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Re: How do I stop appending data

by Kenosis (Priest)
on Mar 07, 2013 at 18:18 UTC ( #1022285=note: print w/ replies, xml ) Need Help??


in reply to How do I stop appending data

toolic expertly provided the solution to your script's concatenation issue. However, consider using Bio::SeqIO for your Fasta-parsing needs:

use strict; use warnings; use Bio::SeqIO; my $in = Bio::SeqIO->new( -fh => \*ARGV, -format => 'Fasta' ); while ( my $seq = $in->next_seq() ) { my $protein; $protein .= codon2aa($_) for $seq->seq =~ /.../g; print '>' . $seq->id . "\n$protein\n"; } #' codon2aa #' #' A subroutine to translate a DNA 3-character codon to an amino acid sub codon2aa { my ($codon) = @_; if ( $codon =~ /GC./i ) { return 'A' } # Alanine elsif ( $codon =~ /TG[TC]/i ) { return 'C' } # Cysteine elsif ( $codon =~ /GA[TC]/i ) { return 'D' } # Aspartic Aci +d elsif ( $codon =~ /GA[AG]/i ) { return 'E' } # Glutamic Aci +d elsif ( $codon =~ /TT[TC]/i ) { return 'F' } # Phenylalanin +e elsif ( $codon =~ /GG./i ) { return 'G' } # Glycine elsif ( $codon =~ /CA[TC]/i ) { return 'H' } # Histidine elsif ( $codon =~ /AT[TCA]/i ) { return 'I' } # Isoleucine elsif ( $codon =~ /AA[AG]/i ) { return 'K' } # Lysine elsif ( $codon =~ /TT[AG]|CT./i ) { return 'L' } # Leucine elsif ( $codon =~ /ATG/i ) { return 'M' } # Methionine elsif ( $codon =~ /AA[TC]/i ) { return 'N' } # Asparagine elsif ( $codon =~ /CC./i ) { return 'P' } # Proline elsif ( $codon =~ /CA[AG]/i ) { return 'Q' } # Glutamine elsif ( $codon =~ /CG.|AG[AG]/i ) { return 'R' } # Arginine elsif ( $codon =~ /TC.|AG[TC]/i ) { return 'S' } # Serine elsif ( $codon =~ /AC./i ) { return 'T' } # Threonine elsif ( $codon =~ /GT./i ) { return 'V' } # Valine elsif ( $codon =~ /TGG/i ) { return 'W' } # Tryptophan elsif ( $codon =~ /TA[TC]/i ) { return 'Y' } # Tyrosine elsif ( $codon =~ /TA[AG]|TGA/i ) { return '_' } # Stop else { return '*'; } }

Output on your data set:

>M01096:4:000000000-A23M1:1:1101:15974:1529 VTECGWQTAGCRMY >M01096:4:000000000-A23M1:1:1101:16525:1548 LSHCDVKDWMCWLL >M01096:4:000000000-A23M1:1:1101:13838:1554 AWTCVEIDGHFSMN


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Re^2: How do I stop appending data
by 4pt8secs (Novice) on Mar 07, 2013 at 19:05 UTC

    Yeah, I'll need to delve into the BioPerl tools. Thanks for the example. That will be helpful too.

      You're most welcome, 4pt8secs!

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