use strict;
use warnings;
my $idsfile = "sample_IDs.txt";
my $seqfile = "sample_reads.fasta";
my %ids  = ();

open FILE, $idsfile;
while(<FILE>) {
  chomp;
  $ids{$_} += 1;
}
close FILE;

local $/ = "\n>";  # read by FASTA record

open FASTA, $seqfile;
while (<FASTA>) {
    chomp;
    my $seq = $_;
    my ($id) = $seq =~ /^>*(\S+)/;  # parse ID as first word in FASTA header
    if (exists($ids{$id})) {
        $seq =~ s/^>*.+\n//;  # remove FASTA header
        $seq =~ s/\n//g;  # remove endlines
        print "$seq\n";
    }
}
close FASTA; 

##</code><code>##

 
sample_ID.txt


>comp10000_c0_seq1	15

>comp10001_c0_seq1	79

>comp10002_c0_seq1	7521

>comp10003_c0_seq1	41

>comp10004_c0_seq1	25

>comp10005_c0_seq1	96

>comp10006_c0_seq1	84

>comp10007_c0_seq1	63

>comp10008_c0_seq1	19

>comp1000_c0_seq1	35

>comp10010_c0_seq1	44

>comp10011_c0_seq1	32

>comp10012_c0_seq1	451

>comp10014_c0_seq1	6845

>comp10015_c0_seq1	521

>comp10016_c0_seq1	254

>comp10017_c0_seq1	51

>comp10018_c0_seq1	4512

>comp10019_c0_seq1	64    

##</code><code>##

sample_reads.fasta

>comp10000_c0_seq0 len=159 path=[12:0-66 885:67-79 1106:80-158]
GGTTAATATTCCCGAGCCACGAGATTGGAGGGACGGCGTCCAGAGCACCTGCGGACTGAT
AGAATAGCCCGTTGGAGGTACTGAGTTGGAGAGGATTAAAAGACTCTCATAATACAAGGC
CCGTACTAAGCCCACTTACGATGGAATAGATGGTAGGAA	

>comp10001_c0_seq2 len=100 path=[1:0-60 177:61-65 600:66-99]
ATCCCGCACGATTCCTGGAAACACTATCTCACCCCCAAAAGTGAAGAACCGTATAGAAAC
TCGAATACCTTGGTTTCGAGTACATCTTGTGCTCTTGAAT

>comp10002_c0_seq3 len=99 path=[2446:0-34 1163:35-98]
TTTTTTGTGATATATTAAATAATATATAAAAATACTATGGCAGGAAGTTTAAATAAAGTC
TTATTAATAGGCCGTTTAGGCGCAGACCCAGATATAAAA	</p>

>comp10003_c0_seq1 len=166 path=[748:0-22 1004:23-46 2527:47-165]
AAGTAGCCTATGCGCTACAGTAAGAAAGACAGGTGAAAAAATGGAAGTAAAACAATTAGA
TGACTACTTTGGATATACAGAAAAGGGCAGTTCCTTAGAGGGGGAATTACGAGCAGGACT
AACGACATTCTTGACAATGGCGTACATTCTGTTTGTGAACCCAGAC 

>comp10004_c0_seq1 len=143 path=[2167:0-44 2322:45-68 2508:69-142]
AATCTTTAATTTAAACTTAAAAAAAATTAACTTTTGAAAGGAATTAAAATGGAAAAAGAA
ATGTTAGTAGTAGCTAAATTAAAAGAAGGTACATTTGAAAAATTTATGGGTTTCATGCAA
TCGCCTGAAGGTTTAGCAGAAAG 


>comp10005_c0_seq1 len=135 path=[2666:0-71 4268:72-134]	
AATATTACCAGAAGTTACAGGTGATGTGACTTATTTACATTGCTTCGGTGAGTGTTCAGG
TGATGGTACAGGTGAATGCCCAAGTGGCGCTGTAACATGGATGCTTACAATGACTGTAAA
TACTGCTAATATCAC 

>comp10006_c0_seq1 len=116 path=[4850:0-56 4046:57-115]
ATATAAGGTAGAAAATTACATTAACTATCTTTATCTATTTTATCACATTAGATATACAAA
CTTTTCCTTACAGAGAGGTCAAAAAATATGGAAGGAACTTTACTCTTAGCTAAATT 


>comp10007_c0_seq1
CCGGGTTAGTCCGAATTTATTTTTTATATAAGGTAGATTTACAAAGTTATATGATTTTTT
TAATAGCCGCAATAGCACTCTTCATCTGGGTTGCATACACCGCAATGGAATTAAGAAAAG
CAACGCT 


>comp10008_c0_seq1 len=298 path=[4908:0-189 5729:190-297]
ATTTTGATTTCAGAAAGATGTGTAACTGATGACGTGTTTACTTCAGTTCATATTGAAGAA
TATGAAATAATGGCAAGAGACACTAAACTAGGTGAAGAAGAAATTACCAGAGATATTCCT
AATGTTAATGAAGAAGCTTTAAAAAATCTTGATGAATCAGGGATAGTTTACATTGGAGCT
GAAGTAAACGCTGGTGATATTTTAGTTGGGAAAGTGACACCCAAAGGCGAGTCGCCAATG
ACCCCAGAAGAAAAATTGCTTCGAGCAATTTTTGGAGAGAAAGCTTCTGATGTAAGGG 
 

 
>comp1000_c0_seq1 len=120 path=[5871:0-53 6857:54-119]
ATTATAACAAGAGGAGTGCACATGAGAAAAATGATATCATTGATTTCTGCGGTGCTAGTA
ATGTTTGCTTTTTCAAGCTCTATTACTTCAATCGCGAAATCAGCAGAGTTCTTTACAATA 


>comp10010_c0_seq1 len=108 path=[7438:0-30 7277:31-107]
ATTCAGACTTTCTAACCAGACAGATGATCTAGATTGGATCGTTGGTCTTTTCTACCAAGA
AAGAGAAGAAGGTTGGGATTTCGAAACGGAAACCCACAACTACAGAAA 

 
>comp10011_c0_seq1 len=105 path=[7198:0-63 8366:64-81 10234:82-104]
ATTGTTAAGTTTGTGTTTTTATGAATTGAAAATAAGAACTACAAACACGCTATTGAAAAT
TGTAAATATGTTTTCGGCTTTCATCGATTAATCAGAAGGTGATTG 


>comp10012_c0_seq1 len=134 path=[8117:0-30 7737:31-54 7822:55-133]
ATATGTTTTTTTTATTAACACTTAAATTAACTAAATGGTACGATTCTTGAATAGATGATC
GAAATAGTTGGAGTTTTGTAATGGATTTAGCCTCCCTAATTGGACTTGTTGGTGCAGTCG
GTATGATTATAGCA 


>comp10014_c0_seq1en=175 path=[7957:0-85 8425:86-174]
CTCGCGGTCTTTCAGAGGATGCTGAGAAATTCCTAGAGAAGGTTCGTGCGAATGGTGGCT
CCAAGATGATTAAGACACACTGCCGAAGTATGTACGTATTACCAGAGATGGTCGGTACTA 


>comp10015_c0_seq1 len=122 path=[8708:0-78 9126:79-121]
AAGTGAATGTTTTTTAATTAAAACTTAGGTGGGAACCTGTAAAAAGGCGCACCATCGACC
GGTCATGGGCTTCGGTCCAAGATCTGAGTATGAGTTTTTATGCTGGGACCCGAAAGATGG
TG 
 

>comp10016_c0_seq1 len=210 path=[9869:0-132 11973:133-209]
TTGTAGTATTTATGAATAAAACTGACCAAGTTGATGATGAAGAACTTGTTGAGCTTGTTG
AAATGGAGCTTCGCGACCTATTAAATGAATATGAATTCCCAGGTGATGATATTCCTATAG
TTAAAGGTTCTGCACTTAAAGCTCTTGATAATGTTTCTGATGAAGCTGCTACTGCTTGTA
TAGCTGAACTTATGGAAGCTTGTGATAGTT 


>comp10017_c0_seq0 len=103 path=[11024:0-19 11107:20-43  <p> 11572:44-48 11236:49-102]
TTTTTTGGTCAACTAGGTGGCTGAGAATCATTATTCTATGGTTATAAGGCACCCTTATTG
ACATTTAAACGTTGGAGGAAATCATAAATGCGTATTAAATCAA 
 

>comp10018_c0_seq2 len=77 path=[12879:0-24 13307:25-76]
ATAAAACACAATACACCGCCCATCTTATGCGGTGTCTAAATATAACTTAACCCTATTAAG
TTTCCTAATAAACTTAT 


>comp10019_c0_seq3 len=112 path=[14245:0-49 14086:50-111]
ATTTAGGACAAGTCTCTGCTGCAATGGGAACAGGAGTTGATCCTGGAGCTGCAATTGGAA
ATGTAGCAGGTGCTGCGATGGCAGCTGAGGGAGCAGGCGGATTAGCAAGTGC