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InfoNucleicAcids.pl - List properties of nucleic acids
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...
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.
NucleicAcidIDs is a space delimited list of values to identify nucleic acids.
For NucleicAcidID mode, input value format is: Code [NucleicAcidName...]. Default: A. Examples:
For NucleicAcidType mode, input value format is: NucleicAcidType [NucleicAcidType...]. Default: A. Possible values are: Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside. Examples:
Print this help message.
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.
Output text file delimiter. Possible values: comma, tab, or semicolon Default value: comma.
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.
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:
An example for NucleicAcidRows output style:
Overwrite existing files.
Precision for listing numerical values. Default: up to 4 decimal places. Valid values: positive integers.
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.
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.
Specify how to list properties for nucleic acids: group by category or an alphabetical by property names. Possible values: ByGroup or Alphabetical. Default: ByGroup
Put quotes around column values in output text file. Possible values: yes or no. Default value: yes.
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.
Location of working directory. Default: current directory.
To list basic properties information for nucleoside A, type:
To list all available properties information for nucleoside A, type:
To list all available information for all available nucleic acids, type:
To list basic properties information for all nucleobases, type:
To list basic properties information for all nucleotides and deoxynulceotides, type:
To list basic properties information for variety of nucleic acids, type:
To list code and molecular weights for nucleosides A, G, C and T, type:
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:
To alphabetically list all the available properties for all available nucleic acids to a file names NucleicAcidsProperties.csv with quotes around the values, type
InfoAminoAcids.pl, InfoPeriodicTableElements.pl
Copyright (C) 2024 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.
