Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/scripts/man1/InfoNucleicAcids.1 @ 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/scripts/man1/InfoNucleicAcids.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,349 @@ +.\" 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 "INFONUCLEICACIDS 1" +.TH INFONUCLEICACIDS 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" +InfoNucleicAcids.pl \- List properties of nucleic acids +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +InfoNucleicAcids.pl NucleicAcidIDs... +.PP +InfoNucleicAcids.pl [\fB\-h, \-\-help\fR] [\fB\-m, \-\-mode\fR NucleicAcidID | NucleicAcidType] +[\fB\-\-OutDelim\fR comma | tab | semicolon] +[\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-OutputStyle\fR NucleicAcidBlock | NucleicAcidRows] +[\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-\-PropertiesMode\fR Categories | Names | All] +[\fB\-p, \-\-properties\fR CategoryName, [CategoryName,...] | PropertyName, [PropertyName,...]] +[\fB\-\-PropertiesListing\fR ByGroup | Alphabetical] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname] +[\fB\-w, \-\-WorkingDir\fR dirname] NucleicAcidIDs... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +List nucleic acid properties. Nucleic acids identification supports two types of IDs: code +or name. Nucleic acid properties data, in addition to basic information about nucleic acids \- code, +name, type, chemical formula and molecular weight \- include information about exact mass and +elemental composition. +.SH "PARAMETERS" +.IX Header "PARAMETERS" +.IP "\fBNucleicAcidIDs\fR \fICode [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]\fR" 4 +.IX Item "NucleicAcidIDs Code [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]" +\&\fINucleicAcidIDs\fR is a space delimited list of values to identify nucleic acids. +.Sp +For \fINucleicAcidID\fR mode, input value format is: \fICode [NucleicAcidName...]\fR. Default: \fIA\fR. +Examples: +.Sp +.Vb 3 +\& A +\& dG AMP +\& Cytidine T UDP dpppA "5\*(Aq\-dATP" +.Ve +.Sp +For \fINucleicAcidType\fR mode, input value format is: \fINucleicAcidType [NucleicAcidType...]\fR. +Default: \fIA\fR. Possible values are: \fINucleobase, Nucleoside, Deoxynucleoside, Nucleotide, +Deoxynucleotide\fR. Default: \fINucleoside\fR. +Examples: +.Sp +.Vb 2 +\& Deoxynucleoside +\& Nucleobase Nucleotide +.Ve +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-m, \-\-mode\fR \fINucleicAcidID | NucleicAcidType\fR" 4 +.IX Item "-m, --mode NucleicAcidID | NucleicAcidType" +Specify nucleic acids for listing properties using one of these methods: nucleic acid +code and/or names or nucleic acid type. +.Sp +Possible values: \fINucleicAcidID or NucleicAcidType\fR. Default: \fINucleicAcidID\fR +.Sp +For \fINucleicAcidType\fR, command line parameters support these type: \fINucleobase, +Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide\fR. +.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--OutDelim comma | tab | semicolon" +Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR. +.IP "\fB\-\-output\fR \fI\s-1STDOUT\s0 | File\fR" 4 +.IX Item "--output STDOUT | File" +List information at \s-1STDOUT\s0 or write it to a file. Possible values: \fI\s-1STDOUT\s0 or File\fR. Default: +\&\fI\s-1STDOUT\s0\fR. \fB\-r, \-\-root\fR option is used to generate output file name. +.IP "\fB\-\-OutputStyle\fR \fINucleicAcidBlock | NucleicAcidRows\fR" 4 +.IX Item "--OutputStyle NucleicAcidBlock | NucleicAcidRows" +Specify how to list nucleic acid information: add a new line for each property and present it as a block +for each nucleic acid; or include all properties in one line and show it as a single line. +.Sp +Possible values: \fINucleicAcidBlock | NucleicAcidRows\fR. Default: \fINucleicAcidBlock\fR +.Sp +An example for \fINucleicAcidBlock\fR output style: +.Sp +.Vb 7 +\& Code: Ado +\& OtherCodes: A +\& Name: Adenosine +\& Type: Nucleoside +\& MolecularFormula: C10H13O4N5 +\& MolecularWeight: 267.2413 +\& ... ... +.Ve +.Sp +An example for \fINucleicAcidRows\fR output style: +.Sp +.Vb 1 +\& Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight +.Ve +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-\-precision\fR \fInumber\fR" 4 +.IX Item "--precision number" +Precision for listing numerical values. Default: up to \fI4\fR decimal places. +Valid values: positive integers. +.IP "\fB\-\-PropertiesMode\fR \fICategories | Names | All\fR" 4 +.IX Item "--PropertiesMode Categories | Names | All" +Specify how property names are specified: use category names; explicit list of property names; or +use all available properties. Possible values: \fICategories, Names, or All\fR. Default: \fICategories\fR. +.Sp +This option is used in conjunction with \fB\-p, \-\-properties\fR option to specify properties of +interest. +.IP "\fB\-p, \-\-properties\fR \fICategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]\fR" 4 +.IX Item "-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]" +This option is \fB\-\-propertiesmode\fR specific. In general, it's a list of comma separated category or +property names. +.Sp +Specify which nucleic acid properties information to list for the nucleic acid IDs specified using +command line parameters: list basic information; list all available information; or specify a comma +separated list of nucleic acid property names. +.Sp +Possible values: \fIBasic | BasicPlus | PropertyName,[PropertyName,...]\fR. +Default: \fIBasic\fR. +.Sp +\&\fIBasic\fR includes: \fICode, OtherCodes, Name, Type, MolecularFormula, MolecularWeight\fR +.Sp +\&\fIBasicPlus\fR includes: \fICode, OtherCodes, Name, Type, MolecularFormula, MolecularWeight, ExactMass, +ElementalComposition\fR +.Sp +Here is a complete list of available properties: \fICode, OtherCodes, BasePair, Name, Type, MolecularFormula, +MolecularFormulaAtpH7.5, MolecularWeight, ExactMass, ElementalComposition\fR. +.IP "\fB\-\-PropertiesListing\fR \fIByGroup | Alphabetical\fR" 4 +.IX Item "--PropertiesListing ByGroup | Alphabetical" +Specify how to list properties for nucleic acids: group by category or an alphabetical by +property names. Possible values: \fIByGroup or Alphabetical\fR. Default: \fIByGroup\fR +.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4 +.IX Item "-q, --quote yes | no" +Put quotes around column values in output text file. Possible values: \fIyes or +no\fR. Default value: \fIyes\fR. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New text file name is generated using the root: <Root>.<Ext>. File name is only +used during \fIFile\fR value of \fB\-o, \-\-output\fR option. +.Sp +Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files respectively. +.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4 +.IX Item "-w, --WorkingDir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To list basic properties information for nucleoside A, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl +.Ve +.PP +To list all available properties information for nucleoside A, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl \-\-propertiesmode all A +.Ve +.PP +To list all available information for all available nucleic acids, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl \-\-propertiesmode All All +.Ve +.PP +To list basic properties information for all nucleobases, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl \-m NucleicAcidType Nucleoside +.Ve +.PP +To list basic properties information for all nucleotides and deoxynulceotides, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl \-m NucleicAcidType Nucleotide Deoxynucleotide +.Ve +.PP +To list basic properties information for variety of nucleic acids, type: +.PP +.Vb 1 +\& % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5\*(Aq\-dATP" +.Ve +.PP +To list code and molecular weights for nucleosides A, G, C and T, type: +.PP +.Vb 2 +\& % InfoNucleicAcids.pl \-\-PropertiesMode Names \-\-properties +\& Code,MolecularWeight A G C T +.Ve +.PP +To alphabetically list all the available properties for nucleotides dAMP, dGMP, +dCMP, and dTMP in rows instead of nucleic acid blocks with quotes around the values, type: +.PP +.Vb 3 +\& % InfoNucleicAcids.pl \-\-PropertiesMode All \-\-PropertiesListing +\& Alphabetical \-\-OutputStyle NucleicAcidRows \-q yes dAMP dGMP +\& dCMP dTMP +.Ve +.PP +To alphabetically list all the available properties for all available nucleic acids to +a file names NucleicAcidsProperties.csv with quotes around the values, type +.PP +.Vb 3 +\& % InfoNucleicAcids.pl \-\-PropertiesMode All \-\-PropertiesListing +\& Alphabetical \-\-output File \-\-OutputStyle NucleicAcidRows \-r +\& NucleicAcidsProperties \-o \-q Yes All +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoAminoAcids.pl, InfoPeriodicTableElements.pl +.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.