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Replace multiple text with corresponding text

Hi,

I run an analysis and the software replaced the bacteria name with codes, and I have txt file as below:

Order   Original Name   Code
1   Allostreptomyces_psammosilenae_DSM_42178    S1_f1
2   Embleya_hyalina_NBRC_13850  S2_f2
3   Embleya_scabrispora_DSM_41855   S3_f3

Because the analysis involved few hundreds bacteria, it would be difficult to replace it one by one in the output txt file. May I know any method for me replace the code back to my bacteria original name? Thanks in advance.

Best regards,

Felix

replacement text
• 3,101 views • link
written by fec2 • fec2

1 answer

This is a perfect task for sed.

I would suggest modifying the file in to a set of sed commands. Assume your input above is called subs.txt:

awk 'BEGIN {OFS=","} {print $3, $2}' subs.txt | tail -n+2 | sed -e "s|^|s\/|" -e "s|,|\/|" -e "s|$|\/g|" > changes.sed

Given your input, this will create:

s/S1_f1/Allostreptomyces_psammosilenae_DSM_42178/g
s/S2_f2/Embleya_hyalina_NBRC_13850/g
s/S3_f3/Embleya_scabrispora_DSM_41855/g

You can then feed this in as a sed script to alter your original file:

sed -f changes.sed file_to_be_changed.txt
• 0 views • link
written by Joe Joe

Hi, the changes.sed file is empty. Anyway I am using Macbook, I have also tried using gawk and gsed but the changes.sed file still empty.

• 0 views • link
written by fec2 • fec2

Mac implements sed etc slightly differently. It may also do the same for awk. Try building the pipe up part by part.

I'm afraid that's not enough information for me to be able to tell you why it isn't working

• 0 views • link
written by Joe Joe

Hi, I generated the changes.sed file using excel and save as .txt file as below:

s/S1_f1/Allostreptomyces_psammosilenae_DSM_42178/g
s/S2_f2/Embleya_hyalina_NBRC_13850/g
s/S3_f3/Embleya_scabrispora_DSM_41855/g

But when run the second command I got error as below:

sed: file changes.txt line 1: unknown option to `s'

Any suggestion?

• 0 views • link
written by fec2 • fec2

Make sure you are using GNU sed as distributed in coreutils.

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written by Joe Joe

I have changed my command to gsed, but result remain the same.

• 0 views • link
written by fec2 • fec2

It may be due to you producing the file with Excel. How did you export the file? Any invisible characters will break this.

• 0 views • link
written by Joe Joe

I saved the file as tab delimitated text file.

• 0 views • link
written by fec2 • fec2

OK, so how did you make the file you showed above? did you use the sed commands I gave you on the tab-separated file?

• 0 views • link
written by Joe Joe

Sorry, I don't know why the command is not working on my side. But still, thanks for your sed command, I manually run all the sed command one by one using && in the terminal.

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written by fec2 • fec2

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