Let's suppose for a moment that you wanted to split the data at the lines containing "INPUT SEQUENCE=" and use the number following the = as part of the file name for the output file, then you could:

use strict;
use warnings;

$/ = 'INPUT SEQUENCE=';

while (<DATA>) {
    chomp;
    next unless length;
    
    next unless s/^(\d+)\n//;
    print "Start of file seq$1.dat\n";
    print "$_\n";
}


__DATA__

[download]
INPUT SEQUENCE=6618
>P40757|ALN_RANCA Allantoinase, mitochondrial precursor - Rana catesbe
+iana (Bull frog)
MALKSKPGIMNITPGSKISVIRSKRVIQANTISSCDIIISDGKISSVLAWGKHVTSGAKLLDVGDLVVMA
GIIDPHVHVNEPGRTDWEGYRTATLAAAAGGITAIVDMPLNSLPPTTSVTNFHTKLQAAKRQCYVDVAFW
GGVIPDNQVELIPMLQAGVAGFKCFLINSGVPEFPHVSVTDLHTAMSELQGTNSVLLFHAELEIAKPAPE
IGDSTLYQTFLDSRPDDMEIAAVQLVADLCQQYKVRCHIVHLSSAQSLTIIRKAKEAGAPLTVETTHHYL
SLSSEHIPPGATYFKCCPPVRGHRNKEALWNALLQGHIDMVVSDHSPCTPDLKLLKEGDYMKAWGGISSL
QFGLPLFWTSARTRGFSLTDVSQLLSSNTAKLCGLGIVKEPLKWVMMLIWSSGILTKSFRCKKMIFITRI
SSPHIWDSFFKEKSWLLLFEGLLFISKGSMLPNQLENLFLYTLWSLVKPVHPVHPIIRKNLPHI
                                                                      
+                                                                     
+                  
Total Number of residues in the sequence =484
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 5
AAAAG                                                               96
+ to 100
AAAGG                                                               97
+ to 101
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 7
AGVAGFK                                                            157
+ to 163
GGISSLQ                                                            345
+ to 351
----------------------------------------------------------------------
+----------­-------------------------
Minimum number of amino-acids present in the distant repeat is  = 5
Maximum number of amino-acids present in the distant repeat is  = 7
Total number of distant repeats found = 62
______________________________________________________________________
+__________­_________________________
INPUT SEQUENCE=6619
>Q9RKU5|ALN_STRCO Probable allantoinase - Streptomyces coelicolor
MSEAELVLRSTRVITPEGTRAASVAVTGEKITAVLPYDAPVPAGARLEDVGDHVVLPGLVDTHVHVNDPG
RTEWEGFWTATRAAAAGGITTLVDMPLNSIPPTTTVDNLRTKREVAADKAHIDVGFWGGALPDNVKDLRP
LHEAGVFGFKAFLSPSGVDEFPHLDQEQLARSLAEIAAFDGLLIVHAEDPHHLAAAPQQGGPKYTHFLAS
RPRDAEDTAIATLLAQAKRFNARVHVLHLSSSDALPLIAEARADGVRVTVETCPHYLTLTAEEVPDGASE
FKCCPPIREAANQDLLWQALADGTIDCVVTDHSPSTADLKTDDFATAWGGIAGLQLSLPAMWTAARGRGL
GLEDVVRWMSERTAALVGLDARKGAIAPGHDADFAVLAPDETFTVDPAALQHRNRVTAYAGKTLYGVVKS
TWLRGERIVADGAFTDPKGQLLDRA
                                                                      
+                                                                     
+                  
Total Number of residues in the sequence =445
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 5
AAAAG                                                               83
+ to 87
AAAGG                                                               84
+ to 88
PSTAD                                                              314
+ to 318
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 6
AAAGGI                                                              84
+ to 89
SSSDAL                                                             240
+ to 245
----------------------------------------------------------------------
+----------­-------------------------
Minimum number of amino-acids present in the distant repeat is  = 5
Maximum number of amino-acids present in the distant repeat is  = 8
Total number of distant repeats found = 94
______________________________________________________________________
+__________­_________________________

[download]

Prints:

Start of file seq6618.dat
>P40757|ALN_RANCA Allantoinase, mitochondrial precursor - Rana catesbe
+iana (Bull frog)
MALKSKPGIMNITPGSKISVIRSKRVIQANTISSCDIIISDGKISSVLAWGKHVTSGAKLLDVGDLVVMA
GIIDPHVHVNEPGRTDWEGYRTATLAAAAGGITAIVDMPLNSLPPTTSVTNFHTKLQAAKRQCYVDVAFW
GGVIPDNQVELIPMLQAGVAGFKCFLINSGVPEFPHVSVTDLHTAMSELQGTNSVLLFHAELEIAKPAPE
IGDSTLYQTFLDSRPDDMEIAAVQLVADLCQQYKVRCHIVHLSSAQSLTIIRKAKEAGAPLTVETTHHYL
SLSSEHIPPGATYFKCCPPVRGHRNKEALWNALLQGHIDMVVSDHSPCTPDLKLLKEGDYMKAWGGISSL
QFGLPLFWTSARTRGFSLTDVSQLLSSNTAKLCGLGIVKEPLKWVMMLIWSSGILTKSFRCKKMIFITRI
SSPHIWDSFFKEKSWLLLFEGLLFISKGSMLPNQLENLFLYTLWSLVKPVHPVHPIIRKNLPHI
                                                                      
+                                                                     
+                  
Total Number of residues in the sequence =484
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 5
AAAAG                                                               96
+ to 100
AAAGG                                                               97
+ to 101
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 7
AGVAGFK                                                            157
+ to 163
GGISSLQ                                                            345
+ to 351
----------------------------------------------------------------------
+----------­-------------------------
Minimum number of amino-acids present in the distant repeat is  = 5
Maximum number of amino-acids present in the distant repeat is  = 7
Total number of distant repeats found = 62
______________________________________________________________________
+__________­_________________________

Start of file seq6619.dat
>Q9RKU5|ALN_STRCO Probable allantoinase - Streptomyces coelicolor
MSEAELVLRSTRVITPEGTRAASVAVTGEKITAVLPYDAPVPAGARLEDVGDHVVLPGLVDTHVHVNDPG
RTEWEGFWTATRAAAAGGITTLVDMPLNSIPPTTTVDNLRTKREVAADKAHIDVGFWGGALPDNVKDLRP
LHEAGVFGFKAFLSPSGVDEFPHLDQEQLARSLAEIAAFDGLLIVHAEDPHHLAAAPQQGGPKYTHFLAS
RPRDAEDTAIATLLAQAKRFNARVHVLHLSSSDALPLIAEARADGVRVTVETCPHYLTLTAEEVPDGASE
FKCCPPIREAANQDLLWQALADGTIDCVVTDHSPSTADLKTDDFATAWGGIAGLQLSLPAMWTAARGRGL
GLEDVVRWMSERTAALVGLDARKGAIAPGHDADFAVLAPDETFTVDPAALQHRNRVTAYAGKTLYGVVKS
TWLRGERIVADGAFTDPKGQLLDRA
                                                                      
+                                                                     
+                  
Total Number of residues in the sequence =445
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 5
AAAAG                                                               83
+ to 87
AAAGG                                                               84
+ to 88
PSTAD                                                              314
+ to 318
----------------------------------------------------------------------
+----------­-------------------------
Number of residues in the repeat = 6
AAAGGI                                                              84
+ to 89
SSSDAL                                                             240
+ to 245
----------------------------------------------------------------------
+----------­-------------------------
Minimum number of amino-acids present in the distant repeat is  = 5
Maximum number of amino-acids present in the distant repeat is  = 8
Total number of distant repeats found = 94
______________________________________________________________________
+__________­_________________________

[download]

which may or may not be anything at all like what you had in mind, but then you haven't actually told us that so guessing is all we can do.

DWIM is Perl's answer to Gödel

In reply to Re: split of files by GrandFather
in thread split of files by boby

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