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up vote 1 down vote favorite

I have the following list of files:

Dorn_Triatomine_A5201_sequence_1_unmappedforTdim_tdim.alleles.tsv
Dorn_Triatomine_A5201_sequence_1_unmappedforTdim_tdim.matches.tsv
Dorn_Triatomine_A5201_sequence_1_unmappedforTdim_tdim.snps.tsv
Dorn_Triatomine_A5201_sequence_1_unmappedforTdim_tdim.tags.tsv
Dorn_Triatomine_T9252_sequence_1_unmappedforTdim_tdim.alleles.tsv
Dorn_Triatomine_T9252_sequence_1_unmappedforTdim_tdim.matches.tsv
Dorn_Triatomine_T9252_sequence_1_unmappedforTdim_tdim.snps.tsv
Dorn_Triatomine_T9252_sequence_1_unmappedforTdim_tdim.tags.tsv

I would like to eliminate some of the repetitive string and rename the file as follow:

A5201_tdim.alleles.tsv
A5201_tdim.matches.tsv
A5201_tdim.snps.tsv

I tried using:

mv Dorn_Triatomine_*_sequence_1_unmappedforTdim_tdim.tags.tsv *_tdim.tags.tsv

What would be the simplest way to achieve this task?

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2 Answers 2

up vote 2 down vote accepted

This script ought to do it:

#!/bin/sh
for f in Dorn_Triatom* ; do
  mv "$f" `echo "$f" | sed -e 's/Dorn_Triatomine_//' -e 's/sequence_1_unmappedforTdim_//'`
done
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NB I assume the two strings after s/ are the ones you want to remove –  Bjorn Munch May 12 at 21:47
    
Worked perfect. Thanks. –  Lucia O May 12 at 21:51
1  
Please note that it would give an error if there is no file starts with Dorn_Triatom and placing $f inside of double quotes would be safer in case of spaces in file names. –  Esref May 12 at 21:54
    
@LuciaO if this is what works for you please remember to accept the answer with the tick mark. –  roaima May 12 at 22:26
up vote 0 down vote

Using grep with PCRE to get the new file name:

#!/bin/bash
for file in *.tsv; do
  newname="$(grep -Po '^[^_]*_[^_]*_\K[^_]*_'<<<"$file")$(grep -Po '.*_\K.*$' <<<"$file")"
  mv "$file" "$newname"
done

newname is combined of output of two grep operations:

  • grep -Po '^[^_]*_[^_]*_\K[^_]*_'<<<"$file" will output the A5201_ like strings from each filename

  • $(grep -Po '.*_\K.*$' <<<"$file") will match the last portion of the filename, after last _

  • $() is the bash command substitution pattern.

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