My sample data File is
$ cat /fullpath/myfile.csv
a#gmail.com, A Singh
k#gmail.com, K Singh
I am using script.sh
#!/bin/bash
while IFS= read -r line
do
email=$(echo $line | awk -F, '{print $1 }')
name=$(echo $line | awk -F, '{print $2 }')
echo | mailx -v -s "Helo $name" -S smtp-use-starttls -S ssl-verify=ignore -S smtp-auth=login -S smtp=smtp://smtp.gmail.com:587 -S from="xxxx#gmail.com(John Smith)" -S smtp-auth-user=xxxx#gmail.com -S smtp-auth-password=xxxxpassword -S ssl-verify=ignore -S nss-config-dir=~/.certs "$name<$email>"
done < /fullpath/myfile.csv
what is the correct syntax of adding receiver name
I am looking for syntax which I am not able to find
I tried below
"$name<$email>"
$name<$email>
-S to:"$name<$email>"
-S To:"$name<$email>"
-S To: "$name <$email>"
-S To: $name <$email>
its picking names (A Singh) as email and say invalid email. if i use To, it pick TO as email. i.e. whatever come 1st after certs code pic that as email.
According to the standard documentation, mailx does not seem to support the -S option, but some systems may add this option.
I recommend you use GNU Mailutils.
To specify a "FROM" name and address, you can use the "-a" option.
-a header:value
--append=header:value
Append the given header to the composed message.
To specify the receiver name and address, just like you did, add name and email to the end of the command will do the work.
#!/bin/bash
while IFS= read -r line
do
email=$(echo $line | awk -F, '{print $1 }')
name=$(echo $line | awk -F, '{print $2 }')
mail -s "Hello $name" -a "From: John Smith<xxxx#gmail.com>" "$name<$email>"
#echo | mailx -v -s "Helo $name" -S smtp-use-starttls -S ssl-verify=ignore -S smtp-auth=login -S smtp=smtp://smtp.gmail.com:587 -S from="xxxx#gmail.com(John Smith)" -S smtp-auth-user=xxxx#gmail.com -S smtp-auth-password=xxxxpassword## -S ssl-verify=ignore -S nss-config-dir=~/.certs "$name<$email>"
done < ./myfile.csv
Related
#!/bin/bash
# I get the newest file in Directory
latest_file=$(ls -t | head -n 1)
getAlldoublicate()
# getting Token syntax error here getAlldoublicate() '{
{
Alldoublicate=$(tr -s ',' ' ' <latest_file | awk '{print $2" "$3" "$4}' | uniq -d)
# here I try to find dublicate rows in csv
}
if [[ -s latest_file]] ; then
# here I check if file is emty
getAlldoublicate
else
cat "$latest_file" | mailx -s "$latest_file is empty" bla..`#bla
fi
I guess this is your code.
#!/bin/bash
# I get the newest file in Directory
latest_file=$(ls -t | head -n 1)
# getting Token syntax error here
getAlldoublicate()
{
# here I try to find dublicate rows in csv
Alldoublicate=$(tr -s ',' ' ' < $1 | awk '{print $2" "$3" "$4}' | uniq -d)
}
if [[ -s $latest_file ]]; then
# here I check if file is emty
getAlldoublicate $latest_file
else
cat $latest_file | mailx -s "$latest_file is empty" bla.. #bla
fi
Three points you need to pay attention:
function must be defined first before being use.
You can pass the latest_file as an argument when calling getAlldoublicate. Then you could use it by $1 in the function. ($0 stands for the function being called itself).
It would be better if you read the How to Format Tutorials before asking questions.
I have a problem
I Have a program general like this gene.sh
that for all file (es file: geneX.csv) make a directory with the name of gene (example: Genex/geneX.csv) next this program compile an other program inside gene.sh but this progrm need a varieble and I dont know how do it.
this is the program gene.sh
#!/bin/bash
# Create a dictory for each file *.xls and *.csv
for fname in *.xlsx *csv
do
dname=${fname%.*}
[[ -d $dname ]] || mkdir "$dname"
mv "$fname" "$dname"
done
# For each gene go inside the directory and compile the programs getChromosomicPositions.sh to have the positions, and getHapolotipeStings.sh to have the variants
for geni in */; do
cd $geni
z=$(tail -n 1 *.csv | tr ';' "\n" | wc -l)
cd ..
cp getChromosomicPositions.sh $geni --->
cp getHaplotypeStrings.sh $geni
cd $geni
export z
./getChromosomicPositions.sh *.csv
export z
./getHaplotypeStrings.sh *.csv
cd ..
done
This is the program getChromosomichPositions.sh:
rm chrPosRs.txt
grep '^Haplotype\ ID' $1 | cut -d ";" -f 4-61 | tr ";" "\n" | awk '{print "select chrom,chromStart,chromEnd,name from snp147 where name=\""$1"\";"}' > listOfQuery.txt
while read l; do
echo $l > query.txt
mysql -h genome-mysql.cse.ucsc.edu -u genome -A -D hg38 --skip-column-names < query.txt > queryResult.txt
if [[ "$(cat queryResult.txt)" == "" ]];
then
cat query.txt |
while read line; do
echo $line | awk '$6 ~/rs/ {print $6}' > temp.txt;
if [[ "$(cat temp.txt)" != "" ]];
then cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g' > temp.txt;
./getHGSVposHG19.sh temp.txt ---> Hear the problem--->
else
echo $line | awk '{num=sub(/.*:g\./,"");num+=sub(/\".*/,"");if(num==2){print};num=""}' > temp2.txt
fi
done
cat query.txt >> varianti.txt
echo "Missing Data" >> chrPosRs.txt
else
cat queryResult.txt >> chrPosRs.txt
fi
done < listOfQuery.txt
rm query*
hear the problem:
I need to enter in the file temp.txt and put automatically at the beginning of the file the variable $geni of the program gene.sh
How can I do that?
Why not pass "$geni" as say the first argument when invoking your script, and treating the rest of the arguments as your expected .csv files.
./getChromosomicPositions.sh "$geni" *.csv
Alternatively, you can set it as environment variable for the script, so that it can be used there (or just export it).
geni="$geni" ./getChromosomicPositions.sh *.csv
In any case, once you have it available in the second script, you can do
if passed as the first argument:
echo "${1}:$(cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g')
or if passed as environment variable:
echo "${geni}:$(cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g')
Hi I have the following batch script where I submitted each file to a separate processing as follows:
for file in ../Positive/*.txt_rn; do
bsub <<EOF
#BSUB -L /bin/bash
#BSUB -W 150:00
#BSUB -M 10000
#BSUB -n 3
#BSUB -e /somefolder/errors/%J.err
#BSUB -o /somefolder/errors/%J.out
while read line; do
name=`cat \$line | awk '{print $1":"$2"-"$3}'`
four=`cat \$line | awk '{print $4}' | cut -d\: -f4`
fasta=\$name".fa"
op=\$name".rs"
echo \$name | xargs samtools faidx /somefolder/rn4/Rattus_norvegicus/UCSC/rn4/Sequence/WholeGenomeFasta/genome.fa > \$fasta
Process -F \$fasta -M "list_"\$four".txt" -p 0.003 | awk '(\$5 >= 0.67)' > \$op
if [ -s "\$op" ]
then
cat "\$line" >> ../Positive_Strand/$file".cons"
fi
rm \$lne
rm \$op
rm \$fasta
done < $file
EOF
done
I am am somehow unable to store the values of the column from the line (which is in $line variable into the $name and $four variable and hence unable to carry on further processes. Also any suggestions to edit the code for a better version of it would be welcome.
If you change EOF to 'EOF' then you will more properly disable shell interpretation. Your problem is that your back-ticks (`) are not escaped.
I've fixed your indentation and cleaned up some of your code. Note that the syntax highlighting here doesn't understand cat <<'EOF'. If you paste that into vim with highlighting enabled, you'll see that block is all the same color since it's just a string.
bsub_helper() {
cat <<'EOF'
#BSUB -L /bin/bash
#BSUB -W 150:00
#BSUB -M 10000
#BSUB -n 3
#BSUB -e /somefolder/errors/%J.err
#BSUB -o /somefolder/errors/%J.out
while read line; do
name=`cat $line | awk '{print $1":"$2"-"$3}'`
four=`cat $line | awk '{print $4}' | cut -d: -f4`
fasta="$name.fa"
op="$name.rs"
genome="/somefolder/rn4/Rattus_norvegicus/UCSC/rn4/Sequence/WholeGenomeFasta/genome.fa"
echo $name | xargs samtools faidx "$genome" > "$fasta"
Process -F "$fasta" -M "list_$four.txt" -p 0.003 | awk '($5 >= 0.67)' > "$op"
if [ -s "$op" ]
then
cat "$line" >> "../Positive_Strand/$file.cons"
fi
rm "$lne" "$op" "$fasta"
EOF
echo " done < \"$1\""
}
for file in ../Positive/*.txt_rn; do
bsub_helper "$file" |bsub
done
I created a helper function because I needed to get the input in two commands. I am assuming that $file is the only variable in that block that you want interpreted. I also surrounded that variable (among others) with quotes so that the code can support file names with spaces in them. The final line of the helper has nested double quotes for this reason.
I left your echo $name | xargs … line alone because it's so odd. Without quotes around $name, xargs will take each whitespace-separated entry as its own file. With quotes, xargs will only supply one (likely invalid) file name to samtools.
If $name is a single file, try:
samtools faidx "$genome" "$name" > "$fasta"
If $name is multiple files and none of them have spaces, try:
samtools faidx "$genome" $name > "$fasta"
The only reason to use xargs here would be if you have too much content for one command line, but if you're running echo $name | xargs then you'll run into the same problem.
I am learning to customize wget in a bash function and having trouble. I would like to display Downloading (file):% instead of the messy output of wget. The function below seems close I am having trouble calling it for my specific needs.
For example, my standard wget is:
cd 'C:\Users\cmccabe\Desktop\wget'
wget -O getCSV.txt http://xxx.xx.xxx.xxx/data/getCSV.csv
and that downloads the .csv as a .txt in the directory specified with all the messy wget output.
This function seems like it will do more-or-less what I need, but I can not seem to get it to function correctly using my data. Below is what I have tried. Thank you :).
#!/bin/bash
download() {
local url=$1 wget -O getCSV.txt http://xxx.xx.xxx.xxx/data/getCSV.csv
local destin=$2 'C:\Users\cmccabe\Desktop\wget'
echo -n " "
if [ "$destin" ]; then
wget --progress=dot "$url" -O "$destin" 2>&1 | grep --line-buffered "%" | \
sed -u -e "s,\.,,g" | awk '{printf("\b\b\b\b%4s", $2)}'
else
wget --progress=dot "$url" 2>&1 | grep --line-buffered "%" | \
sed -u -e "s,\.,,g" | awk '{printf("\b\b\b\b%4s", $2)}'
fi
echo -ne "\b\b\b\b"
echo " DONE"
}
EDITED CODE
#!/bin/bash
download () {
url=http://xxx.xx.xxx.xxx/data/getCSV.csv
destin='C:\Users\cmccabe\Desktop\wget'
echo -n " "
if [ "$destin" ]; then
wget -O getCSV.txt --progress=dot "$url" -O "$destin" 2>&1 | grep --line-buffered "%" | \
sed -u -e "s,\.,,g" | awk '{printf("\b\b\b\b%4s", $2)}'
else
wget -O getCSV.txt --progress=dot $url 2>&1 | grep --line-buffered "%" | \
sed -u -e "s,\.,,g" | awk '{printf("\b\b\b\b%4s", $2)}'
fi
echo -ne "\b\b\b\b"
echo " DONE"
menu
}
menu() {
while true
do
printf "\n Welcome to NGS menu (v1), please make a selection from the MENU \n
==================================\n\n
\t 1 Patient QC\n
==================================\n\n"
printf "\t Your choice: "; read menu_choice
case "$menu_choice" in
1) patient ;;
*) printf "\n Invalid choice."; sleep 2 ;;
esac
done
}
I have the following script, it reads from users.txt the first and second fields and uses them to generate the username and password and creates the accounts for each line. the problem is that the script is only creating accounts for the first 2 lines and not for the rest
#!/bin/bash
FILE=/home/knoppix/users.txt
USERSH=/bin/bash
while IFS=":" read GECOS USRGRP ; do
groupadd -f $USRGRP
USERNM="u$(cat /dev/urandom| tr -dc '0-9' | fold -w 6| head -n 1)"
USERPW=$(cat /dev/urandom| tr -dc 'a-zA-Z0-9' | fold -w 6| head -n 1)
useradd $USERNM -p $USERPW -g $USRGRP -c "$GECOS,$USRGRP" -d $HOME/$USERNM -s $USERSH -m
ACCNT=$(grep $USRNM /etc/passwd)
echo "${tgrn}Account creation successful!${tr}"
echo "$ACCNT"
echo "Credentials"
echo "${tred}Username:${tr} $USERNM ${tred}Password:${tr} $USERPW"
echo
done < $FILE
#!/bin/bash
while IFS=: read GECOS USRGRP; do
# your groupadd and useradd commands here
done < /home/knoppix/users.txt
#!/bin/bash
for line in $file; do
# make the account
done
rm $file
touch $file