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This article mainly introduces how to filter fasta files related knowledge, the content is detailed and easy to understand, the operation is simple and fast, with a certain reference value, I believe you will have a harvest after reading this article on how to filter fasta files, let's take a look at it.

Fasta files have a fixed format, and if some sequences are malformed or appear some characters that should not appear (such as garbled codes), you need to filter out these sequences. The filtering method is relatively simple and can be done with a script to avoid repeated manual deletions.

Script run commands:

Perl fasta.filter.pl-in in.fasta-o out.fasta

Where:

Fasta.filter.pl: script name

-in: enter the option, followed by the name of the file

-o: output option followed by the name of the output file.

The script is as follows:

Use Bio::SeqIO;use Bio::Seq;use Getopt::Long;my% opts;GetOptions (\% opts, "in=s", "oaths", "h"); my$in = Bio::SeqIO- > new (- file = > "$opts {in}",-format = > 'Fasta'); my$out = Bio::SeqIO- > new (- file = > "> $opts {o}",-format = >' Fasta') While (my $seq = $in- > next_seq ()) {my ($id,$seqence,$desc) = ($seq- > id,$seq- > seq,$seq- > desc); next if ($seqence eq ""); next if ($seqence = ~ [^ ATCGNatcgn]); $out- > write_seq ($seq); $out- > close ();} $in- > close (); $out- > close (); this is the end of the article on "how to filter fasta files". Thank you for reading! I believe you all have a certain understanding of the knowledge of "how to filter fasta files". If you want to learn more, you are welcome to follow the industry information channel.

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