Please awk expert!!!! Filter sequence

[demis001]

I want to filter fastafile using awk. The inpute file looks like

Input file:
>cel-miR-49 MIMAT0000020 Caenorhabditis elegans miR-49
AAGCACCACGAGAAGCUGCAGA
>cel-miR-50 MIMAT0000021 Caenorhabditis elegans miR-50
UGAUAUGUCUGGUAUUCUUGGG
>cel-miR-51 MIMAT0000022 Caenorhabditis elegans miR-51
UACCCGUAGCUCCUAUCCAUGUU
>hsa-miR-28-3p MIMAT0004502 Homo sapiens miR-28-3p
CACUAGAUUGUGAGCUCCUGGA
>hsa-miR-29a MIMAT0000086 Homo sapiens miR-29a
UAGCACCAUCUGAAAUCGGUUA
>hsa-miR-30a MIMAT0000087 Homo sapiens miR-30a
UGUAAACAUCCUCGACUGGAAG
>hsa-miR-31 MIMAT0000089 Homo sapiens miR-31
AGGCAAGAUGCUGGCAUAGCU

Is there easy to filter only sequence with >hsa? grep only return the fasta header not the sequence. I need the fasta header with the sequence

Dereje

 

[Annihilannic]

Are you using Linux? If so try grep -A1 '>hsa' inputfile.

If not, awk '/>hsa/ { print; getline; print }' inputfile.

Annihilannic.

 

[demis001]

Many thanks!!

What if If I have unequal sequence line after fasta header?

>hsa
aaaaaaaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>hsa
aaaaaaaaaaaaaaaaaaaaaaaaaa
>hsa
ttttttttttttttttttttttttttt
ttttttttttttttttttttttttttt
ttttttttttttttttttttttttttttt

Dereje

 

[Annihilannic]

awk '
        /^>hsa/ {
                print
                while (getline) {
                        if ($0 ~ /^>/ && $0 !~ /^>hsa/) next
                        print
                }
        }

' inputfile

Annihilannic.

 

[demis001]

Many thanks and really appriciate. I carried out the same task with this perl script followed by the original single line awk script. I really wonder how simple to have awk. Just started learning.


my $seq;
while (<>) {
if (/^>/) { # header line
print "$seq\n" if defined $seq;
print;
$seq='';
} else {
chomp;
$seq .= $_;
}
}
print $seq,"\n";

awk '/>hsa/ { print; getline; print }' inputfile.

 

[Annihilannic]

Have a look at the perl -n and perl -p options (on man perlrun). They make perl behave in a very similar way to awk and are handy for writing one-liners.

Annihilannic.