Mercurial > repos > dcouvin > concatenatemultifasta

comparison concatenateMultiFasta.pl @ 0:640361a4d2ef draft default tip

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author dcouvin
date Fri, 17 Sep 2021 19:23:57 +0000
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-1:000000000000 0:640361a4d2ef
1 #!/usr/bin/perl -w
2 use strict;
3
4 ################################################################
5 # Script allowing to concatenate multiFasta file,
6 # generating an output file containing a single sequence
7 ################################################################
8
9 # example of use: perl concatenateMultiFasta.pl multiFasta_file.fasta
10 # other example: perl concatenateMultiFasta.pl *.fasta
11
12 my @listFastaFiles = @ARGV;
13
14 foreach my $multiFasta ( @listFastaFiles ) {
15 my $outFasta = 'concatenated_'.$multiFasta ;
16 open(FILE,"<$multiFasta") || die ("Error opening $multiFasta $!");
17 #open(OUT, '>', $outFasta) or die $!;
18 print ">$outFasta\n";
19 while (my $row = <FILE>) {
20 chomp $row;
21 if ($row=~m/^>/){
22 }
23 else{
24 print "$row\n";
25 }
26 }
27 }
28
29 close(FILE);
30 #close(OUT);