Bio::Perl - Functional access to BioPerl for people who don't know objects
use Bio::Perl qw(read_sequence read_all_sequences write_sequence new_sequence get_sequence);
# will guess file format from extension $seq_object = read_sequence($filename);
# forces genbank format $seq_object = read_sequence($filename,'genbank');
# reads an array of sequences @seq_object_array = read_all_sequences($filename,'fasta');
# sequences are Bio::Seq objects, so the following methods work # for more info see Bio::Seq, or do 'perldoc Bio/Seq.pm'
print "Sequence name is ",$seq_object->display_id,"\n"; print "Sequence acc is ",$seq_object->accession_number,"\n"; print "First 5 bases is ",$seq_object->subseq(1,5),"\n";
# get the whole sequence as a single string
$sequence_as_a_string = $seq_object->seq();
# writing sequences
write_sequence(">$filename",'genbank',$seq_object); write_sequence(">$filename",'genbank',@seq_object_array);
# making a new sequence from just strings you have # from something else
$seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA","myname","AL12232");
# getting a sequence from a database (assumes internet connection)
$seq_object = get_sequence('swissprot',"ROA1_HUMAN"); $seq_object = get_sequence('embl',"AI129902"); $seq_object = get_sequence('genbank',"AI129902");
Easy first time access to BioPerl via functions
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : read_sequence Usage : $seq = read_sequence('sequences.fa') $seq = read_sequence($filename,'genbank'); # pipes are fine $seq = read_sequence("my_fetching_program $id |",'fasta'); Function: Reads the top sequence from the file. If no format is given, it will try to guess the format from the filename. If a format is given, it forces that format. The filename can be any valid perl open() string - in particular, you can put in pipes Returns : A Bio::Seq object. A quick synopsis: $seq_object->display_id - name of the sequence $seq_object->seq - sequence as a string Args : Two strings, first the filename - any Perl open() string is ok Second string is the format, which is optional
For more information on Seq objects see Bio::Seq.
Title : read_all_sequences Usage : @seq_object_array = read_all_sequences($filename); @seq_object_array = read_all_sequences($filename,'genbank'); Function: Just as the function above, but reads all the sequences in the file and loads them into an array. For very large files, you will run out of memory. When this happens, you've got to use the SeqIO system directly (this is not so hard! Don't worry about it!). Returns : array of Bio::Seq objects Args : two strings, first the filename (any open() string is ok) second the format (which is optional)
See Bio::SeqIO and Bio::Seq for more information
Title : write_sequence Usage : write_sequence(">new_file.gb",'genbank',$seq) write_sequence(">new_file.gb",'genbank',@array_of_sequence_objects) Function: writes sequences in the specified format Returns : true Args : filename as a string, must provide an open() output file format as a string one or more sequence objects
Title : new_sequence Usage : Function: Example : Returns : Args :
Title : get_sequence Usage : $seq_object = get_sequence('swiss',"ROA1_HUMAN"); Function: If the computer has Internet accessibility, gets the sequence from Internet accessible databases. Currently this supports Swissprot, EMBL, GenBank and RefSeq. Swissprot and EMBL are more robust than GenBank fetching. If the user is trying to retrieve a RefSeq entry from GenBank/EMBL, the query is silently redirected. Returns : A Bio::Seq object Args : database type - one of swiss, embl, genbank or refseq identifier or accession number
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.