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.\" ========================================================================
.\"
.IX Title "Bio::Seq::LargeSeq 3pm"
.TH Bio::Seq::LargeSeq 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Seq::LargeSeq \- SeqI compliant object that stores sequence as
files in /tmp
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # normal primary seq usage
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object stores a sequence as a series of files in a temporary
directory. The aim is to allow someone the ability to store very large
sequences (eg, > 100MBases) in a file system without running out
of memory (eg, on a 64 \s-1MB\s0 real memory machine!).
.PP
Of course, to actually make use of this functionality, the programs
which use this object \fBmust\fR not call \f(CW$primary_seq\fR\->seq otherwise
the entire sequence will come out into memory and probably paste your
machine. However, calls \f(CW$primary_seq\fR\->subseq(10,100) will cause
only 90 characters to be brought into real memory.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Email birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "trunc"
.IX Subsection "trunc"
.Vb 3
\& Title   : trunc
\& Usage   : $subseq = $myseq\->trunc(10,100);
\& Function: Provides a truncation of a sequence,
\&
\& Example :
\& Returns : a fresh Bio::SeqI object
\& Args    :
.Ve
.SS "Bio::Seq::LargePrimarySeq methods"
.IX Subsection "Bio::Seq::LargePrimarySeq methods"
.SS "add_sequence_as_string"
.IX Subsection "add_sequence_as_string"
.Vb 7
\& Title   : add_sequence_as_string
\& Usage   : $seq\->add_sequence_as_string("CATGAT");
\& Function: Appends additional residues to an existing LargePrimarySeq object.
\&           This allows one to build up a large sequence without storing
\&           entire object in memory.
\& Returns : Current length of sequence
\& Args    : string to append
.Ve