I figured it out.
GREPOUT=`grep "NOTE: Table $TABLE created," $LOGFILE | awk '{print $6}'`
NIW=`grep "SYMBOLGEN: Macro variable NIW resolves to" $LOGFILE | awk '{print $0}'`
if [ "$GREPOUT" -gt "0" ]; then
echo "$NIW" |\
$MAILX -s "SUCESSFUL BATCH RUN: $PROG $RPTDATE" $MAILLIST
fi
from the body of the sent email
SYMBOLGEN: Macro variable NIW resolves to 8
My script runs a SAS code and sends out an email after it completes.
I'm looking to print the contents of a table or list of macro variables in the email.
The SAS code has a %put all; statement at the end so all macro variables are listed in the log.
Thanks.
#If it's gotten this far, we can safely grab the number of rows
#of output from $LOGFILE.
GREPOUT=`grep "NOTE: Table $TABLE created," $LOGFILE | awk '{print $6}'`
NIW=`grep "GLOBAL NIW" $LOGFILE | '(print $6)'`
if [ "$GREPOUT" -gt "0" ]; then
#echo "$GREPOUT rows found in $TABLE." |\
echo "$NIW NIW" |\
$MAILX -s "SUCESSFUL BATCH RUN: $PROG $RPTDATE" $MAILLIST
else
echo "$GREPOUT rows found in $TABLE." |\
$MAILX -s "SUCESSFUL BATCH RUN: $PROG $RPTDATE" $MAILLIST
fi
Related
I'm having a terrible go trying to pass some variables from the shell to R. I am hesitant to post this because I can't figure out a reasonable way to make this reproducible, since it involves a tool that has to be downloaded, and really it's more of a general methodology issue that I don't think needs to be reproducible, if you can just suspend your disbelief and bear with me for a quick minute.
I have arguments that are defined in a bash script: $P, $G, and $O.
I have some if/then statements and everything is fine until I get to the $O options.
This is the first part of the $O section and it works fine. It grabs data from $P and passes it to the twoBitToFa utility from UCSC's genome project and outputs the data correctly in a .fa file. Beautiful. (Although I think using 'stdout' and '>' is perhaps redundant?)
if [ "$O" = "fasta" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout > "${P%.bed}".fa
fi
The next section is where I am stuck. If the $O option is "bed", then I want to invoke the Rscript command and pass my stuff over to R. I am able to pass my $P, $G, and $O variables without issue, but now I also need to pass the output from the twoBitToFa function. I could add a step and make the .fa file and then pick that up in R, but I am trying to skip the .fa file creation step and output a different file type instead (.bed). Here are some things I have tried:
# try saving twoBitToFa output to variable and including it in the variables passed to R:
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
myvar=$(twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout) \
Rscript \
GetSeq_R.r \
$P \
$G \
$O \
$myvar
fi
To check what variables come through, my GetSeq_R.r script starts with:
args = commandArgs(trailingOnly=TRUE)
print(args)
and with the above code, the output only includes my $P, $G, and $O variables. $myvar doesn't make it. $P is the TAD-1 file, $G is "hg38", and $O is "bed".
[1] "TAD-1_template.bed" "hg38" "bed"
I am not sure if the way I am trying to pass the data in the variable is wrong. From everything I've read, it seems like it should work. I've also tried using tee to see what is in my stdout at that step like so:
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout | tee \
Rscript \
GetSeq_R.r \
$P \
$G \
$O
fi
And the data I want to pass to R is correctly shown in my console by using tee. I've tried saving stdout and tee to a variable and passing that variable to R, thinking maybe it's something about twoBitToFa that refuses to be put inside a variable, but was unsuccessful. I've spent hours looking up info about tee, stdout, and passing variables from bash to R. I feel like I'm missing something fundamental, or trying to do something impossible, and would really appreciate some other eyes on this.
Here's the whole bash script, in case that's illuminating. Do I need to define a variable in "$#" for what I am trying to pass to R, even though it's not something I want the user to be aware of? Am I capturing the variable with $myvar incorrectly? Can I get the contents of stdout or tee to show up in R?
Thanks in advance.
for arg in "$#"; do
shift
case "$arg" in
"--path") set -- "$#" "-P" ;;
"--genome") set -- "$#" "-G" ;;
"--output") set -- "$#" "-O" ;;
"--help") set -- "$#" "-h" ;;
*) set -- "$#" "$arg"
esac
done
while getopts ":P:G:O:h" OPT
do
case $OPT in
P) P=$OPTARG;;
G) G=$OPTARG;;
O) O=$OPTARG;;
h) help ;;
\?)
echo "Invalid option: -$OPTARG" >&2
usage
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
usage
exit 1
;;
esac
done
num_col=$(cat "$P" | awk "{print NF; exit}")
if [ "$num_col" = 3 ]
then
echo -e "\n\n3 column bed file detected; no directional considerations for sequences \n\n"
if [ "$G" = "hg38" ]
then
twobit="https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.2bit"
fi
if [ "$G" = "hg19" ]
then
twobit="https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.2bit"
fi
if [ "$O" = "fasta" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout > "${P%.bed}".fa
fi
if [ "$O" = "bed" ]
then
awk '{print $0" "$1":"$2"-"$3}' "$P" |
#myvar=$(twoBitToFa -bed=stdin -udcDir=. "$twobit" stdout) \
Rscript \
GetSeq_R.r \
$P \
$G \
$O \
$myvar
fi
fi
I have the below code which adds Logger.info line after every function definition which I need to run on a python script which is the requirement.
The only question is this has to be written back to the same file so the new file has all these looger.info statements below each function definition.
e.g. the file abc.py has currently below code :
def run_func(sql_query):
return run_func(sql_query)
and the code below should create the same abc.py file but with all the logger.info added to this new file
def run_func(sql_query):
LOGGER.info (''MIPY_INVOKING run_func function for abc file in directory'
return run_func(sql_query)
I am not able to write the sed in this file to the new file (with same file name) so that the original file gets replaced by same file name and so that I have all the logger.info statements in there.
for i in $(find * -name '*.py');
do echo "#############################################" | tee -a auto_logger.log
echo "File Name : $i" | tee -a auto_logger.log
echo "Listing the python files in the current script $i" | tee -a auto_logger.log
for j in $(grep "def " $i | awk '{print $2}' | awk -F"(" '{print $1}');
do
echo "Function name : $j" | tee -a auto_logger.log
echo "Writing the INVOKING statements for $j function definition" | tee -a auto_logger.log
grep "def " $i |sed '/):/w a LOGGER.info (''INVOKING1 '"$j"' function for '"$i"' file in sam_utilities'')'
if [ $? -ne 0 ] ; then
echo " Auto Logger for $i filename - Not Executed Successfully" | tee -a auto_logger.log
else
echo "Auto Logger for $i filename - Executed Successfully" | tee -a auto_logger.log
fi
done
done
Following code read the test.txt contents and based on first field it redirect third field to result.txt
src_fld=s1
type=11
Logic_File=`cat /home/script/test.txt`
printf '%s\n' "$Logic_File" |
{
while IFS=',' read -r line
do
fld1=`echo $line | cut -d ',' -f 1`
if [[ $type -eq $fld1 ]];then
query=`echo $line | cut -d ',' -f 3-`
echo $query >> /home/stg/result.txt
fi
done
}
Following is the contents of test.txt:
6,STRING TO DECIMAL WITHOUT DEFAULT,cast($src_fld as DECIMAL(15,2) $tgt_fld
7,STRING TO INTERGER WITHOUT DEFAULT,cast($src_fld as integer) $tgt_fld
11,DEFAULT NO RULE,$src_fld
everything works fine except output in result.txt is $src_fld instead of s1. Can anyone please tell me what is wrong in the code?
Try replacing the below line
echo $query >> /home/stg/result.txt
with this one
eval "echo $query" >> /home/stg/result.txt
How do I check if a file is empty in a korn script
I want to test in my korn script if the output CSV file is empty or not and if it is not empty then it should give the count of values.
Thanks.
The test(1) program has a -s switch:
-s FILE
FILE exists and has a size greater than zero
This is just another way of doing it, albeit a roundabout one:
if [ `ls -l <file> | awk '{print $5}'` -eq 0 ]
then
//condition for being empty
else
//condition for not being empty
fi
if [ ! -f manogna.txt ]
then
echo " Error: manogna.txt does not exist "
else
echo " manogna.txt exist "
echo " no of records in manogna.txt are `cat manogna.txt | wc -l`"
fi
Consider I have a file abcde.txt which may contain one or more lines of text. I want a script that will DELETE the file if it contains single line.
Something like, if 'wc -l abscde.txt' = 1 then rm abscde.txt
My system : Solaris
Here's a simple bash script:
#!/bin/bash
LINECOUNT=`wc -l abscde.txt | cut -f1 -d' '`
if [[ $LINECOUNT == 1 ]]; then
rm -f abscde.txt
fi
delifsingleline () {
if [ $(cat $1 | wc -l) = "1" ]
then
echo "Deleting $1"
echo "rm $1"
fi
}
Lightly tested on zsh. Should work on bash as well.
This is (mostly) just a reformat of Ben's answer:
wc -l $PATH | grep '^1 ' > /dev/null && rm -f $PATH