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Renaming files in one file from names in other

 
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Top Forums UNIX for Dummies Questions & Answers Renaming files in one file from names in other
# 8  
Old 03-14-2011
I'm using a bash shell

1. Yes all my U_P*.ab1 files are located in the same directory.
2. Although all my K*-* names are located in a different file.

I'm still having problems to figure this out. So to clarify, K*-* names are stored as a .txt file, and these nales have to be used to rename the U_P*.ab1 files to give rise to renamed K*-*.ab1 files.

Thank you for your help and input.

Have a nice day

---------- Post updated at 05:35 AM ---------- Previous update was at 05:33 AM ----------

Correction in previous reply :
I'm still having problems to figure this out. So to clarify, K*-* names are stored as a .txt file, and these nales (names) have to be used to rename the U_P*.ab1 files to give rise to renamed K*-*.ab1 files.

Cheers
# 9  
Old 03-14-2011
Please give more infos :
give the full PATH of WHERE all your K* and U*.ab1 files are located as well as WHERE your *.txt files are located (those which contain the lists of their K* and U*.ab1 names)
and use ksh when running the code i provide.
# 10  
Old 03-14-2011
my U*.ab1 files are located in the directory:
Code:
/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results

my .txt file containing the K* names is located:
Code:
/Users/pawannoel/Desktop

And how do I change to ksh from bash to run your scripts?

Cheers
# 11  
Old 03-14-2011
once renamed, do you want them to be in

/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results ?

or in

/Users/pawannoel/Desktop ?
# 12  
Old 03-14-2011
I want to rename them in
Code:
/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results

# 13  
Old 03-14-2011
Please also provide what output you have when running the following command :
Code:
uname -a

---------- Post updated at 12:54 PM ---------- Previous update was at 12:53 PM ----------

Ok then try this :
Code:
cd /Users/pawannoel/Desktop
ksh
MYDIR=/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results
paste b.txt a.txt | while read a b
do
t=${b##*_}
v=$(echo $b | sed 's/.*_//;s/-/+/')
n=${b%$t}$(( ($v) / 2 )).${a#*.}
mv "$MYDIR/$a $MYDIR/$n"
done

---------- Post updated at 01:01 PM ---------- Previous update was at 12:54 PM ----------

You shouldn't get errors ... except if some files mentionned in *.txt does not exist in

/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results
# 14  
Old 03-14-2011
I'm afraid, due to data protection I cant provide you my machine ID as I am on an institutional machine, but I am getting the following results after your script

Notice that I am trying to work inside the "test" directory in the MYDIR path

Code:
u830-tro-6-35-6647:~ pawannoel$ ksh
$ MYDIR=/Users/pawannoel/Documents/Sequences/Sanger_Sequencing_results/test
$ paste b.txt a.txt | while read a b
> do
> t=${b##*_}
> v=$(echo $b | sed 's/.*_//;s/-/+/')
> n=${b%$t}$(( ($v) / 2 )).${a#*.}
> mv "$MYDIR/$a $MYDIR/$n"
> done
paste: b.txt: No such file or directory
$

Both a.txt and b.txt are on the Desktop and look like this

a.txt :
Code:
K7_S5_279891-280489
K7_S6_279891-280489
K7_S7_279891-280489
K7_S8a_279891-280489
K7_S5_1083565-1084163
K7_S6_1083565-1084163
K7_S7_1083565-1084163
K7_S8a_1083565-1084163

b.txt:

Code:
U3244_AN_PN_11_03_11_1_A08_002.ab1
U3244_AN_PN_11_03_11_2_B08_004.ab1
U3244_AN_PN_11_03_11_3_C08_006.ab1
U3244_AN_PN_11_03_11_4_D08_008.ab1
U3244_AN_PN_11_03_11_5_E08_010.ab1
U3244_AN_PN_11_03_11_6_F08_012.ab1
U3244_AN_PN_11_03_11_7_G08_014.ab1
U3244_AN_PN_11_03_11_8_H08_016.ab1

Do a.txt and b.txt need to be in the MYDIR path?

Thanks

---------- Post updated at 07:37 AM ---------- Previous update was at 07:31 AM ----------

I have tried to run the same commands after copying both a.txt and b.txt in the MYDIR path and I get the same result as above !!

Any idea?
 
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