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Bio-Procedural-1.7.3
River stage one • 6 direct dependents • 7 total dependents
/ Bio::Perl

NAME

Bio::Perl - Functional access to BioPerl for people who don't know objects

VERSION

version 1.7.3

SYNOPSIS

use Bio::Perl;

# 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 a string

$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");

# BLAST a sequence (assumes an internet connection)

$blast_report = blast_sequence($seq_object);

write_blast(">blast.out",$blast_report);

DESCRIPTION

Easy first time access to BioPerl via functions.

read_sequence

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.

read_all_sequences

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

write_sequence

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

new_sequence

Title   : new_sequence
Usage   : $seq_obj = new_sequence("GATTACA", "kino-enzyme");

Function: Construct a sequency object from sequence string
Returns : A Bio::Seq object

Args    : sequence string
          name string (optional, default "no-name-for-sequence")
          accession - accession number (optional, no default)

blast_sequence

Title   : blast_sequence
Usage   : $blast_result = blast_sequence($seq)
          $blast_result = blast_sequence('MFVEGGTFASEDDDSASAEDE');

Function: If the computer has Internet accessibility, blasts
          the sequence using the NCBI BLAST server against nrdb.

          It chooses the flavour of BLAST on the basis of the sequence.

          This function uses Bio::Tools::Run::RemoteBlast, which itself
          use Bio::SearchIO - as soon as you want to know more, check out
          these modules
Returns : Bio::Search::Result::GenericResult.pm

Args    : Either a string of protein letters or nucleotides, or a
          Bio::Seq object

write_blast

Title   : write_blast
Usage   : write_blast($filename,$blast_report);

Function: Writes a BLAST result object (or more formally
          a SearchIO result object) out to a filename
          in BLAST-like format

Returns : none

Args    : filename as a string
          Bio::SearchIO::Results object

get_sequence

Title   : get_sequence
Usage   : $seq_object = get_sequence('swiss',"ROA1_HUMAN");

Function: If the computer has Internet access this method gets
          the sequence from Internet accessible databases. Currently
          this supports Swissprot ('swiss'), EMBL ('embl'), GenBank
          ('genbank'), GenPept ('genpept'), and RefSeq ('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, genpept, or
          refseq

translate

Title   : translate
Usage   : $seqobj = translate($seq_or_string_scalar)

Function: translates a DNA sequence object OR just a plain
          string of DNA to amino acids
Returns : A Bio::Seq object

Args    : Either a sequence object or a string of
          just DNA sequence characters

translate_as_string

Title   : translate_as_string
Usage   : $seqstring = translate_as_string($seq_or_string_scalar)

Function: translates a DNA sequence object OR just a plain
          string of DNA to amino acids
Returns : A string of just amino acids

Args    : Either a sequence object or a string of
          just DNA sequence characters

reverse_complement

Title   : reverse_complement
Usage   : $seqobj = reverse_complement($seq_or_string_scalar)

Function: reverse complements a string or sequence argument
          producing a Bio::Seq - if you want a string, you
          can use reverse_complement_as_string
Returns : A Bio::Seq object

Args    : Either a sequence object or a string of
          just DNA sequence characters

revcom

Title   : revcom
Usage   : $seqobj = revcom($seq_or_string_scalar)

Function: reverse complements a string or sequence argument
          producing a Bio::Seq - if you want a string, you
          can use reverse_complement_as_string

          This is an alias for reverse_complement
Returns : A Bio::Seq object

Args    : Either a sequence object or a string of
          just DNA sequence characters

reverse_complement_as_string

Title   : reverse_complement_as_string
Usage   : $string = reverse_complement_as_string($seq_or_string_scalar)

Function: reverse complements a string or sequence argument
          producing a string
Returns : A string of DNA letters

Args    : Either a sequence object or a string of
          just DNA sequence characters

revcom_as_string

Title   : revcom_as_string
Usage   : $string = revcom_as_string($seq_or_string_scalar)

Function: reverse complements a string or sequence argument
          producing a string
Returns : A string of DNA letters

Args    : Either a sequence object or a string of
          just DNA sequence characters

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

FEEDBACK

Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bio-procedural/issues

AUTHOR

Ewan Birney <birney@ebi.ac.uk>

COPYRIGHT

This software is copyright (c) by many people (see the individual modules for their copyright holders).

This software is available under the same terms as the perl 5 programming language system itself.