length of specific sequences from multi fasta file

Question

[balathumma10]

I have a list of fasta headers in a file (list.txt). I want to get the size or the length of the sequences of list.txt file from a big multi fasta file (main.fasta). Please let me know how to do this, Thank you,

[balathumma10]

The awk commands do the job. Thank you.

[GenoMax]

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Answer 1

[cpad0112]

$ grep --no-group-separator -h -A 1 -wf file.txt *.fa | awk -v OFS="\t" 'NR==1 {print "sequence","length"}; BEGIN{RS=">"} NR>1 {print $1, length($2)}'

if you have one fasta file, try following line:

$ awk -v OFS="\t" 'NR==FNR {a[$1]=$1; next} BEGIN{RS=">"}  ($1 in a) {print a[$1], length($2)}' file.txt a.fa

Assuming that all fasta files are linearized. If you have smaller number of fasta files, try:

$ awk -v OFS="\t"  'BEGIN{RS=">"} {print $1, length($2)}' *.fa | grep -f file.txt

Answer 2

[Mensur Dlakic]

I suspect you will get several different solutions. For this one you will need a program called esl-seqstat from the HMMer package.

esl-seqstat -a main.fasta | grep -f list.txt > list-lengths.txt

Sequence length will be in third column of list-lengths.txt.