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Re^18: how to read input from a file, one section at a time?

by poj (Abbot)
on Apr 02, 2019 at 19:20 UTC ( [id://1232047]=note: print w/replies, xml ) Need Help??


in reply to Re^17: how to read input from a file, one section at a time?
in thread how to read input from a file, one section at a time?

I would suggest developing a separate program to clean up your data and leave the working program alone. It's always preferable to have 'clean data' to process and 2 steps I think are easier to debug. For example

#!/usr/bin/perl # cleanup.pl use strict; use warnings; print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: '; chomp( my $prot_filename = <STDIN> ); open my $PROTFILE, '<', $prot_filename or die "Cannot open '$prot_filename' because: $!"; my $out_filename = 'cleaned_'.$prot_filename; open my $OUTFILE, '>', $out_filename or die "Cannot open '$out_filename' because: $!"; $/ = ''; # Set paragraph mode my %fasta_seen; # sequences seen so far my $header; my $count_in; my $count_out; while ( my $record = <$PROTFILE> ) { ++$count_in; if ( $record =~ s/^>(.*)//m ){ $header = $1; # skip fragments next if $header =~ /\(Fragments\)/i; }; # Remove comment line(s) $record =~ s/^\s*#.*//mg; # trim trailing spaces $record =~ s/\s+$//; # skip duplicated if ( $fasta_seen{ $record }++ ){ print $OUTFILE "\n"; } else { print $OUTFILE $header.$record."\n\n"; ++$count_out; } } close $OUTFILE; close $PROTFILE; printf "%d records read from %s\n",$count_in,$prot_filename; printf "%d records written to %s\n",$count_out,$out_filename;

I'm sure acknowledge of perlmonks.org would be appreciated by the community here.

poj

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Re^19: how to read input from a file, one section at a time?
by davi54 (Sexton) on Apr 02, 2019 at 21:11 UTC
    Thank you so much Poj. Will do.
    :)
Re^19: how to read input from a file, one section at a time?
by davi54 (Sexton) on Apr 03, 2019 at 16:49 UTC
    Hi, can someone tell me what's the mistake I'm doing in the following code? To be precise, in line- 'printf "%d duplicate records written\n",$name,$para,$out_filename;'?
    I get an error:
    Argument "sdAb_1193_LgLlama" isn't numeric in printf at ../duplicate.p +l line 35, <$PROTFILE> chunk 165. 'Redundant argument in printf at ../duplicate.pl line 35, <$PROTFILE> +chunk 1164.'
    #!/usr/bin/perl # cleanup.pl use strict; use warnings; print 'Enter protein sequence filename: '; chomp( my $prot_filename = <STDIN> ); open my $PROTFILE, '<', $prot_filename or die "Cannot open '$prot_filename' because: $!"; my $out_filename = 'duplicates_entries_in_'.$prot_filename; open my $OUTFILE, '>', $out_filename or die "Cannot open '$out_filename' because: $!"; $/ = ''; # Set paragraph mode my $name; my %fasta_seen; FASTA_RECORD: while ( my $para = <$PROTFILE> ) { # Remove fasta header line if ( $para =~ s/^>(.*)//m ){ $name = $1; }; # Remove comment line(s) $para =~ s/^\s*#.*//mg; # Trim trailing white space $para =~ s/\s+$//; # next FASTA_RECORD if $fasta_seen{ $para }++; if ( $fasta_seen{ $para }++ ){ printf "%d duplicate records written\n",$name,$para,$out_filename; next FASTA_RECORD; } } print "\n";

    2019-04-07 Athanasius added code tags and removed break tags within code

      printf "%d duplicate records written\n",$name,$para,$out_filename;

      see printf and sprintf. You need to put %s in the print format for strings, %d for integers

      while ( my $para = <$PROTFILE> ) { # Remove fasta header line if ( $para =~ s/^>(.*)//m ){ $name = $1; }; # Remove comment line(s) $para =~ s/^\s*#.*//mg; # Trim trailing white space $para =~ s/\s+$//; # next FASTA_RECORD if $fasta_seen{ $para }++; if ( $fasta_seen{ $para }++ ){ printf "duplicate record %s %s \nwritten to %s\n",$name,$para,$out +_filename; print $OUTFILE '>'.$name.$para."\n\n"; } }
      poj
        Ohh.. okay.. still learning.. Thanks.. :)

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