Shell Programming and Scripting

Mon Jan 16 14:39:05 CST 2017
/home/cmccabe/Desktop/NGS/API/R_2017_01_13_14_46_04_user_S5-00580-25-Medexome/IonXpress_008_xx-xxx_R_2017_01_13_14_46_04_user_S5-00580-25-Medexome.bam.bai: OK
/home/cmccabe/Desktop/NGS/API/R_2017_01_13_14_46_04_user_S5-00580-25-Medexome/IonXpress_007_xx-xxx_R_2017_01_13_14_46_04_user_S5-00580-25-Medexome.bam: OK
/home/cmccabe/Desktop/NGS/API/R_2017_01_13_14_46_04_user_S5-00580-25-Medexome/IonXpress_007_xx-xxx_R_2017_01_13_14_46_04_user_S5-00580-25-Medexome.bam.bai: OK

#!/bin/bash

DIR=/home/cmccabe/Desktop/NGS/API
cd $DIR
line_no=$(ls | awk -F . '{print $NF}' | sort | uniq -c | awk '{print $2,$1}') # count folder type and store as variable
echo "The folders detected are:
$line_no"

# Get rid of old log file
rm $HOME/virus-scan.log 2> /dev/null
 
for FILE in $DIR;
do
     # check file length is nonzero otherwise commands may be repeated
     if [ -s $FILE ]; then
          date > $HOME/virus-scan.log
          clamscan -r $FILE >> $HOME/virus-scan.log
if grep -iq "OK" "${file}"; then
        echo "echo nothing detected by scan"
    else
        if [[ -f "$f" ]]; then
               mv -f "$f" /home/cmccabe/Desktop/API/$filename /home/cmccabe/quarantine
            # rm -f "$f"
            echo "The files infected have been moved to the folder at /home/cmccabe/quarantine"
        fi
     fi
done

#!/bin/bash
DIR=/home/cmccabe/Desktop/NGS/API
log=$HOME/virus-scan.log

{
echo "The extensions are"
ls | awk -F'\.' 'NF>1 {ext[$NF]++} END {for (i in ext) print ext[i],i}'
} > $log

scanned=0
for FILE in "$DIR"/*
do
     # check file length is nonzero otherwise commands may be repeated
     if [ -s "$FILE" ]; then
          {
          date
          clamscan -r "$FILE"
          } >> $log
          ((scanned++))
     if grep -iq "OK" "${file}"; then
        echo "echo nothing detected by scan"
    else
        if [[ -f "$f" ]]; then
               mv -f "$f" /home/cmccabe/Desktop/API/$filename /home/cmccabe/quarantine
            # rm -f "$f"
            echo "The files infected have been moved to the folder at /home/cmccabe/quarantine"
        fi
     fi
done
[ $scanned -eq 0 ] && echo "nothing detected by scan" >> $log

        while read line
        do
           line="${line% FOUND}"
           virus_name="${line#* }"
           file_name="${line%: *}"
           ((virus_count=$virus_count+1))

           printf "  %s\n" "${file_name}"            # Output to screen
           printf "%s\n" "${file_name}" >&3          # Output to log_file
        done < <(grep " FOUND$" $scan_log) 3>log_file

#!/bin/bash
DIR=/home/cmccabe/Desktop/NGS/API
log=$HOME/virus-scan.log

{
echo "The extensions are"
ls | awk -F'\.' 'NF>1 {ext[$NF]++} END {for (i in ext) print ext[i],i}'
} > $log

scanned=0
for FILE in "$DIR"/*
do
     # check file length is nonzero otherwise commands may be repeated
     if [ -s "$FILE" ]; then
          {
          date
          clamscan -r "$FILE"
          } >> $log
          ((scanned++))
          while read line
          do
              line="${line% FOUND}"
              virus_name="${line#* }"
              file_name="${line%: *}"
              ((virus_count=$virus_count+1))

              printf "  %s\n" "${file_name}"            # Output to screen
              printf "%s\n" "${file_name}" >&3          # Output to log
          done < <(grep " FOUND$" $scan_log) 3>log
          echo "The files infected have been moved to the folder at /home/cmccabe/quarantine"
        fi
     fi
done
[ $scanned -eq 0 ] && echo "nothing detected by scan" >> $log