How to split one file into multiple files using perl?

Question

I have the file as ftp.txt which contains many versions of lines such as

>KCY60942 pep:novel supercontig:GCA_000682575.1:ab248605.contig.36_1:19:588:-1 gene:J738_3590 transcript:KCY60942 description:"putative transposase 1"
MTHLNELYLILNKYLKWNKSHLKCFALIMLVIILKQTCNLSSASKALPIKCLPQSFYRRM
QRFFAGQYFDYRQISQLIFNMFSFDQVQLTLDRTNWKWGKRNINILMLAIVYRGIAIPIL
WTLLNKRGNSDTKERIALIQRFIAIFGKDRIVNVFADREFIGEQWFTWLIEQDINFCIRV
KKTSLSPII

>KCY61710 pep:novel supercontig:GCA_000682575.1:ab248605.contig.22_1:4164:6320:1 gene:J738_2986 transcript:KCY61710 description:"tonB-dependent siderophore receptor family protein"
MQRTTKHFQINALALAIAMSTISAHAETDQQTSEYGTLPTIKVKAGSGQENEKSYIAGKT
DTAVPLGLSVREVPQSVSVITQQRLQDQQLSTLVEVAENVTGVSVNRYETNRGGIYSRGF
VVDNYIIDGIPTTYSLPWSSGEIFSSMALYDHIDVVRGATGLTFGAGNPSAAINMVRKRA
TSTEPTANVEVSAGSWDNYRVMGDIANSLNQSGTVRGRAVAQYEQGDSYTDLLSKEKLSL
LLSAEADLSENTLLSGGVTYQEDDPRGPMWGGLPVWFSDGTKTNWSKNITTSADWTRWNV
KYTNLFADLTHKFNDNWSAKLSYSHGKRDANSKLLYVSGSVDKNTGLGLSPYASAYDLEV
EQDNASLQLNGSFDLWGLEQKVVLGYQYSNQDFTAYARSTDTKMEIGNFFEWNGSMPEPV
WNAPTLNEKYNIEQNALFAATYLNPIEPLKFILGGRFTNYEKNIYGRSSSIKYDHEFVPY
AGIIYDFNDVYTAYASYTSIFQPQDKKDFDGNYLDPVEGNSTEVGLKSAWFDGRLNGTLA
LYHIKQDNLAQEAGDVTRNGVKEIYYRAAKGATSEGFEVEVSGQITPDWNITAGYSQFSA
KDTNDVDVNTQLPRKMIQTFTTYKLSGKLENITVGGGVNWQSSTYINAENPKEVIEKVEQ
GDYALVNLMARYQITKDFSAQLNINNVFDKKYYGVFPAYGQITLGAPRNAALTLQYKF

my query is to separate each version and want to save it each version with different file names? i tried the below code but i get only the line which startsup

#!/usr/local/bin/perl
open( FILE, "/home/httpd/cgi-bin/r/ftp.txt" );
while ( $line = <FILE> ) {
    if ( $line =~ m/^\>/g ) {
        print $line;
    }
}

my desired output should be those two different versions which starts as like this >KCY60942 and >KCY61710 must saved in different filenames such as >KCY60942 should be saved in one file name and >KCY61710 it should be saved in another file name.

Answer 1

Here's another option:

use strict;
use warnings;

local $/ = '';

while (<>) {
    my ($fileName) = /^>([^\s]+)/;
    open my $fh, '>', "$fileName.txt" or die "Can't write to '$fileName.txt'";
    print $fh $_;
    close $fh;
}

Usage: perl script.pl inFile

Since each (FASTA?) record is a paragraph, $/ is set to empty ( '' ) to read the file in paragraph mode--one 'record' at a time. Each record's id is captured for use as that record's file name, and then that record is written to its file.

Hope this helps!

Answer 2

Something like this should do the trick:

#!/usr/local/bin/perl

use strict;
use warnings;

open( my $file, "<", "/home/httpd/cgi-bin/r/ftp.txt" );
open( my $output, ">", "pre-match" ) or die $!;

while ( my $line = <$file> ) {
    if ( $line =~ m/^\>/g ) {
        my ($output_name) = ( $line =~ m/^\>(\w+)/ );
        close($output);
        open( $output, ">", $output_name . ".output" ) or die $!;
    }
    print {$output} $line;
}

close($output);

If your line matches that regular expression, we 'pick out' the first word (so KCY61710 etc.) and open a file called KCY61710.output .

We print each line as we go to this output, closing and re-opening each time we hit one of those lines.

A pre-match file exists in case the first line(s) don't match this pattern.