With the use of perl regex, if two consecutive lines match than count the number of lines.
I want the number of lines until matches the pattern
D001
0000
open ($file, "$file") || die;
my #lines_f = $file;
my $total_size = $#lines_f +1;
foreach my $line (#lines_f)
{
if ($line =~ /D001/) {
$FSIZE = $k + 1;
} else {
$k++;}
}
Instead of just D001, I also want to check if the next line is 0000. If so $FSIZE is the $file size.
The $file would look something like this
00001
00002
.
.
.
D0001
00000
00000
Here is an example. This sets $FSIZE to undef if it cannot find the marker lines:
use strict;
use warnings;
my $fn = 'test.txt';
open ( my $fh, '<', $fn ) or die "Could not open file '$fn': $!";
chomp (my #lines = <$fh>);
close $fh;
my $FSIZE = undef;
for my $i (0..$#lines) {
if ($lines[$i] =~ /D0001/) {
if ( $i < $#lines ) {
if ( $lines[$i+1] =~ /00000/ ) {
$FSIZE = $i + 1;
last;
}
}
}
}
Related
I have 2 csv and text files, file 1 has 2 columns one with gene id and two with gene name,file 2 has many columns with part of the string in columns being gene id e.g gene id(genome) or pseudo gene id(genome). i want to compare each gene id in file 1 with each gene id in file 2 and replace the gene id in file 2 with the gene name in file 1 printing in file 3.
file 1;
SPAR5_0024, coA binding domain protein
SPAR5_0025, hypothetical protein
SPAR5_0026, hypothetical protein
file 2;
SPAR5_0024(72.AFAX01.1.gb) SPAR5_0026(72.AFAX01.1.gbff) SPAR5_0025(72.AFAX01.1.gbff)
desired output (file 3);
coA binding domain protein(72.AFAX01.1.gb) hypothetical protein(72.AFAX01.1.gbff) hypothetical protein(72.AFAX01.1.gbff)
with my code am getting an empty file 3
This is what am running;
#!/usr/local/bin/perl -w
use strict;
use warnings;
my $file1 = "annot.txt";
my $file2 = "orthomcl.csv";
my $file3 = "combi.csv";
open (FILE1,"$file1") || die;
open (FILE2,"$file2") || die;
open (FILE3,">$file3") || die;
my #file1 = <FILE1>;
my #file2 = <FILE2>;
my %file1;
while ( my $value = <FILE1> ) {
chomp $value;
my #file1 = split /\s+/, $_;
$file1{$value} = 1;
}
my %file2;
while (my $value = <FILE2>) {
chomp $value;
my #file2 = split /\s+/, $_;
if ( $file1{ $value } ) {
$file2 = $file1{ $file2 };
print join( "\t" => #file2 ), $/;
}
}
close (FILE1);
close (FILE2);
close (FILE3);
desired output (file 3)
coA binding domain protein(72.AFAX01.1.gb) hypothetical protein(72.AFAX01.1.gbff) hypothetical protein(72.AFAX01.1.gbff)
The primary error is that
my #file1 = <FILE1>;
my #file2 = <FILE2>;
consume all data from the files, so that there's nothing left to read for the
while ( my $value = <FILE1> ) {
and
while (my $value = <FILE2>) {
Here is an example of how you can insert the annotations from the first file annot.txt into the second file orthomcl.csv:
use feature qw(say);
use strict;
use warnings;
{
my $map = read_annot();
my ($regex) = map {qr /$_/} join '|', map {quotemeta} keys %$map;
my $fn = 'orthomcl.csv';
open ( my $fh, '<', $fn ) or die "Could not open file '$fn': $!";
my $str = do { local $/; <$fh> };
close $fh;
$str =~ s/($regex)/$map->{$1}/ge;
save_combi( $str );
}
sub save_combi {
my ( $str ) = #_;
my $fn = 'combi.csv';
open ( my $fh, '>', $fn ) or die "Could not open file '$fn': $!";
print $fh $str;
close $fh;
say "Saved: '$fn'";
}
sub read_annot {
my $fn = 'annot.txt';
open ( my $fh, '<', $fn ) or die "Could not open file '$fn': $!";
my %map;
while (my $line = <$fh> ) {
chomp $line;
my ( $key, $value ) = $line =~ /^(\S+),\s+(.*)$/;
$value =~ s/\s+$//;
if (defined $key) {
$map{$key} = $value;
}
}
close $fh;
return \%map;
}
I have a fasta file. I need to remove sequences containing “N” or did not contain at least 3 unique bases.
The code so far is below. Also how would I remove the sequence ID line as go along for sequences I delete.
#!/usr/bin/perl
use strict;
use warnings;
open FILE, '<', $ARGV[0] or die qq{Failed to open "$ARGV[1]" for input: $!\n};
open match_fh, ">$ARGV[0]_trimmed.fasta"
or die qq{Failed to open for output: $!\n};
while ( my $line = <FILE> ) {
chomp($line);
if ( $line =~ m/^>/ ) {
print match_fh "$line\n";
my #data = split( /\|/, $line );
my $nextline = <FILE>;
if ( $nextline !~ /N+/g ) {
if ( $nextline =~ /[ATGC]{3}/g ) {
}
print match_fh "$nextline";
}
}
}
close FILE;
close match_fh;
INPUT
>seq1
ATGCGGGATGATCCGAACGTTTAATCTCGTATGCCGTCTTCTATCTCNNN
>seq2
GATGAGCTTGACTCTAGTCCATCTCGTATGCCGTCTTCTGCTATCTCGTA
>seq3
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC
>seq4
TGGTACTGTAAGCATGAGAGTAATCTCGTATGCCGTCTTCTGCTTGAAAA
OUTPUT
>seq2
GATGAGCTTGACTCTAGTCCATCTCGTATGCCGTCTTCTGCTATCTCGTA
>seq4
TGGTACTGTAAGCATGAGAGTAATCTCGTATGCCGTCTTCTGCTTGAAAA
while(my $head = <FILE>) {
next if($head !~ /^>/);
$_=<FILE>;
if(!/N+/ && /A/+/T/+/G/+/C/ >= 3) {
print match_fh $head, $_;
}
}
I am trying to find pattern Pattern String , once it found , I need to get the next line of pattern, which contains page number, I need extract the page number 2 in below sample text file Page: 2 of 5. Here is my try:
my $filename="sample.txt";
$i=1;
open(FILE, "<$filename") or die "File couldn't be matched $filename\n";
#array = <FILE>;
foreach $line(#array){
chomp($line);
if ($array[$i]=~/(\s+)Pattern String(\s+)/) {
if ($array[$i]=~/(\s+)Page:(\s+)(.*) of (.*)/) {
$page = $3;
}
}
Here is my sample text file :
Pattern String
MCN: 349450A0 NCP Account ID: 999 600-0089 Page: 2 of 5
=============================================================================
Customer Name: PCS HEALTH SYSTEMS
Customer Number: 349450A0
What about this? Is that what you want? After a match and if next line is not empty then show the line. Let me know if worked for you.
# Perl:
my $filename="sample.txt";
my $match = undef;
my $line = "";
open(my $fh, "<", $filename) or die "Failed to open file: $!";
foreach (<$fh>) {
$line = $_;
if ( $line =~ /.*Pattern\sString.*/ ) {
$match = 1;
next;
}
if (($match == "1") && ($line !~ /^$/)){
print $line;
$match = undef;
}
}
I think this will solve the problem (I'm assuming that the sample files will always have the same format). I hope this will help you, please let me know if it worked.
my $filename="sample.txt";
my $count = 0;
my $tgline = 0;
open(my $fh, "<", $filename) or die "Failed to open file: $!";
my #lines = <$fh>;
foreach (#lines) {
if ( $_ =~ /.*Pattern\sString.*/ ) {
$tgline = $count + 2;
if ( $lines[$tgline] =~ /.*Page\:\s(\d+)\sof\s(\d+)$/ ) {
print "Current page: " . $1 . "\n";
print "Total page #: " . $2 . "\n";
}
}
$count+=1;
}
I don't know why are you matching Pattern String, if your target is achieveing 2 from Page: 2 of 5 from your input file. This is a way to get this:
use warnings;
use strict;
my $filename = "sample.txt";
open my $fh, "<","$filename" or die "Couldn't open $filename: $!";
while (my $line = <$fh>)
{
if($line =~ m/.*Page:\s(\d+)\sof\s(\d+)$/)
{
print "$1\n";
}
}
sample.txt:
Pattern String
MCN: 349450A0 NCP Account ID: 999 600-0089 Page: 2 of 5
=============================================================================
Customer Name: PCS HEALTH SYSTEMS
Customer Number: 349450A0
Output:
2
I am trying to glob files from a directory and print out regexp matches,
Trying to match
<110>
*everything here*
<120>
My matches would be
SCHALLY, ANDREW V.
CAI, REN ZHI
ZARANDI, MARTA
However when i try to split this by newline and join using "|", I am not getting the desired output that is
Applicant : SCHALLY, ANDREW V. | CAI, REN ZHI | ZARANDI, MARTA
My current output is only
| ZARANDI, MARTA
Can someone see any obvious mistakes?
#!/usr/bin/perl
use warnings;
use strict;
use IO::Handle;
open (my $fh, '>', '../logfile.txt') || die "can't open logfile.txt";
open (STDERR, ">>&=", $fh) || die "can't redirect STDERR";
$fh->autoflush(1);
my $input_path = "../input/";
my $output_path = "../output/";
my $whole_file;
opendir INPUTDIR, $input_path or die "Cannot find dir $input_path : $!";
my #input_files = readdir INPUTDIR;
closedir INPUTDIR;
foreach my $input_file (#input_files)
{
$whole_file = &getfile($input_path.$input_file);
if ($whole_file){
$whole_file =~ /[<][1][1][0][>](.*)[<][1][2][0][>]/s ;
if ($1){
my $applicant_string = "Applicant : $1";
my $op = join( "|", split("\n", $applicant_string) );
print $op;
}
}
}
close $fh;
sub getfile {
my $filename = shift;
open F, "< $filename " or die "Could not open $filename : $!" ;
local $/ = undef;
my $contents = <F>;
close F;
return $contents;
}
EDIT 1
I Ran Code on a single file
#!/usr/bin/perl
use warnings;
use strict;
use IO::Handle;
my $input_file = "01.txt-WO13_090919_PD_20130620";
my $input_path = "../input/";
my $whole_file = &getfile($input_path.$input_file);
if ($whole_file =~ /[<][1][1][0][>](.*)[<][1][2][0][>]/s ) {
print $1;
my #split_string = split("\n", $1);
my $new_string = join("|", #split_string) ;
print "$new_string \n";
}
sub getfile {
my $filename = shift;
open F, "< $filename " or die "Could not open $filename : $!" ;
local $/ = undef;
my $contents = <F>;
close F;
return $contents;
}
Output
Chen, Guokai
Thomson, James
Hou, Zhonggang
Hou, Zhonggang
Replace
$whole_file =~ /[<][1][1][0][>](.*)[<][1][2][0][>]/s ;
if ($1) {
with
if ($whole_file =~ /[<][1][1][0][>](.+)[<][1][2][0][>]/s) {
The problem with your original code is that $1 is unchanged (i.e. retained from the previous file) if the regexp doesn't match.
If that doesn't solve the problem, then double check and make sure that you have the correct value if $applicant_string. Your join + split line looks correct.
I run your code and get
|SCHALLY, ANDREW V. |CAI, REN ZHI| ZARANDI, MARTA
Which is pretty close. all you need to do is trim whitespace before you join. So replace this
my #split_string = split("\n", $1);
my $new_string = join("|", #split_string) ;
With this:
my #split_string = split("\n", $1);
my #names;
foreach my $name ( #split_string ) {
$name =~ s/^\s*(.*)\s*$/$1/;
next if $name =~ /^$/;
push #names, $name;
}
my $new_string = join("|", #names);
#pts is correct, the regex capture variables do not get reset to UNDEF
upon a negative match, looks like they retain their last value.
So his solution should work for you. Use the if ( $whole_file =~ // ) {} form.
Beyond that, you could clean up the operation a little by doing something like this
use strict;
use warnings;
$/ = undef;
my $whole_file = <DATA>;
if ( $whole_file =~ /[<][1][1][0][>](.*)[<][1][2][0][>]/s )
{
my $applicant_string = $1;
$applicant_string =~ s/^\s+|\s+$//g;
my $op = "Applicant : " . join( " | ", split( /\s*\r?\n\s*/, $applicant_string) );
print $op;
}
__DATA__
<110>
SCHALLY, ANDREW V.
CAI, REN ZHI
ZARANDI, MARTA
<120>
Output:
Applicant : SCHALLY, ANDREW V. | CAI, REN ZHI | ZARANDI, MARTA
I have 2 files, as follows:
file1.txt:
0 117nt, >gene_73|GeneMark.hm... *
0 237nt, >gene_3097|GeneMark.... *
0 237nt, >gene_579|GeneMark.h... *
0 237nt, >gene_988|GeneMark.h... *
0 189nt, >gene_97|GeneMark.hm... *
0 183nt, >gene_97|GeneMark.hm... *
file2.fasta:
>gene_735|GeneMark.hmm|237_nt|+|798985|799221
TTGTGGTTCGTGCCGCGCGACGCGTTGCGTCTGCAAACGCCCGACGAAGACATCGCGACCTATCTGTTCAACAAGCATGTGATTCGGCATCGGTTCTGTCCGACCTGCGGGATTCATCCGTTCGCGGAAGGCACGGACCCGAAGGGCAACGCGATGGCGGCCGTCAATCTTCGCTGCGTCGACGGCGTCGATCTCGACGCGTTGAGCGTCCGCCATTTCGACGGGCGCGCGCTCTGA
>gene_579|GeneMark.hmm|237_nt|+|667187|667423
ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCCAACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTCAACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACCAAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA
>gene_1876|GeneMark.hmm|234_nt|-|2168498|2168731
ATGCTGTTCTTTTCGCGCGCGGGCGTGTCGCGTGCGGCCGGCGGCCAATCATGCGGCGAGTCGTTTTGTCGCGGCTCGCGGCGCTTGCCGACGTTGGAATCGCGCGCGCCGATGCGCGGATCGGGGCGGCAACGTTTGCGTATGAGGAATGATGCGTTTGCGCATCGGGAATGGGCGCCTCGCCCCGGTTTCGCCGCGATTCCGCCCGACTCGAGGCAGTCGTTTTTCCGCTAA
>gene_3097|GeneMark.hmm|237_nt|-|3467022|3467258
GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGGCGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGCTCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAAACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA
>gene_988|GeneMark.hmm|237_nt|+|1121027|1121263
ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCGGTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTCCGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGGCTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA
>gene_97|GeneMark.hmm|105_nt|+|90122|90226
GTGACGCGTTTCGCGACGCGCGTCGATGGGGCGGGCGCGAAACCCGTTCGCCGCGATGCGGCGGACGGGGTATGGCCGAGCGCCGTCCGTCGCGGCGAGAGTTGA
>gene_97|GeneMark.hmm|183_nt|-|107002|107184
ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTCATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGCGACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCACTAA
>gene_97|GeneMark.hmm|189_nt|-|98624|98812
GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCGAACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGCGATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGCCATCGATGA
>gene_97|GeneMark.hmm|234_nt|+|105494|105727
ATGAAGATTCAAATCGCCATTGTTTATTTTGTCGCCCGTCACGCAAACGAGCAGGCGCGAAGCGGATCGGCGCGCATTGGCGAAGAGCCGGCGCGCATCGGCATCGCGCTCGCGCGACACATGCGCGCCGCGCGCGGCCGGTCGACGCCGGATTCGCCTGTCGATCGATCCGGTGCGCCCCGAGCCGATGAGCGGTACGCTTCGGCGCGCGCGCGACACGCGCGACACGCGTGA
>gene_979|GeneMark.hmm|225_nt|-|1115442|1115666
TTGATCGACGCGCGGGGCCGGCCGGGCCGCGGGGTATCGAAGGCGATCGACGCGCAACACGAATCGCCGCCGCGCGCCGAAACCTCGCTATGCGCGTCGCGCGCACGCGCGGCCGGCGGCGCACGCGCGGGTGTGCGCGGGCCGGCGGCGCGGCCGCTCGCACTGCGCGACCGCTCGCGCGCACGCCTTCCTCGGCACGCGCCGGGAATCCCGGCCCTTCAATGA
The output that I expect is:
>gene_579|GeneMark.hmm|237_nt|+|667187|667423
ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCCAACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTCAACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACCAAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA
>gene_3097|GeneMark.hmm|237_nt|-|3467022|3467258
GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGGCGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGCTCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAAACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA
>gene_988|GeneMark.hmm|237_nt|+|1121027|1121263
ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCGGTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTCCGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGGCTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA
>gene_97|GeneMark.hmm|183_nt|-|107002|107184
ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTCATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGCGACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCACTAA
>gene_97|GeneMark.hmm|189_nt|-|98624|98812
GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCGAACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGCGATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGCCATCGATGA
There are 4 sequences with gene number 97, but all in different length. I want the sequence with the correct gene length only which listed in file1.txt to output in the output.fasta file. What I've done so far is as follows (but failed and have some errors):
#!/usr/bin/perl
use strict;
use warnings;
my #genes;
open my $list, '<file1.txt';
while (my $line = <$list>) {
push (#genes, $1) if $line =~/\>(.*?)\|/gs;
}
my $tag1 = "0\t";
my $tag2 = "nt";
while (my $line = <$list>) {
if ($line =~ /$tag1(.*?)$tag2/) {
my $match1 = $1;
}
}
my $input;
{
local $/ = undef;
open my $fasta, '<file2.fasta';
my $tag3 = "GeneMark.hmm";
my $tag4 = "_nt";
while (my $input = <$fasta>) {
if ($input =~ /$tag3(.*?)$tag4/) {
my $match2 = $1; }}
close $fasta;
}
my #lines = split(/>/,$input);
foreach my $l (#lines) {
if ($l =~ /(.+?)\|/) {
my $real_name = $1;
if ($real_name ~~ #genes) {
if ($match2 = $match1) {
open (OUTFILE, '>>output.fasta');
print OUTFILE ">$l"; }
}
}
}
Can anyone give me some guide to correct the code? Or is there any better way to do this? Any help will be very much appreciated! Thanks! :)
Here's an option that uses Bio::SeqIO:
use strict;
use warnings;
use Bio::SeqIO;
my %hash;
open my $fh, '<', $ARGV[0] or die $!;
while (<$fh>) {
push #{ $hash{$2} }, $1 if /\s+(\d+)nt,.+?>(gene_\d+)\|/;
}
close $fh;
my $in = Bio::SeqIO->new( -file => $ARGV[1], -format => 'Fasta' );
my $out = Bio::SeqIO->new( -fh => \*STDOUT, -format => 'Fasta' );
while ( my $seq = $in->next_seq() ) {
$out->write_seq($seq)
if $seq->id =~ /(gene_\d+)\|.+?\|(\d+)_nt\|/ and grep /$2/, #{ $hash{$1} };
}
Usage: perl script.pl file1.txt file2.fasta [>outFile.fasta]
The second, optional parameter directs output to a file.
Output from your data:
>gene_579|GeneMark.hmm|237_nt|+|667187|667423
ATGTACCACGGCGCCGAATTTGCCGCTGCCAAGGGCATGCGCTGGCTGCGAGATGCCGCC
AACGGCTCTGCCTTCATCGCACCGGGCAGTCCGTGGCAAAACGGTTTCGTCGAGCGTTTC
AACGGCAAGCTGCATGACGAATTGCTGAACCGGGAATGGTTCCGCGGCCGTGCCGAGACC
AAGATGCTCATCGAACGCTCCGGCTACGGTCCGTCGAGTCTGACCGGATTCCGATGA
>gene_3097|GeneMark.hmm|237_nt|-|3467022|3467258
GTGTCGAACGAACGTCGCGGCGAACGGCCGCTGCGGGCATCGCCGCAGGACGTCACACGG
CGAACGTCGCGCGCGATCCTCGGCGGCCGCGAACGTGGGCCGTCCCGTGGCACGTTCGGC
TCGCTCGGCATGGCGAACGACCGCCGCATCGCGCATCGCCGTCGCGCGGCCTCCAAAAAA
ACGGCGGTCAGCGACCGCCGGCTTTGGCCGAAACCGATGCGTCGTACGAATCAGTGA
>gene_988|GeneMark.hmm|237_nt|+|1121027|1121263
ATGACCTTGTCAGGCAACATCAAGGACGGCGACTGGACGGTCGAGGTGACGACATCGCCG
GTGCAGGGCGGTTACGTGTGCGACATCGAGGTGATGCACGGCGCGCCGGGCGGCGCGTTC
CGGCACGCGTTCCGGCACGGCGGCACTTATCCGGCCGAGCGCGACGCGATGATCGAGGGG
CTGCGCGCGGGCATGACCTGGATCGAGCTGAAGATGTCGAAAGCATTCAATCTGTAA
>gene_97|GeneMark.hmm|183_nt|-|107002|107184
ATGGAGGCAATCGTGATCGAGCAAGTGATACTGGGCGTCTTTCTCGTACTGCCGCTTCTC
ATCGTCGCGGTGCTGTACTCCGACGAACTCTGGCAAGAACACCGCCTGCAGCATCCGCGC
GACGAGCACACGCCACATATCGACTGGCGTCATCCGTGGCGGATCCTGCGGCGAGGGCAC
TAA
>gene_97|GeneMark.hmm|189_nt|-|98624|98812
GTGAAATACACGAGCGACCATTACGCGGGCGTCAAATTTGGCGCGCTGTACGGGTTCTCG
AACGCGGCGAACTTCGCCGACAACCGCGCTCGCCGGCGCATGCGCGGCGTTCGCATACGC
GATCGGCAAAAGCGGCGTGATGTGCGGTTGCCTGCCGCGCTCGCGCTATGCGCGGCACGC
CATCGATGA
Bio::SeqIO lives to parse fasta (and other such) files, so the above leverages this capability. After creating a hash of arrays (HoA) from file1.txt, the fasta file is processed, and only matching fasta records are printed.
Hope this helps!