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How to count the length of fasta sequences?

I know, how to count the length of a particular fasta sequence. But, I need to count the length of a particular fasta sequence based on the header listed in another txt file. The base length to be printed in another/specified excel file at column number 3. Therefore, please help me to do the same. Thank you in advance.

fasta shell scripting python awk grep
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updated by fhsantanna fhsantanna • written by Kumar Kumar

What have you tried? There are definitely solutions for this on the forum already.

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written by Joe Joe

Dear healey, The below command can list out the base length of each fasta sequences of the file,

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta

But, I do not know, how to print the specified header's length listed in another txt file. Moreover, how to print the length in another excel sheet.

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written by Kumar Kumar

You will have to provide sample data.

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written by Kevin Blighe Kevin Blighe

Suppose, I have a multi fasta sequences in org1.fasta as given below,

>seq1
ATGCTA

>seq2
GCTAGTT

>seq3
TAGC

I need to count the length of following header's listed in id.txt as given below,

seq1
seq2

And the results(length) to be printed at 3rd coloumn (Total length) of another csv file org.csv as shown below,

ID       hit_length    Total length
seq1    3                  **6**
seq2    4                  **7**
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updated by lakhujanivijay lakhujanivijay • written by Kumar Kumar

ID and hit_length columns are the existing data of csv file. I need to print the length at 3rd column as I specified with in * symbol.

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written by Kumar Kumar

just add |paste - -

unique.fasta

>seq1
ATGCTA

>seq2
GCTAGTT

>seq3
TAGC

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta |paste - -

stdout

>seq1   6
>seq2   7
>seq3   4

If you need hit_length as the 2nd column there, then use a combination of GNU utilities paste and cut

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta |paste - - |cut -f 2 > col3

col3

6
7
4

Combine the files together

paste file-with-ID-as-col1-and-hit_length-as-col2 col3 > final.result

This assumes that the order is the same in your results example and in the unique.fasta file

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written by jean.elbers jean.elbers

1 answer

I suggest using faslen from FAST tools. https://github.com/tlawrence3/FAST

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written by fhsantanna fhsantanna

Thank you fhsantanna,

faslen does the same thing what this does

awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta

But, I need to get the length of listed fasta headers only.

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written by Kumar Kumar

You could do a faslen, and then "grep > file.fasta > headers.txt" will capture the headers.

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written by fhsantanna fhsantanna

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