Re: how to read input from a file, one section at a time?

This may work: (UNTESTED)

open my $out_file, '>', 'aa_report.txt' or die "Cannot open 'aa_report
+.txt' because: $!";

print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename or die "Cannot open '$prot_file
+name' because: $!";

$/ = ''; # Set paragraph mode

while ( my $para = <$PROTFILE> ) {
    # Remove fasta header line
    $para =~ s/^>.*//m;
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    my %prot;
    $para =~ s/([A-Z])/ ++$prot{ $1 } /eg;

    print $out_file join( ' ', map "$_=$prot{$_}", sort keys %prot ), 
+"\n";
    }
[download]

Comment on Re: how to read input from a file, one section at a time? Download Code

Replies are listed 'Best First'.
Re^2: how to read input from a file, one section at a time? by davi54 (Sexton) on Feb 21, 2019 at 23:38 UTC
Hi, thank you so much. It works. I have a following question. Once I have the output in the output file, I want to read the number of alphabets present in the output file for each sequence. Example: for the output: "A=27 C=3 D=16 E=14 F=1 G=11 H=4 I=12 K=10 L=13 M=2 N=6 P=10 Q=6 R=6 S=14 T=20 V=11 W=4 Y=10" I want it to count the alphabets in each result and return how many alphabets are present. In the above example, 20 alphabets are present. So I want my final output to look something like: number of alphabets = 20. How can I do it?	[reply]
Re^3: how to read input from a file, one section at a time? by Cristoforo (Curate) on Feb 22, 2019 at 00:48 UTC
The line below will give you those counts. `print $out_file "Number of proteins = ", scalar keys %prot, "\n";` [download]	[reply] [d/l]
Re^4: how to read input from a file, one section at a time? by davi54 (Sexton) on Feb 22, 2019 at 21:10 UTC
Hi, Thank you. It works perfectly. One last thing I would like my script to do is tho look at those "number of proteins" and tell me which entry in the original input file has the smallest number of proteins. So, it should look like following in the output: A=11 D=5 E=12 F=1 G=5 I=6 K=3 L=7 M=2 N=4 P=2 Q=9 R=10 T=4 V=10 Number of proteins = 15 Entry ">sp\|Q2M7X4\|YICS_ECOLI Uncharacterized protein YicS OS=Escherichia coli (strain K12) OX=83333 GN=yicS PE=4 SV=1" has the least number of proteins	[reply]
Re^5: how to read input from a file, one section at a time? by poj (Abbot) on Feb 23, 2019 at 11:05 UTC
Re^6: how to read input from a file, one section at a time? by davi54 (Sexton) on Feb 26, 2019 at 17:26 UTC
Re^6: how to read input from a file, one section at a time? by davi54 (Sexton) on Oct 15, 2019 at 19:10 UTC
Some notes below your chosen depth have not been shown here
Re^6: how to read input from a file, one section at a time? by davi54 (Sexton) on Mar 28, 2019 at 16:45 UTC
Some notes below your chosen depth have not been shown here
Re^3: how to read input from a file, one section at a time? by BillKSmith (Monsignor) on Feb 22, 2019 at 03:06 UTC
`>type davi54.pl use strict; use warnings; my $string = "A=27 C=3 D=16 E=14 " . "F=1 G=11 H=4 I=12 " . "K=10 L=13 M=2 N=6 " . "P=10 Q=6 R=6 S=14 " . "T=20 V=11 W=4 Y=10" ; print $string =~ tr/A-Z/A-Z/; >perl davi54.pl 20` [download] Bill	[reply] [d/l]


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