.\" 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::PopGen::Utilities 3pm" .TH Bio::PopGen::Utilities 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::PopGen::Utilities \- Utilities for working with PopGen data and objects .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& use Bio::PopGen::Utilities; \& use Bio::AlignIO; \& \& my $in = Bio::AlignIO\->new(\-file => \*(Aqt/data/t7.aln\*(Aq, \& \-format => \*(Aqclustalw\*(Aq); \& my $aln = $in\->next_aln; \& # get a population, each sequence is an individual and \& # for the default case, every site which is not monomorphic \& # is a \*(Aqmarker\*(Aq. Each individual will have a \*(Aqgenotype\*(Aq for the \& # site which will be the specific base in the alignment at that \& # site \& my $pop = Bio::PopGen::Utilities\->aln_to_population(\-alignment => $aln); \& \& # get the synonymous sites from the alignemt only as the \*(Aqgenotypes\*(Aq \& # for the population \& my $synpop = Bio::PopGen::Utilities\->aln_to_population(\-site_model => \*(Aqcod\*(Aq, \& \-alignment => $aln); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object provides some convience function to turn sequence alignments into usable objects for the Population genetics modules (Bio::PopGen). .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 the Bioperl mailing list. 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 of 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 \- Jason Stajich" .IX Header "AUTHOR - Jason Stajich" Email jason-at-bioperl-dot-org .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "aln_to_population" .IX Subsection "aln_to_population" .Vb 4 \& Title : aln_to_population \& Usage : my $pop = Bio::PopGen::Utilities\->aln_to_population($aln); \& Function: Turn and alignment into a set of L \& objects grouped in a L object \& \& Sites are treated as \*(AqMarkers\*(Aq in the Bioperl PopGen object \& model in the sense that a site is a unique location for which \& an individual will have a genotype (a set of alleles). \& In this implementation we are assuming that each individual \& has a single entry in the alignment file. \& \& Specify a site model as one of those listed \& \*(Aqall\*(Aq \-\- every base in the alignment is considered a site \& \*(Aqcod\*(Aq \-\- codons \& \& The option \-site_model \& for All sites : \*(Aqall\*(Aq \& Codon sites : \*(Aqcod\*(Aq or \*(Aqcodon\*(Aq \& \& To see all sites, including those which are fixed in the population \& add \-include_monomorphic => 1 \& to the arguments \& Returns : \& Args : \-include_monomorphic => 1 to specify all sites, \& even those which are monomorphic \& in the population \& (useful for HKA test mostly) \& [default is false] \& \-phase => specify a phase for the data, this is only \& used if the site_mode is codon \& [default is 0] \& \-site_model => one\-of \*(Aqall\*(Aq, \*(Aqcodon\*(Aq \& to specify a site model for the data extraction \& from the alignment \& [default is all] \& \-alignment => provide a L object [required] .Ve