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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -0500 |
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1 NAME | |
2 InfoAminoAcids.pl - List properties of amino acids | |
3 | |
4 SYNOPSIS | |
5 InfoAminoAcids.pl AminoAcidIDs... | |
6 | |
7 InfoAminoAcids.pl [-h, --help] [--outdelim comma | tab | semicolon] | |
8 [--output STDOUT | File] [--outputstyle AminoAcidBlock | AminoAcidRows] | |
9 [-o, --overwrite] [--precision number] [--propertiesmode Categories | | |
10 Names | All] [-p, --properties CategoryName,[CategoryName,...] | | |
11 PropertyName,[PropertyName,...]] [--propertieslinting ByGroup | | |
12 Alphabetical] [-q, --quote yes | no] [-r, --root rootname] [-w, | |
13 --workingdir dirname] AminoAcidIDs... | |
14 | |
15 DESCRIPTION | |
16 List amino acid properties. Amino acids identification supports these | |
17 three types of IDs: one letter code, three letter code or name. Amino | |
18 acid properties data, in addition to basic information about amino acids | |
19 - one and three letter codes, name, DNA and RNA codons, molecular weight | |
20 - include variety of other properties: polarity, acidity, | |
21 hydrophobicity, and so on. | |
22 | |
23 PARAMETERS | |
24 AminoAcidIDs *ThreeLetterCode [OneLetterCode AminoAcidName...]* | |
25 *AminoAcidIDs* is a space delimited list of values to identify amino | |
26 acids. | |
27 | |
28 Input value format is: *ThreeLetterCode [OneLetterCode | |
29 AminoAcidName...]*. Default: *Ala*. Examples: | |
30 | |
31 Ala | |
32 Glu A | |
33 Alanine Glu Y "Aspartic acid" | |
34 | |
35 OPTIONS | |
36 -h, --help | |
37 Print this help message. | |
38 | |
39 --outdelim *comma | tab | semicolon* | |
40 Output text file delimiter. Possible values: *comma, tab, or | |
41 semicolon* Default value: *comma*. | |
42 | |
43 --output *STDOUT | File* | |
44 List information at STDOUT or write it to a file. Possible values: | |
45 *STDOUT or File*. Default: *STDOUT*. -r, --root option is used to | |
46 generate output file name. | |
47 | |
48 --outputstyle *AminoAcidBlock | AminoAcidRows* | |
49 Specify how to list amino acid information: add a new line for each | |
50 property and present it as a block for each amino acid; or include | |
51 all properties in one line and show it as a single line. | |
52 | |
53 Possible values: *AminoAcidBlock | AminoAcidRows*. Default: | |
54 *AminoAcidBlock* | |
55 | |
56 An example for *AminoAcidBlock* output style: | |
57 | |
58 ThreeLetterCode: Ala | |
59 OneLetterCode: A | |
60 AminoAcid: Alanine | |
61 MolecularWeight: 89.0941 | |
62 ... ... | |
63 ... ... | |
64 ... ... | |
65 | |
66 ThreeLetterCode: Glu | |
67 OneLetterCode: E | |
68 AminoAcid: Glutamic acid | |
69 MolecularWeight: 147.1308 | |
70 ... ... | |
71 ... ... | |
72 ... ... | |
73 | |
74 An example for *AminoAcidRows* output style: | |
75 | |
76 ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight | |
77 Ala,A,Alanine,89.0941.. | |
78 Glu,E,Glutamic acid,147.1308.. | |
79 | |
80 -o, --overwrite | |
81 Overwrite existing files. | |
82 | |
83 --precision *number* | |
84 Precision for listing numerical values. Default: up to *4* decimal | |
85 places. Valid values: positive integers. | |
86 | |
87 --propertiesmode *Categories | Names | All* | |
88 Specify how property names are specified: use category names; | |
89 explicit list of property names; or use all available properties. | |
90 Possible values: *Categories, Names, or All*. Default: *Categories*. | |
91 | |
92 This option is used in conjunction with -p, --properties option to | |
93 specify properties of interest. | |
94 | |
95 -p, --properties *CategoryName,[CategoryName,...] | | |
96 PropertyName,[PropertyName,...]* | |
97 This option is --propertiesmode specific. In general, it's a list of | |
98 comma separated category or property names. | |
99 | |
100 Specify which amino acid properties information to list for the | |
101 amino acid IDs specified using command: line parameters: list basic | |
102 and/or hydrophobicity information; list all available information; | |
103 or specify a comma separated list of amino acid property names. | |
104 | |
105 Possible values: *Basic | BasicPlus | BasicAndHydrophobicity | | |
106 BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]*. | |
107 Default: *Basic*. | |
108 | |
109 *Basic* includes: *ThreeLetterCode, OneLetterCode, AminoAcid, | |
110 DNACodons, RNACodons, ChemicalFormula, MolecularWeight, | |
111 LinearStructure, LinearStructureAtpH7.4* | |
112 | |
113 *BasicPlus* includes: *ThreeLetterCode, OneLetterCode, AminoAcid, | |
114 DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, | |
115 HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, | |
116 ChemicalFormula, MolecularWeight, ExactMass, | |
117 ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), | |
118 ExactMassMinusH2O(18.01056), LinearStructure, | |
119 LinearStructureAtpH7.4* | |
120 | |
121 *BasicAndHydrophobicity* includes: *ThreeLetterCode, OneLetterCode, | |
122 AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, | |
123 LinearStructure, LinearStructureAtpH7.4, | |
124 HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, | |
125 HydrophobicityJanin, HydrophobicityKyteAndDoolittle, | |
126 HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers* | |
127 | |
128 *BasicAndHydrophobicityPlus* includes: *(ThreeLetterCode, | |
129 OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, | |
130 MolecularWeight, LinearStructure, LinearStructureAtpH7.4, | |
131 HydrophobicityAbrahamAndLeo, HydrophobicityBlack, | |
132 HydrophobicityBullAndBreese, HydrophobicityChothia, | |
133 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, | |
134 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, | |
135 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, | |
136 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, | |
137 HydrophobicityJanin, HydrophobicityKyteAndDoolittle, | |
138 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, | |
139 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, | |
140 HydrophobicityRfMobility, HydrophobicityRoseAndOthers, | |
141 HydrophobicityRoseman, HydrophobicityWellingAndOthers, | |
142 HydrophobicityWolfendenAndOthers* | |
143 | |
144 Here is a complete list of available properties: ThreeLetterCode, | |
145 OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, | |
146 PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, | |
147 IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, | |
148 ExactMass, ChemicalFormulaMinusH2O, | |
149 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), | |
150 vanderWaalsVolume, %AccessibleResidues, %BuriedResidues, | |
151 AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, | |
152 AminoAcidsComposition, AminoAcidsCompositionInSwissProt, | |
153 AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, | |
154 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, | |
155 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, | |
156 Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, | |
157 HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, | |
158 HydrophobicityAbrahamAndLeo, HydrophobicityBlack, | |
159 HydrophobicityBullAndBreese, HydrophobicityChothia, | |
160 HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, | |
161 HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, | |
162 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, | |
163 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, | |
164 HydrophobicityJanin, HydrophobicityKyteAndDoolittle, | |
165 HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, | |
166 HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, | |
167 HydrophobicityRfMobility, HydrophobicityRoseAndOthers, | |
168 HydrophobicityRoseman, HydrophobicityWellingAndOthers, | |
169 HydrophobicityWolfendenAndOthers, ParallelBetaStrand, | |
170 PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, | |
171 RecognitionFactors, Refractivity, RelativeMutability, | |
172 TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4 | |
173 | |
174 --propertieslisting *ByGroup | Alphabetical* | |
175 Specify how to list properties for amino acids: group by category or | |
176 an alphabetical by property names. Possible values: *ByGroup or | |
177 Alphabetical*. Default: *ByGroup*. | |
178 | |
179 -q, --quote *yes | no* | |
180 Put quotes around column values in output text file. Possible | |
181 values: *yes or no*. Default value: *yes*. | |
182 | |
183 -r, --root *rootname* | |
184 New text file name is generated using the root: <Root>.<Ext>. File | |
185 name is only used during *File* value of -o, --output option. | |
186 | |
187 Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv <Ext> | |
188 values are used for comma/semicolon, and tab delimited text files | |
189 respectively. | |
190 | |
191 -w, --workingdir *dirname* | |
192 Location of working directory. Default: current directory. | |
193 | |
194 EXAMPLES | |
195 To list basic properties information for amino acid Ala, type: | |
196 | |
197 % InfoAminoAcids.pl | |
198 | |
199 To list all available properties information for amino acid Ala, type: | |
200 | |
201 % InfoAminoAcids.pl --propertiesmode all | |
202 | |
203 To list basic properties information for amino acids Ala, Arg, and Asp | |
204 type: | |
205 | |
206 % InfoAminoAcids.pl Ala Arg Asp | |
207 % InfoAminoAcids.pl A Arg "Aspartic acid" | |
208 | |
209 To list all available properties information for amino acids Ala, Arg, | |
210 and Asp type: | |
211 | |
212 % InfoAminoAcids.pl --propertiesmode all Ala Arg Asp | |
213 | |
214 To list basic and hydrophobicty properties information for amino acids | |
215 Ala, Arg, and Asp type: | |
216 | |
217 % InfoAminoAcids.pl --propertiesmode Categories | |
218 --properties BasicAndHydrophobicity Ala Arg Asp | |
219 | |
220 To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight | |
221 for amino acids Ala, Arg, and Asp type: | |
222 | |
223 % InfoAminoAcids.pl --propertiesmode Names | |
224 --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight | |
225 Ala Arg Asp | |
226 | |
227 To alphabetically list basic and hydrophobicty properties information | |
228 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks | |
229 with quotes around the values, type: | |
230 | |
231 % InfoAminoAcids.pl --propertiesmode Categories | |
232 --properties BasicAndHydrophobicity --propertieslisting alphabetical | |
233 --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp | |
234 | |
235 To alphabetically list basic and hydrophobicty properties information | |
236 for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks | |
237 with quotes around the values and write them into a file | |
238 AminoAcidProperties.csv, type: | |
239 | |
240 % InfoAminoAcids.pl --propertiesmode Categories | |
241 --properties BasicAndHydrophobicity --propertieslisting alphabetical | |
242 --outdelim comma --outputstyle AminoAcidRows --quote yes | |
243 --output File -r AminoAcidProperties -o Ala Arg Asp | |
244 | |
245 AUTHOR | |
246 Manish Sud <msud@san.rr.com> | |
247 | |
248 SEE ALSO | |
249 InfoNucleicAcids.pl InfoPeriodicTableElements.pl | |
250 | |
251 COPYRIGHT | |
252 Copyright (C) 2015 Manish Sud. All rights reserved. | |
253 | |
254 This file is part of MayaChemTools. | |
255 | |
256 MayaChemTools is free software; you can redistribute it and/or modify it | |
257 under the terms of the GNU Lesser General Public License as published by | |
258 the Free Software Foundation; either version 3 of the License, or (at | |
259 your option) any later version. | |
260 |