comparison mayachemtools/docs/scripts/man1/InfoNucleicAcids.1 @ 0:73ae111cf86f draft

Uploaded

0:73ae111cf86f

.\" 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 <[e-mail]>
.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.