Keep current and previous line only if current line fulfills a given condition - awk

Question

I have a file which looks like this:
>4RYF_1
MAENTKNENITNILTQKLIDTRTVLIYGEINQELAEDVSKQLLLLESISNDPITIFINSQGGHVEAGDTIHDMIKFIKPTVKVVGTGWVASAGITIYLAAEKENRFSLPNTRYMIHQPAGGVQGQSTEIEIEAKEIIRMRERINRLIAEATGQSYEQISKDTDRNFWLSVNEAKDYGIVNEIIENRDGLKMASWSHPQFEK
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
I want to keep the sequence and previous line only if the sequence has a given length. For selecting only lines with that condition I use:
awk 'length($0) > 50 && length($0) <=800)' sample.txt
But how can I keep lines starting with > as well if this condition is met?

Answer 1

Yet another awk solution:
awk '/^>/ { header = $0; next } length > 50 && length <= 800 { print header ORS $0 }'

Answer 2

Would you please try the following:
awk -v RS='>' -F'\n' '
length($2) > 50 && length($2) <= 800 {printf ">%s", $0}
' sample.txt
Assigning RS to '>' tells awk to split the file on > into records,
treating the header line and the sequence line in the same record.
Assigning FS to '\n' splits the record to the header and
sequence, each assigning $1 to the header and $2 to the sequence.
As the leading > is chopped off as a delimiter, we need to prepend it
when printing the matched records.

Answer 3

Here is one-liner:
LANG=C grep -B1 '^.\{51,800\}$' < sample.txt
The command was really slow with LANG=en_US.UTF-8 that I set by default, so using LANG=C instead.
man grep tells you that '-B NUM' means ' Print NUM lines of leading context before matching lines.'.
'^' means start of line
'.' means any character
'{51,800}' means we want between 51 and 800 of the previous thing
'$' means end of line.
Or in other words, we want to match lines that are between 51 and 800 characters, and print it and the previous line.

Answer 4

A potential solution with AWK is:
awk '!/^>/ {next}; {getline s}; length(s) > 50 && length(s) <= 800 { print $0 "\n" s }' example.fasta
e.g. if example.fasta contains
>4RYF_1
WLSVNEAKDYGIVNEIIENRDGLKMASWSHPQFEK
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
>1000_chars
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
It will only print
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH
Edit
The method that I would recommend to better handle edge-cases is to use purpose-built bioinformatics software, e.g. seqkit
seqkit seq -m 50 -M 800 example.fasta
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDI
FLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEI
MIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEA
KDYGLIDDIIINKSGLKGHHHHHH

Answer 5

Is perl an option?
perl -nle '$prev && print if length() >50 and length() < 800 && print $prev; $prev = $_' input_file
$prev - Create a variable which will hold every line. When the length condition is met, and there has been a previous line $prev, then it prints the condition matched in $prev and prints the last line.
$prev = $_ Assigns the current line to the prev line variable
If the upper limit 800 is not essential, could sed be an option?
$ sed -En '/>/ {N;/[a-zA-Z0-9]{50,}/p}' input_file
/>/ - Match > and read into the pattern space
N; Run the condition on the next line after the match and append that to the pattern space also:
{50,} - If the length is 50 or more
\1/p - Return it and print
Output
>4RYF_2
MNLIPTVIEQTSRGERAYDIYSRLLKDRIIMLGSAIDDNVANSIVSQLLFLDAQDPEKDIFLYINSPGGSISAGMAIYDTMNFVKADVQTIGMGMAASMGSFLLTAGANGKRFALPNAEIMIHQPLGGAQGQATEIEIAARHILKIKERMNTIMAEKTGQPYEVIARDTDRDNFMTAQEAKDYGLIDDIIINKSGLKGHHHHHH

Answer 6

With your shown samples, please try following awk code. Written and tested with GNU awk.
awk -v RS= '
{
val=""
delete arr
while(match($0,/>[^\n]*\n*[^\n]*/)){
val=substr($0,RSTART,RLENGTH)
split(val,arr,"\n")
if(length(arr[2])>50 && length(arr[2])<=800){
print val
}
$0=substr($0,RSTART+RLENGTH)
}
}
' Input_file

Answer 7

If only the next line should meet the length restrictions, you can match and store the line that starts with > in a variable, for example previous
Then for the next line, check for the length and if the previous line is not empty.
If is is not, print the previous and the current line.
At the end, set the previous variable to an empty string.
awk '{
if (/^>/) {
previous = $0
next
}
if (length(previous) != 0 && length($0) > 50 && length($0) <= 800) {
print previous ORS $0
}
previous=""
}' sample.txt
See an AWK demo