Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/man3/SequenceFileUtil.3 @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/SequenceFileUtil.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,357 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" 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" '' +'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 turned on, 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. +.ie \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.el \{\ +. de IX +.. +.\} +.\" +.\" 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 "SEQUENCEFILEUTIL 1" +.TH SEQUENCEFILEUTIL 1 "2015-03-29" "perl v5.14.2" "MayaChemTools" +.\" 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" +SequenceFileUtil +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use SequenceFileUtil ; +.PP +use SequenceFileUtil qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBSequenceFileUtil\fR module provides the following functions: +.PP +AreSequenceLengthsIdentical, CalcuatePercentSequenceIdentity, +CalculatePercentSequenceIdentityMatrix, GetLongestSequence, GetSequenceLength, +GetShortestSequence, IsClustalWSequenceFile, IsGapResidue, IsMSFSequenceFile, +IsPIRFastaSequenceFile, IsPearsonFastaSequenceFile, IsSupportedSequenceFile, +ReadClustalWSequenceFile, ReadMSFSequenceFile, ReadPIRFastaSequenceFile, +ReadPearsonFastaSequenceFile, ReadSequenceFile, RemoveSequenceAlignmentGapColumns, +RemoveSequenceGaps, WritePearsonFastaSequenceFile +SequenceFileUtil module provides various methods to process sequence +files and retreive appropriate information. +.SH "FUNCTIONS" +.IX Header "FUNCTIONS" +.IP "\fBAreSequenceLengthsIdentical\fR" 4 +.IX Item "AreSequenceLengthsIdentical" +.Vb 1 +\& $Status = AreSequenceLengthsIdentical($SequencesDataRef); +.Ve +.Sp +Checks the lengths of all the sequences available in \fISequencesDataRef\fR and returns 1 +or 0 based whether lengths of all the sequence is same. +.IP "\fBCalcuatePercentSequenceIdentity\fR" 4 +.IX Item "CalcuatePercentSequenceIdentity" +.Vb 3 +\& $PercentIdentity = +\& AreSequenceLengthsIdenticalAreSequenceLengthsIdentical( +\& $Sequence1, $Sequence2, [$IgnoreGaps, $Precision]); +.Ve +.Sp +Returns percent identity between \fISequence1\fR and \fISequence2\fR. Optional arguments +\&\fIIgnoreGaps\fR and \fIPrecision\fR control handling of gaps in sequences and precision of the +returned value. By default, gaps are ignored and precision is set up to 1 decimal. +.IP "\fBCalculatePercentSequenceIdentityMatrix\fR" 4 +.IX Item "CalculatePercentSequenceIdentityMatrix" +.Vb 3 +\& $IdentityMatrixDataRef = CalculatePercentSequenceIdentityMatrix( +\& $SequencesDataRef, [$IgnoreGaps, +\& $Precision]); +.Ve +.Sp +Calculate pairwise percent identity between all the sequences available in \fISequencesDataRef\fR +and returns a reference to identity matrix hash. Optional arguments \fIIgnoreGaps\fR and +\&\fIPrecision\fR control handling of gaps in sequences and precision of the returned value. By default, gaps +are ignored and precision is set up to 1 decimal. +.IP "\fBGetSequenceLength\fR" 4 +.IX Item "GetSequenceLength" +.Vb 1 +\& $SeqquenceLength = GetSequenceLength($Sequence, [$IgnoreGaps]); +.Ve +.Sp +Returns length of the specified sequence. Optional argument \fIIgnoreGaps\fR controls handling +of gaps. By default, gaps are ignored. +.IP "\fBGetShortestSequence\fR" 4 +.IX Item "GetShortestSequence" +.Vb 2 +\& ($ID, $Sequence, $SeqLen, $Description) = GetShortestSequence( +\& $SequencesDataRef, [$IgnoreGaps]); +.Ve +.Sp +Checks the lengths of all the sequences available in \f(CW$SequencesDataRef\fR and returns \f(CW$ID\fR, +\&\f(CW$Sequence\fR, \f(CW$SeqLen\fR, and \f(CW$Description\fR values for the shortest sequence. Optional arguments \f(CW$IgnoreGaps\fR +controls handling of gaps in sequences. By default, gaps are ignored. +.IP "\fBGetLongestSequence\fR" 4 +.IX Item "GetLongestSequence" +.Vb 2 +\& ($ID, $Sequence, $SeqLen, $Description) = GetLongestSequence( +\& $SequencesDataRef, [$IgnoreGaps]); +.Ve +.Sp +Checks the lengths of all the sequences available in \fISequencesDataRef\fR and returns \fB\s-1ID\s0\fR, +\&\fBSequence\fR, \fBSeqLen\fR, and \fBDescription\fR values for the longest sequence. Optional argument +$\fIIgnoreGaps\fR controls handling of gaps in sequences. By default, gaps are ignored. +.IP "\fBIsGapResidue\fR" 4 +.IX Item "IsGapResidue" +.Vb 1 +\& $Status = AreSequenceLengthsIdentical($Residue); +.Ve +.Sp +Returns 1 or 0 based on whether \fIResidue\fR corresponds to a gap. Any character other than A to Z is +considered a gap residue. +.IP "\fBIsSupportedSequenceFile\fR" 4 +.IX Item "IsSupportedSequenceFile" +.Vb 1 +\& $Status = IsSupportedSequenceFile($SequenceFile); +.Ve +.Sp +Returns 1 or 0 based on whether \fISequenceFile\fR corresponds to a supported sequence +format. +.IP "\fBIsClustalWSequenceFile\fR" 4 +.IX Item "IsClustalWSequenceFile" +.Vb 1 +\& $Status = IsClustalWSequenceFile($SequenceFile); +.Ve +.Sp +Returns 1 or 0 based on whether \fISequenceFile\fR corresponds to Clustal sequence alignment +format. +.IP "\fBIsPearsonFastaSequenceFile\fR" 4 +.IX Item "IsPearsonFastaSequenceFile" +.Vb 1 +\& $Status = IsPearsonFastaSequenceFile($SequenceFile); +.Ve +.Sp +Returns 1 or 0 based on whether \fISequenceFile\fR corresponds to Pearson \s-1FASTA\s0 sequence +format. +.IP "\fBIsPIRFastaSequenceFile\fR" 4 +.IX Item "IsPIRFastaSequenceFile" +.Vb 1 +\& $Status = IsPIRFastaSequenceFile($SequenceFile); +.Ve +.Sp +Returns 1 or 0 based on whether \fISequenceFile\fR corresponds to \s-1PIR\s0 \s-1FASTA\s0 sequence +format. +.IP "\fBIsMSFSequenceFile\fR" 4 +.IX Item "IsMSFSequenceFile" +.Vb 1 +\& $Status = IsClustalWSequenceFile($SequenceFile); +.Ve +.Sp +Returns 1 or 0 based on whether \fISequenceFile\fR corresponds to \s-1MSF\s0 sequence alignment +format. +.IP "\fBReadSequenceFile\fR" 4 +.IX Item "ReadSequenceFile" +.Vb 1 +\& $SequenceDataMapRef = ReadSequenceFile($SequenceFile); +.Ve +.Sp +Reads \fISequenceFile\fR and returns reference to a hash containing following key/value +pairs: +.Sp +.Vb 5 +\& $SequenceDataMapRef\->{IDs} \- Array of sequence IDs +\& $SequenceDataMapRef\->{Count} \- Number of sequences +\& $SequenceDataMapRef\->{Description}{$ID} \- Sequence description +\& $SequenceDataMapRef\->{Sequence}{$ID} \- Sequence for a specific ID +\& $SequenceDataMapRef\->{Sequence}{InputFileType} \- File format +.Ve +.IP "\fBReadClustalWSequenceFile\fR" 4 +.IX Item "ReadClustalWSequenceFile" +.Vb 1 +\& $SequenceDataMapRef = ReadClustalWSequenceFile($SequenceFile); +.Ve +.Sp +Reads ClustalW \fISequenceFile\fR and returns reference to a hash containing following key/value +pairs as describes in \fBReadSequenceFile\fR method. +.IP "\fBReadMSFSequenceFile\fR" 4 +.IX Item "ReadMSFSequenceFile" +.Vb 1 +\& $SequenceDataMapRef = ReadMSFSequenceFile($SequenceFile); +.Ve +.Sp +Reads \s-1MSF\s0 \fISequenceFile\fR and returns reference to a hash containing following key/value +pairs as describes in \fBReadSequenceFile\fR method. +.IP "\fBReadPIRFastaSequenceFile\fR" 4 +.IX Item "ReadPIRFastaSequenceFile" +.Vb 1 +\& $SequenceDataMapRef = ReadPIRFastaSequenceFile($SequenceFile); +.Ve +.Sp +Reads \s-1PIR\s0 \s-1FASTA\s0 \fISequenceFile\fR and returns reference to a hash containing following key/value +pairs as describes in \fBReadSequenceFile\fR method. +.IP "\fBReadPearsonFastaSequenceFile\fR" 4 +.IX Item "ReadPearsonFastaSequenceFile" +.Vb 1 +\& $SequenceDataMapRef = ReadPearsonFastaSequenceFile($SequenceFile); +.Ve +.Sp +Reads Pearson \s-1FASTA\s0 \fISequenceFile\fR and returns reference to a hash containing following key/value +pairs as describes in \fBReadSequenceFile\fR method. +.IP "\fBRemoveSequenceGaps\fR" 4 +.IX Item "RemoveSequenceGaps" +.Vb 1 +\& $SeqWithoutGaps = RemoveSequenceGaps($Sequence); +.Ve +.Sp +Removes gaps from \fISequence\fR and return a sequence without any gaps. +.IP "\fBRemoveSequenceAlignmentGapColumns\fR" 4 +.IX Item "RemoveSequenceAlignmentGapColumns" +.Vb 2 +\& $NewAlignmentDataMapRef = RemoveSequenceAlignmentGapColumns( +\& $AlignmentDataMapRef); +.Ve +.Sp +Using input alignment data map ref containing following keys, generate a new hash with +same set of keys after residue columns containg only gaps have been removed: +.Sp +.Vb 4 +\& {IDs} : Array of IDs in order as they appear in file +\& {Count}: ID count +\& {Description}{$ID} : Description data +\& {Sequence}{$ID} : Sequence data +.Ve +.IP "\fBWritePearsonFastaSequenceFile\fR" 4 +.IX Item "WritePearsonFastaSequenceFile" +.Vb 2 +\& WritePearsonFastaSequenceFile($SequenceFileName, $SequenceDataRef, +\& [$MaxLength]); +.Ve +.Sp +Using sequence data specified via \fISequenceDataRef\fR, write out a Pearson \s-1FASTA\s0 sequence +file. Optional argument \fIMaxLength\fR controls maximum length sequence in each line; default is +80. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +PDBFileUtil.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.