.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::LiveSeq::Transcript 3pm"
.TH Bio::LiveSeq::Transcript 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::LiveSeq::Transcript \- Transcript class for LiveSeq
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # documentation needed
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This stores information about coding sequences (\s-1CDS\s0).
The implementation is that a Transcript object accesses a collection of
Exon objects, inferring from them the nucleotide structure and sequence.
.SH "AUTHOR \- Joseph A.L. Insana"
.IX Header "AUTHOR - Joseph A.L. Insana"
Email:  Insana@ebi.ac.uk, jinsana@gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 2
\&  Title   : new
\&  Usage   : $transcript = Bio::LiveSeq::Transcript\->new(\-exons => \e@obj_refs);
\&
\&  Function: generates a new Bio::LiveSeq::Transcript
\&  Returns : reference to a new object of class Transcript
\&  Errorcode \-1
\&  Args    : reference to an array of Exon object references
.Ve
.SS "all_Exons"
.IX Subsection "all_Exons"
.Vb 6
\& Title   : all_Exons
\& Usage   : $transcript_obj\->all_Exons()
\& Function: returns references to all Exon objects the Transcript is composed of
\& Example : foreach $exon ($transcript\->all_Exons()) { do_something }
\& Returns : array of object references
\& Args    : none
.Ve
.SS "downstream_seq"
.IX Subsection "downstream_seq"
.Vb 10
\& Title   : downstream_seq
\& Usage   : $transcript_obj\->downstream_seq()
\&         : $transcript_obj\->downstream_seq(64)
\& Function: returns a string of nucleotides downstream of the end of the
\&           CDS. If there is some information of the real mRNA, from features in
\&           an attached Gene object, it will return up to those boundaries.
\&           Otherwise it will return 1000 nucleotides.
\&           If an argument is given it will override the default 1000 number
\&           and return instead /that/ requested number of nucleotides.
\&           But if a Gene object is attached, this argument will be ignored.
\& Returns : string
\& Args    : an optional integer number of nucleotides to be returned instead of
\&           the default if no gene attached
.Ve
.SS "upstream_seq"
.IX Subsection "upstream_seq"
.Vb 6
\& Title   : upstream_seq
\& Usage   : $transcript_obj\->upstream_seq()
\&         : $transcript_obj\->upstream_seq(64)
\& Function: just like downstream_seq but returns nucleotides before the ATG
\& Note    : the default, if no Gene information present and no nucleotides
\&           number given, is to return up to 400 nucleotides.
.Ve
.SS "get_Translation"
.IX Subsection "get_Translation"
.Vb 6
\&  Title   : valid
\&  Usage   : $translation = $obj\->get_Translation()
\&  Function: retrieves the reference to the object of class Translation (if any)
\&            attached to a LiveSeq object
\&  Returns : object reference
\&  Args    : none
.Ve
.SS "translation_table"
.IX Subsection "translation_table"
.Vb 7
\& Title   : translation_table
\& Usage   : $name = $obj\->translation_table;
\&         : $name = $obj\->translation_table(11);
\& Function: Returns or sets the translation_table used for translating the
\&           transcript.
\&           If it has never been set, it will return undef.
\& Returns : an integer
.Ve
.SS "frame"
.IX Subsection "frame"
.Vb 11
\& Title   : frame
\& Usage   : $frame = $transcript\->frame($label);
\& Function: Returns the frame of a particular nucleotide.
\&           Frame can be 0 1 or 2 and means the position in the codon triplet
\&           of the particulat nucleotide. 0 is the first codon_position.
\&           Codon_position (1 2 3) is simply frame+1.
\&           If the label asked for is not inside the Transcript, \-1 will be
\&           returned.
\& Args    : a label
\& Returns : 0 1 or 2
\& Errorcode \-1
.Ve