp://jicdiejy:wymhi-bison-83@bsg-ftp.well.ox.ac.uk lftp jicdiejy@bsg-ftp.well.ox.ac.uk:/> set ftp:proxy lftp jicdiejy@bsg-ftp.well.ox.ac.uk:/> ls drwxrwsr-x 2 ftp ftp 16384 Feb 07 03:17 180202_K00150_0283_AHNJ22BBXX drwxrwsr-x 2 ftp ftp 49152 Feb 16 13:10 180213_K00150_0289_BHNFTCBBXX drwxrwsr-x 2 ftp ftp 16384 Mar 09 07:43 180307_K00150_0299_BHTCYJBBXX lftp jicdiejy@bsg-ftp.well.ox.ac.uk:/> cd 180202_K00150_0283_AHNJ22BBXX/

rsync

rsync -avz me@remote.url:somedir/somefile .

wget https://www.labnol.org/software/wget-command-examples/28750/

Download a file and save it in a specific folder wget ‐‐directory-prefix=folder/subfolder example.com

compressing files pigz - use for fast parallel compression of files

find see also http://javarevisited.blogspot.co.uk/2011/03/10-find-command-in-unix-examples-basic.html also has good advice on using with exec and xargs (see note on print0 if filenames might have spaces in them) about prune parameter http://www.theunixschool.com/2012/07/find-command-15-examples-to-exclude.html

find a file anywhere at or below your current position with blap in the name

find . -name ‘*’

dont descend into directories you dont have permission for find . ! -readable -prune -o -name ‘blap’ or find . ! -perm u+r,g+r,o+r -prune -o -name ‘blap

! means not -readable evaluates to true if the file/directory is readable -perm u+r,g+r,o+r does the same as -readable -prune will ignore everything that meets prior conditions (i.e. will not attempt to descend into directories for which it does not have permission) -o is the or operator for find -name

carry out a command on every file returned by find find . -name “A1-AD*.fastq.gz” -exec ls -1 {} \;

carry out a command on everyfile returned by find using xargs removing files find . -name “*.tmp” -print | xargs rm –f

grep files find . –name "*.txt" –print | xargs grep "Exception"

it is possible to access the list item from within xargs: try; find . -name “*.bak” -print0 | xargs -0 -I file mv file ~/old.files where -I (replace-string) assigns the STDIN to the ‘variable’ called file Read more: http://javarevisited.blogspot.com/2011/03/10-find-command-in-unix-examples-basic.html#ixzz3rkRSxT2P

xargs

seq 1 3 | xargs -n 1 -t ./test.sh where test.sh is

#!/bin/bash #test.sh echo $1

-n 1 = take 1 argument at a time from stdin (can also use 2,3,….) -t = echo the command before executing it -p = prompt the user before executing

xargs –show-limits will display limits set by OS on xargs -P = sets the maximum number of processes that will execute at once note that many processes may simultaneously write to STDOUT

xargs advanced One of the problems with running xargs as multiple parallel processes is that all of them may write to STDOUT and if this happens, the output from multiple processes will all be jumbled. optimally, you would like each process to write to a separate log file. to do this, you could use something like:

seq 1 3 xargs -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out”

let’s decompress this

-I THIS the -I parameter of xargs will assign the input to the variable name THIS. this varaible can then be referenced in the following section of the code. note that you sometime see this written as -I{} and then the captured input value is referenced using ‘{}’

sh -c “…” instead of passing our test.sh script to xargs as we did above, we pass it a call to the shell (sh) with the -c parameter which allows us to specify a command string that can have spaces in it so long as the entire command is encapsulated in quotes

./test.sh ‘THIS’ this calls our original script with a single parameter specified by the value in the THIS variable. The single quotes ensure that values of THIS with a space in them will be passed as a single argument

‘THIS’.out STDOUT is redirected to a file called 1.out note the single quotes again for the same reason

The above command can now be run using multiple parallel processes using -P:

seq 1 3 xargs -P 2 -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out”

#something a little more daring seq 1 100 | xargs -P 100 -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out”

#alter test.sh to make it non-trivial sleep 5s

#then compare these two seq 1 10 | xargs -P 10 -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out” seq 1 10 | xargs -P 1 -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out”

you can always write time ….one of the above lines or some other command…. to get an exact measure of time taken (real, user and system)

finally, you might consider using parallel to run jobs in parallel

copying large numbers of files suppose you want to move 7200 fastq files that are in various subdirectories try passing to xargs two files at a time (-n 2) and using 5 processes -P 5:

nohup find . -name “*_R2.fastq” xargs –verbose -P 5 -n 2 cp -t /target_dir/. 1>~/nohup.cp.out 2>&1 &

#or try just using find and exec nohup find . -name “*_R2.fastq” exec cp -t /target_dir/. {} + 1>~/nohup.cp.out 2>&1 &

to mv files you need to use

find . -name “*.fastq.gz” | xargs -I ‘{}’ mv ‘{}’ new_location

#N.B. {}+ notation will send as many file names to copy to the cp command as it can at once as opposed to just one at a time if you used the notation … find . -name “*_R2.fastq” exec cp -t /target_dir/. {} \;

trying to use rsync to copy a subset of files using –exclude and –include is possible but it has an unwieldy syntax that is difficult to use; you would need to review the man page for rsync (whole section on filters). once rsynced, you would have to search for and move all of the files you wanted into a single directory if you were not happy to leave them in the original directory structure

something like this nohup rsync -a \ –include ‘subdir_exprs’ \ –include ‘_R2.fastq’ \ source_dir_name \ target_dir_name \ 1>~/nohup.cp.out 2>&1 & followed by a find …| xargs mv command or find fastq_demultiplex -name “_R2.fastq” -exec mv -t . {} +

parallel

sudo apt install parallel man parallel # excellent man page has same params as xargs plus lots more and simplified syntax

seq 1 10 parallel -P 10 -n 1 -t -I THIS sh -c “./test.sh ‘THIS’ > ‘THIS’.out”

but now there is no need for the sh -c seq 1 10 | parallel -P 10 -n 1 -t -I THIS “./test.sh ‘THIS’ > ‘THIS’.out”

screen

#to start a new session screen #do something #cntrl-a will send commands (usually just one letter) to the screen application instead of to the console, so, for example, if you wanted to detach from the screen session, you yould type cntrl-a d

‘d’ means to detach from the session

#go home and log in to the machine, then type screen -r # to re-attach to an existing screen session

#getting help: #https://www.rackaid.com/blog/linux-screen-tutorial-and-how-to/ #man screen