Shell Programming and Scripting

analysis done using v1.5 by cmccabe at 02/08/17 12:19:08 PM
patients analyzed: 
00-0000_Last-First
11-1111_LastName-FirstName
22-2222_LastLastName-FirstFirstName

metrics.txt

linesToSkip=2
{
    for ((i=$linesToSkip;i--;)) ;do
        read
        done
files=( /home/cmccabe/Desktop/list/QC/metrics.txt )
i=0
while read -r new_name; do
  mv "${files[$i]}" "$new_name"
  (( i++ ))
}
done < /home/cmccabe/Desktop/test/list.txt

LinesToSkip=2
((StartLine=$LinesToSkip+1))

files=($(cat /home/cmccabe/Desktop/list/QC/metrics.txt ))

i=1

while read -r new_name
do
   mv "${files[$i]}" "$new_name"
   ((i=$i+1))
done < <(sed -n "${StartLine},\$p" /home/cmccabe/Desktop/test/list.txt

linesToSkip=2
{
    for ((i=$linesToSkip;i--;)) ;do
        read
        done
files=( /home/cmccabe/Desktop/list/QC/metrics.txt )
i=0
while read -r new_name; do
  mv "${files[$i]}" "$new_name"
  (( i++ ))
}
done < /home/cmccabe/Desktop/test/list.txt

linesToSkip=2
{	for((i = 1; i <= linesToSkip; i++))
	do	read
	done

	while read -r new_name && read -ru4 old_name
	do	mv "$old_name" "$new_name"
	done
} < /home/cmccabe/Desktop/test/list.txt 4< /home/cmccabe/Desktop/list/QC/metrics.txt

linesToSkip=2   # skip lines 1 and 2
{	for((i = 1; i <= linesToSkip; i++))   # start at line 3
	do	read   # read lines 3,4,5
	done   # stop

	while read -r new_name && %s\"_"\n && read -ru4 old_name   # read metrics.txt in variable
	do	mv "$old_name" "$new_name"   copy orignal metrics.txt 3 times
	done   # stop
} < /home/cmccabe/Desktop/QC/test/metrics.txt 4< /home/cmccabe/Desktop/QC/analysis.txt   # rename each metrics.txt using lines 3,4,5 of analysis.txt

R_Index	ISP Loading	Pre-Enrichment	Total Reads	Read Length	Key Signal	Usable Sequence	Enrichment	Polyclonal	Low Quality	Test Fragment	Aligned Bases	Unaligned Bases	Exception
1	89	.	78402052	201	77	61	98.6	29.2	10.4	79	98.8	1.2

analysis done using v1.5 by cmccabe at 02/08/17 12:19:08 PM
patients analyzed:
00-0000_Last-First
11-1111_LastName-FirstName
22-2222_LastLastName-FirstFirstName

00-0000_Last-First_metrics.txt
11-1111_LastName-FirstName_metrics.txt
22-2222_LastLastName-FirstFirstName_metrics.txt