Re: missing character when reading input file

It now appears that your data file was created on a windows system and you are reading it with a unix-like system. Perl can handle this, but you have to tell it using IO layers in the open statement. (Refer perlio)

use strict;
use warnings;
BEGIN {
    my $win_file # memory file simulates windows file.
    = ">symbB.v1.2.017277.t1|scaffold1325.1|size176917|3\r\n"

    . "acggaccgcggcatttgccaatttgcgcgt"
    . "cgtcgggggtcgccatgatgtttcgcttgg"
    . "caggcttttttgctttggcactgctggtcg"
    . "cgggaaagcc\r\n"

    . "caagggtggcaaaggtgcaaaaggagaaca"
    . "agaccccttctctgagcttagccgcctcgc"
    . "agacaatttgaaagatgctaaagaacagcc"
    . "ggagaaggcc\r\n"

    . "aagaatgctctgaacatgatggatccagaa"
    . "agtttaggcgattctatggccaacatgatg"
    . "gtgatggcaatggataaggaccaggatggt"
    . "gtgttgtcag\r\n"
    ;
    $ARGV[0] = \do{$win_file};
}

open( my $input, '<:crlf', $ARGV[0] )
    or die( "Could not open input file $ARGV[0].\n" );

my $seq;
while ( my $line = <$input> ) {
    chomp($line);
    unless ( $line =~ m/>/ ) {
        $line = uc($line);
        $seq .= $line;
    }
}
print "Length of \$seq is ", length($seq), " characters\n";
[download]

Bill

Comment on Re: missing character when reading input file Download Code

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Re^2: [OT]: missing character when reading input file by AnomalousMonk (Archbishop) on Sep 12, 2018 at 17:41 UTC
I agree with your example of using open to handle a CRLFish file on a nix system. The rest of this post is just to satisfy my curiosity. `$ARGV[0] = \do{$win_file};`* I don't understand the purpose of munging `@ARGV` in this way. Any scalar can be opened by reference as a RAM file. If the reason for initializing the scalar in a `BEGIN` block was to create a lexically private scalar, then assigning a reference to it to an element of the global `@ARGV` array defeats this purpose. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]
Re^3: [OT]: missing character when reading input file by BillKSmith (Monsignor) on Sep 12, 2018 at 18:36 UTC
The array @ARGV was used to preserve as much of the original OP as possible. The 'BEGIN' is unnecessary, but I feel that it serves to separate the file simulation from the relevant code. No excuse for the 'do' block. It is a leftover from an earlier attempt at the file simulation. Bill	[reply]
Re^4: [OT]: missing character when reading input file by AnomalousMonk (Archbishop) on Sep 12, 2018 at 18:56 UTC
The array @ARGV was used to preserve as much of the original OP as possible. Ah, ok. I understand better now. It occurred to me after I posted that this might have been part of the motivation. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l]
Re^2: missing character when reading input file by bliako (Abbot) on Sep 12, 2018 at 09:03 UTC
hey that's a cool new trick I learned today, setting `$ARGV[0] = \do{$win_file};` I like your method as an easy way to produce a CRLF file in non-windows machine (e.g. for tests).	[reply] [d/l]