Pseq - print protein sequence
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Print sequence (in one letter format) of protein in a readable way in console. | Print sequence (in one letter format) of protein in a readable way in console. | ||
+ | |||
+ | Usage: | ||
+ | pseq | ||
+ | pseq <sequence_file> | ||
+ | |||
+ | default name for sequence file is ./seq | ||
author: [[User:Evgeny Fadeev|Evgeny Fadeev]] | author: [[User:Evgeny Fadeev|Evgeny Fadeev]] | ||
+ | |||
<source lang="perl"> | <source lang="perl"> | ||
#!/usr/bin/perl | #!/usr/bin/perl |
Revision as of 22:26, 10 March 2009
Print sequence (in one letter format) of protein in a readable way in console.
Usage:
pseq pseq <sequence_file>
default name for sequence file is ./seq
author: Evgeny Fadeev
#!/usr/bin/perl my $file = './seq'; $file = $ARGV[0] if not -f $file; open F, "<$file" or die "$!"; my @lines = <F>; s/\s//g foreach @lines; chomp foreach @lines; my $seq = join('',@lines); my @seq = split /|/, $seq; my $num,$aa; my $w=4; print "\n"; for (my $i=0; $i<@seq; $i++) { $num .= sprintf "%4d", $i+1; $aa .= sprintf "%4s", $seq[$i]; if ((($i+1)*$w)%80 == 0) { print "$num\n"; print "$aa\n\n"; $aa = ''; $num = ''; } } print "$num\n"; print "$aa\n\n";