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Fixed typo and quoting and now I can upvote

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edited Mar 9, 2017 at 10:34

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718

This should work for bash:

for filename in *.fasta; do
  index=00$index="00${filename%_*}"
  addme=$addme="${index:((-3)):3}"
  sed "s/^>/>$addme-/g" 1_nc.fasta>$addme_tagged"$filename" > "$addme"_tagged.fasta
done

The trick was to expand the index to three-digit. Then you need " instead of ' to allow for expansion of $addme

This should work for bash:

for filename in *.fasta; do
  index=00${filename%_*}
  addme=${index:((-3)):3}
  sed "s/^>/>$addme-/g" 1_nc.fasta>$addme_tagged.fasta
done

The trick was to expand the index to three-digit. Then you need " instead of ' to allow for expansion of $addme

This should work for bash:

for filename in *.fasta; do
  index="00${filename%_*}"
  addme="${index:((-3)):3}"
  sed "s/^>/>$addme-/g" "$filename" > "$addme"_tagged.fasta
done

The trick was to expand the index to three-digit. Then you need " instead of ' to allow for expansion of $addme

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answered Mar 7, 2017 at 18:39

Philippos

13.7k
2
42
82

This should work for bash:

for filename in *.fasta; do
  index=00${filename%_*}
  addme=${index:((-3)):3}
  sed "s/^>/>$addme-/g" 1_nc.fasta>$addme_tagged.fasta
done

The trick was to expand the index to three-digit. Then you need " instead of ' to allow for expansion of $addme