Replace lowercase characters with -

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I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase.
I would like to change them to gaps. I could do it in higher language but I would like to know the solution in bash.
I have found simple solution to replace all lowercase to uppercase:

awk 'BEGINFS=" "if(!/>/)print toupper($0)elseprint $1' in.fna > out.fna

but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks

asked 7 hours ago

robinj

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awk 'BEGINFS=" "if(!/>/)print toupper($0)elseprint $1' in.fna > out.fna

but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks

asked 7 hours ago

robinj

New contributor

add a commentÂ |Â

up vote
1
down vote

favorite

awk 'BEGINFS=" "if(!/>/)print toupper($0)elseprint $1' in.fna > out.fna

but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks

asked 7 hours ago

robinj

New contributor

awk 'BEGINFS=" "if(!/>/)print toupper($0)elseprint $1' in.fna > out.fna

but I would like to replace lowercase with -. The first row need to be omitted. Could you help me? Thanks

bash shell

asked 7 hours ago

robinj

New contributor

asked 7 hours ago

robinj

New contributor

asked 7 hours ago

robinj

New contributor

asked 7 hours ago

robinj

asked 7 hours ago

robinj

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3 Answers
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The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

answered 6 hours ago

arupgsh

430111

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up vote
2
down vote

You could try it with sed.

Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

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up vote
1
down vote

You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

answered 4 hours ago

Ammar Sabir Cheema

548213

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3 Answers
3

active

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3 Answers
3

active

oldest

votes

up vote
3
down vote

The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

answered 6 hours ago

arupgsh

430111

add a commentÂ |Â

up vote
3
down vote

The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

answered 6 hours ago

arupgsh

430111

add a commentÂ |Â

up vote
3
down vote

The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

answered 6 hours ago

arupgsh

430111

The following sed command will do the trick.

sed -e '/^[^>]/ s/[a-z]/-/g' in.fna > out.fna

Lines starting with > will be escaped and the lowercase characters will be replaced with - .

answered 6 hours ago

arupgsh

430111

answered 6 hours ago

arupgsh

430111

answered 6 hours ago

arupgsh

430111

answered 6 hours ago

arupgsh

430111

add a commentÂ |Â

up vote
2
down vote

You could try it with sed.

Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

add a commentÂ |Â

up vote
2
down vote

You could try it with sed.

Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

add a commentÂ |Â

up vote
2
down vote

You could try it with sed.

Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

You could try it with sed.

Replace all lower-case chars with - in lines not starting with >:

sed -e '/^>/!s/[a-z]/-/g' in.fa

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

edited 5 hours ago

Llopis

2,5471628

edited 5 hours ago

Llopis

2,5471628

edited 5 hours ago

Llopis

2,5471628

answered 6 hours ago

Peter Menzel

1137

answered 6 hours ago

Peter Menzel

1137

answered 6 hours ago

Peter Menzel

1137

add a commentÂ |Â

up vote
1
down vote

You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

answered 4 hours ago

Ammar Sabir Cheema

548213

add a commentÂ |Â

up vote
1
down vote

You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

answered 4 hours ago

Ammar Sabir Cheema

548213

add a commentÂ |Â

up vote
1
down vote

You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

answered 4 hours ago

Ammar Sabir Cheema

548213

You can also use this solution where tr command from linux can solve your problem:

tail -n +2 in.fna | tr '[:lower:]' '-'

answered 4 hours ago

Ammar Sabir Cheema

548213

answered 4 hours ago

Ammar Sabir Cheema

548213

answered 4 hours ago

Ammar Sabir Cheema

548213

answered 4 hours ago

Ammar Sabir Cheema

548213

add a commentÂ |Â

robinj is a new contributor. Be nice, and check out our Code of Conduct.

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