perl

Print the next line after match

My input:

# BLASTN 2.13.0+
# Query: ;HaelonEVm219174t4;
# Database: /data1/IxoSca/Databases/nt/nt
# Fields: subject id, subject sci names, % identity, alignment length, mismatches, gap opens, evalue, bit score, % query coverage per hsp, subject title
# 1 hits found
gi|1962480099|emb|LR990882.1|   Endotricha flammealis   80.702  57  11  0   0.043    54.5   10  Endotricha flammealis genome assembly, chromosome: 29
# BLASTN 2.13.0+
# Query: ;HaelonEVm2775195t2;
# Database: /data1/IxoSca/Databases/nt/nt
# Fields: subject id, subject sci names, % identity, alignment length, mismatches, gap opens, evalue, bit score, % query coverage per hsp, subject title
# 1 hits found
gi|2452922202|emb|OX438846.1|   Eudonia truncicolella   88.372  43  3   1   0.009   53.6    29  Eudonia truncicolella genome assembly, chromosome: 21

My code:

}
elsif($line =~ m/\s[1] hit/){
    print "1 hits found: ".$name."\n";
            $flag=1;
}

My output:

HaelonEVm219174t4   1 hits found: # Query: ;HaelonEVm219174t4;
HaelonEVm2775195t2  1 hits found: # Query: ;HaelonEVm2775195t2;

I want to print the next line in place of "1 hits found: # Query: ;HaelonEVm219174t4;"

Expected output:

HaelonEVm219174t4   LR990882.1   Endotricha flammealis   80.702  57  11  0   0.043    54.5   10  Endotricha flammealis genome assembly, chromosome: 29
HaelonEVm2775195t2  OX438846.1   Eudonia truncicolella   88.372  43  3   1   0.009   53.6    29  Eudonia truncicolella genome assembly, chromosome: 21
Solution

  • When the regex matches, set the flag but don't print anything for that line. When the flag is set, print the current line, then clear the flag.

    use warnings;
use strict;

my $flag = 0;
while (<DATA>) {
    if (m/\s[1] hit/) {
        $flag = 1;
    }
    elsif ($flag) {
        print;
        $flag = 0;
    }
}

__DATA__
# BLASTN 2.13.0+
# Query: ;HaelonEVm219174t4;
# Database: /data1/IxoSca/Databases/nt/nt
# Fields: subject id, subject sci names, % identity, alignment length, mismatches, gap opens, evalue, bit score, % query coverage per hsp, subject title
# 1 hits found
gi|1962480099|emb|LR990882.1|   Endotricha flammealis   80.702  57  11  0   0.043    54.5   10  Endotricha flammealis genome assembly, chromosome: 29
# BLASTN 2.13.0+
# Query: ;HaelonEVm2775195t2;
# Database: /data1/IxoSca/Databases/nt/nt
# Fields: subject id, subject sci names, % identity, alignment length, mismatches, gap opens, evalue, bit score, % query coverage per hsp, subject title
# 1 hits found
gi|2452922202|emb|OX438846.1|   Eudonia truncicolella   88.372  43  3   1   0.009   53.6    29  Eudonia truncicolella genome assembly, chromosome: 21

    Prints:

    gi|1962480099|emb|LR990882.1|   Endotricha flammealis   80.702  57  11  0   0.043    54.5   10  Endotricha flammealis genome assembly, chromosome: 29
gi|2452922202|emb|OX438846.1|   Eudonia truncicolella   88.372  43  3   1   0.009   53.6    29  Eudonia truncicolella genome assembly, chromosome: 21