diff docs/scripts/txt/InfoNucleicAcids.txt @ 0:4816e4a8ae95 draft default tip

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+NAME
+    InfoNucleicAcids.pl - List properties of nucleic acids
+
+SYNOPSIS
+    InfoNucleicAcids.pl NucleicAcidIDs...
+
+    InfoNucleicAcids.pl [-h, --help] [-m, --mode NucleicAcidID |
+    NucleicAcidType] [--OutDelim comma | tab | semicolon] [--output STDOUT |
+    File] [--OutputStyle NucleicAcidBlock | NucleicAcidRows] [-o,
+    --overwrite] [--precision number] [--PropertiesMode Categories | Names |
+    All] [-p, --properties CategoryName, [CategoryName,...] | PropertyName,
+    [PropertyName,...]] [--PropertiesListing ByGroup | Alphabetical] [-q,
+    --quote yes | no] [-r, --root rootname] [-w, --WorkingDir dirname]
+    NucleicAcidIDs...
+
+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.
+
+PARAMETERS
+    NucleicAcidIDs *Code [NucleicAcidName...] | NucleicAcidType
+    [NucleicAcidType...]*
+        *NucleicAcidIDs* is a space delimited list of values to identify
+        nucleic acids.
+
+        For *NucleicAcidID* mode, input value format is: *Code
+        [NucleicAcidName...]*. Default: *A*. Examples:
+
+            A
+            dG AMP
+            Cytidine T UDP dpppA "5'-dATP"
+
+        For *NucleicAcidType* mode, input value format is: *NucleicAcidType
+        [NucleicAcidType...]*. Default: *A*. Possible values are:
+        *Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
+        Deoxynucleotide*. Default: *Nucleoside*. Examples:
+
+            Deoxynucleoside
+            Nucleobase Nucleotide
+
+OPTIONS
+    -h, --help
+        Print this help message.
+
+    -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.
+
+        Possible values: *NucleicAcidID or NucleicAcidType*. Default:
+        *NucleicAcidID*
+
+        For *NucleicAcidType*, command line parameters support these type:
+        *Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
+        Deoxynucleotide*.
+
+    --OutDelim *comma | tab | semicolon*
+        Output text file delimiter. Possible values: *comma, tab, or
+        semicolon* Default value: *comma*.
+
+    --output *STDOUT | File*
+        List information at STDOUT or write it to a file. Possible values:
+        *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to
+        generate output file name.
+
+    --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.
+
+        Possible values: *NucleicAcidBlock | NucleicAcidRows*. Default:
+        *NucleicAcidBlock*
+
+        An example for *NucleicAcidBlock* output style:
+
+            Code: Ado
+            OtherCodes: A
+            Name: Adenosine
+            Type: Nucleoside
+            MolecularFormula: C10H13O4N5
+            MolecularWeight: 267.2413
+            ... ...
+
+        An example for *NucleicAcidRows* output style:
+
+            Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    --precision *number*
+        Precision for listing numerical values. Default: up to *4* decimal
+        places. Valid values: positive integers.
+
+    --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: *Categories, Names, or All*. Default: *Categories*.
+
+        This option is used in conjunction with -p, --properties option to
+        specify properties of interest.
+
+    -p, --properties *CategoryName,[CategoryName,...] |
+    PropertyName,[PropertyName,...]*
+        This option is --propertiesmode specific. In general, it's a list of
+        comma separated category or property names.
+
+        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.
+
+        Possible values: *Basic | BasicPlus |
+        PropertyName,[PropertyName,...]*. Default: *Basic*.
+
+        *Basic* includes: *Code, OtherCodes, Name, Type, MolecularFormula,
+        MolecularWeight*
+
+        *BasicPlus* includes: *Code, OtherCodes, Name, Type,
+        MolecularFormula, MolecularWeight, ExactMass, ElementalComposition*
+
+        Here is a complete list of available properties: *Code, OtherCodes,
+        BasePair, Name, Type, MolecularFormula, MolecularFormulaAtpH7.5,
+        MolecularWeight, ExactMass, ElementalComposition*.
+
+    --PropertiesListing *ByGroup | Alphabetical*
+        Specify how to list properties for nucleic acids: group by category
+        or an alphabetical by property names. Possible values: *ByGroup or
+        Alphabetical*. Default: *ByGroup*
+
+    -q, --quote *yes | no*
+        Put quotes around column values in output text file. Possible
+        values: *yes or no*. Default value: *yes*.
+
+    -r, --root *rootname*
+        New text file name is generated using the root: <Root>.<Ext>. File
+        name is only used during *File* value of -o, --output option.
+
+        Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv
+        <Ext> values are used for comma/semicolon, and tab delimited text
+        files respectively.
+
+    -w, --WorkingDir *dirname*
+        Location of working directory. Default: current directory.
+
+EXAMPLES
+    To list basic properties information for nucleoside A, type:
+
+        % InfoNucleicAcids.pl
+
+    To list all available properties information for nucleoside A, type:
+
+        % InfoNucleicAcids.pl --propertiesmode all A
+
+    To list all available information for all available nucleic acids, type:
+
+        % InfoNucleicAcids.pl --propertiesmode All All
+
+    To list basic properties information for all nucleobases, type:
+
+        % InfoNucleicAcids.pl -m NucleicAcidType Nucleoside
+
+    To list basic properties information for all nucleotides and
+    deoxynulceotides, type:
+
+        % InfoNucleicAcids.pl -m NucleicAcidType Nucleotide Deoxynucleotide
+
+    To list basic properties information for variety of nucleic acids, type:
+
+        % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5'-dATP"
+
+    To list code and molecular weights for nucleosides A, G, C and T, type:
+
+        % InfoNucleicAcids.pl --PropertiesMode  Names --properties
+          Code,MolecularWeight A G C T
+
+    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:
+
+        % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
+          Alphabetical --OutputStyle NucleicAcidRows -q yes dAMP dGMP
+          dCMP dTMP
+
+    To alphabetically list all the available properties for all available
+    nucleic acids to a file names NucleicAcidsProperties.csv with quotes
+    around the values, type
+
+        % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
+          Alphabetical --output File --OutputStyle NucleicAcidRows -r
+          NucleicAcidsProperties -o -q Yes All
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    InfoAminoAcids.pl, InfoPeriodicTableElements.pl
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+