I have the following FASTA file:
>header1
CGCTCTCTCCATCTCTCTACCCTCTCCCTCTCTCTCGGATAGCTAGCTCTTCTTCCTCCT
TCCTCCGTTTGGATCAGACGAGAGGGTATGTAGTGGTGCACCACGAGTTGGTGAAGC
>header2
GGT
>header3
TTATGAT
My desired output:
>header1
117
>header2
3
>header3
7
# 3 sequences, total length 127.
This is my code:
awk '/^>/ {print; next; } { seqlen = length($0); print seqlen}' file.fa
The output I get with this code is:
>header1
60
57
>header2
3
>header3
7
I need a small modification in order to deal with multiple sequence lines.
I also need a way to have the total sequences and total length. Any suggestion will be welcome... In bash or awk, please. I know that is easy to do it in Perl/BioPerl and actually, I have a script to do it in those ways.
An awk
/ gawk
solution can be composed by three stages:
Every time header
is found these actions should be performed:
sequence
lines we just need to accumulate totals.END
stage we print the remnant seqlen.Commented code:
awk '/^>/ { # header pattern detected
if (seqlen){
# print previous seqlen if exists
print seqlen
}
# pring the tag
print
# initialize sequence
seqlen = 0
# skip further processing
next
}
# accumulate sequence length
{
seqlen += length($0)
}
# remnant seqlen if exists
END{if(seqlen){print seqlen}}' file.fa
A oneliner:
awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa
For the totals:
awk '/^>/ { if (seqlen) {
print seqlen
}
print
seqtotal+=seqlen
seqlen=0
seq+=1
next
}
{
seqlen += length($0)
}
END{print seqlen
print seq" sequences, total length " seqtotal+seqlen
}' file.fa