|
0
|
1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
|
|
|
2 .\"
|
|
|
3 .\" Standard preamble:
|
|
|
4 .\" ========================================================================
|
|
|
5 .de Sp \" Vertical space (when we can't use .PP)
|
|
|
6 .if t .sp .5v
|
|
|
7 .if n .sp
|
|
|
8 ..
|
|
|
9 .de Vb \" Begin verbatim text
|
|
|
10 .ft CW
|
|
|
11 .nf
|
|
|
12 .ne \\$1
|
|
|
13 ..
|
|
|
14 .de Ve \" End verbatim text
|
|
|
15 .ft R
|
|
|
16 .fi
|
|
|
17 ..
|
|
|
18 .\" Set up some character translations and predefined strings. \*(-- will
|
|
|
19 .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
|
|
|
20 .\" double quote, and \*(R" will give a right double quote. \*(C+ will
|
|
|
21 .\" give a nicer C++. Capital omega is used to do unbreakable dashes and
|
|
|
22 .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
|
|
|
23 .\" nothing in troff, for use with C<>.
|
|
|
24 .tr \(*W-
|
|
|
25 .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
|
|
|
26 .ie n \{\
|
|
|
27 . ds -- \(*W-
|
|
|
28 . ds PI pi
|
|
|
29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
|
|
|
30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
|
|
|
31 . ds L" ""
|
|
|
32 . ds R" ""
|
|
|
33 . ds C` ""
|
|
|
34 . ds C' ""
|
|
|
35 'br\}
|
|
|
36 .el\{\
|
|
|
37 . ds -- \|\(em\|
|
|
|
38 . ds PI \(*p
|
|
|
39 . ds L" ``
|
|
|
40 . ds R" ''
|
|
|
41 'br\}
|
|
|
42 .\"
|
|
|
43 .\" Escape single quotes in literal strings from groff's Unicode transform.
|
|
|
44 .ie \n(.g .ds Aq \(aq
|
|
|
45 .el .ds Aq '
|
|
|
46 .\"
|
|
|
47 .\" If the F register is turned on, we'll generate index entries on stderr for
|
|
|
48 .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
|
|
|
49 .\" entries marked with X<> in POD. Of course, you'll have to process the
|
|
|
50 .\" output yourself in some meaningful fashion.
|
|
|
51 .ie \nF \{\
|
|
|
52 . de IX
|
|
|
53 . tm Index:\\$1\t\\n%\t"\\$2"
|
|
|
54 ..
|
|
|
55 . nr % 0
|
|
|
56 . rr F
|
|
|
57 .\}
|
|
|
58 .el \{\
|
|
|
59 . de IX
|
|
|
60 ..
|
|
|
61 .\}
|
|
|
62 .\"
|
|
|
63 .\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
|
|
|
64 .\" Fear. Run. Save yourself. No user-serviceable parts.
|
|
|
65 . \" fudge factors for nroff and troff
|
|
|
66 .if n \{\
|
|
|
67 . ds #H 0
|
|
|
68 . ds #V .8m
|
|
|
69 . ds #F .3m
|
|
|
70 . ds #[ \f1
|
|
|
71 . ds #] \fP
|
|
|
72 .\}
|
|
|
73 .if t \{\
|
|
|
74 . ds #H ((1u-(\\\\n(.fu%2u))*.13m)
|
|
|
75 . ds #V .6m
|
|
|
76 . ds #F 0
|
|
|
77 . ds #[ \&
|
|
|
78 . ds #] \&
|
|
|
79 .\}
|
|
|
80 . \" simple accents for nroff and troff
|
|
|
81 .if n \{\
|
|
|
82 . ds ' \&
|
|
|
83 . ds ` \&
|
|
|
84 . ds ^ \&
|
|
|
85 . ds , \&
|
|
|
86 . ds ~ ~
|
|
|
87 . ds /
|
|
|
88 .\}
|
|
|
89 .if t \{\
|
|
|
90 . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
|
|
|
91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
|
|
|
92 . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
|
|
|
93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
|
|
|
94 . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
|
|
|
95 . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
|
|
|
96 .\}
|
|
|
97 . \" troff and (daisy-wheel) nroff accents
|
|
|
98 .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
|
|
|
99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
|
|
|
100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
|
|
|
101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
|
|
|
102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
|
|
|
103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
|
|
|
104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
|
|
|
105 .ds ae a\h'-(\w'a'u*4/10)'e
|
|
|
106 .ds Ae A\h'-(\w'A'u*4/10)'E
|
|
|
107 . \" corrections for vroff
|
|
|
108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
|
|
|
109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
|
|
|
110 . \" for low resolution devices (crt and lpr)
|
|
|
111 .if \n(.H>23 .if \n(.V>19 \
|
|
|
112 \{\
|
|
|
113 . ds : e
|
|
|
114 . ds 8 ss
|
|
|
115 . ds o a
|
|
|
116 . ds d- d\h'-1'\(ga
|
|
|
117 . ds D- D\h'-1'\(hy
|
|
|
118 . ds th \o'bp'
|
|
|
119 . ds Th \o'LP'
|
|
|
120 . ds ae ae
|
|
|
121 . ds Ae AE
|
|
|
122 .\}
|
|
|
123 .rm #[ #] #H #V #F C
|
|
|
124 .\" ========================================================================
|
|
|
125 .\"
|
|
|
126 .IX Title "INFONUCLEICACIDS 1"
|
|
|
127 .TH INFONUCLEICACIDS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
|
|
|
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
|
|
|
129 .\" way too many mistakes in technical documents.
|
|
|
130 .if n .ad l
|
|
|
131 .nh
|
|
|
132 .SH "NAME"
|
|
|
133 InfoNucleicAcids.pl \- List properties of nucleic acids
|
|
|
134 .SH "SYNOPSIS"
|
|
|
135 .IX Header "SYNOPSIS"
|
|
|
136 InfoNucleicAcids.pl NucleicAcidIDs...
|
|
|
137 .PP
|
|
|
138 InfoNucleicAcids.pl [\fB\-h, \-\-help\fR] [\fB\-m, \-\-mode\fR NucleicAcidID | NucleicAcidType]
|
|
|
139 [\fB\-\-OutDelim\fR comma | tab | semicolon]
|
|
|
140 [\fB\-\-output\fR \s-1STDOUT\s0 | File] [\fB\-\-OutputStyle\fR NucleicAcidBlock | NucleicAcidRows]
|
|
|
141 [\fB\-o, \-\-overwrite\fR] [\fB\-\-precision\fR number] [\fB\-\-PropertiesMode\fR Categories | Names | All]
|
|
|
142 [\fB\-p, \-\-properties\fR CategoryName, [CategoryName,...] | PropertyName, [PropertyName,...]]
|
|
|
143 [\fB\-\-PropertiesListing\fR ByGroup | Alphabetical] [\fB\-q, \-\-quote\fR yes | no] [\fB\-r, \-\-root\fR rootname]
|
|
|
144 [\fB\-w, \-\-WorkingDir\fR dirname] NucleicAcidIDs...
|
|
|
145 .SH "DESCRIPTION"
|
|
|
146 .IX Header "DESCRIPTION"
|
|
|
147 List nucleic acid properties. Nucleic acids identification supports two types of IDs: code
|
|
|
148 or name. Nucleic acid properties data, in addition to basic information about nucleic acids \- code,
|
|
|
149 name, type, chemical formula and molecular weight \- include information about exact mass and
|
|
|
150 elemental composition.
|
|
|
151 .SH "PARAMETERS"
|
|
|
152 .IX Header "PARAMETERS"
|
|
|
153 .IP "\fBNucleicAcidIDs\fR \fICode [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]\fR" 4
|
|
|
154 .IX Item "NucleicAcidIDs Code [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]"
|
|
|
155 \&\fINucleicAcidIDs\fR is a space delimited list of values to identify nucleic acids.
|
|
|
156 .Sp
|
|
|
157 For \fINucleicAcidID\fR mode, input value format is: \fICode [NucleicAcidName...]\fR. Default: \fIA\fR.
|
|
|
158 Examples:
|
|
|
159 .Sp
|
|
|
160 .Vb 3
|
|
|
161 \& A
|
|
|
162 \& dG AMP
|
|
|
163 \& Cytidine T UDP dpppA "5\*(Aq\-dATP"
|
|
|
164 .Ve
|
|
|
165 .Sp
|
|
|
166 For \fINucleicAcidType\fR mode, input value format is: \fINucleicAcidType [NucleicAcidType...]\fR.
|
|
|
167 Default: \fIA\fR. Possible values are: \fINucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
|
|
|
168 Deoxynucleotide\fR. Default: \fINucleoside\fR.
|
|
|
169 Examples:
|
|
|
170 .Sp
|
|
|
171 .Vb 2
|
|
|
172 \& Deoxynucleoside
|
|
|
173 \& Nucleobase Nucleotide
|
|
|
174 .Ve
|
|
|
175 .SH "OPTIONS"
|
|
|
176 .IX Header "OPTIONS"
|
|
|
177 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
178 .IX Item "-h, --help"
|
|
|
179 Print this help message.
|
|
|
180 .IP "\fB\-m, \-\-mode\fR \fINucleicAcidID | NucleicAcidType\fR" 4
|
|
|
181 .IX Item "-m, --mode NucleicAcidID | NucleicAcidType"
|
|
|
182 Specify nucleic acids for listing properties using one of these methods: nucleic acid
|
|
|
183 code and/or names or nucleic acid type.
|
|
|
184 .Sp
|
|
|
185 Possible values: \fINucleicAcidID or NucleicAcidType\fR. Default: \fINucleicAcidID\fR
|
|
|
186 .Sp
|
|
|
187 For \fINucleicAcidType\fR, command line parameters support these type: \fINucleobase,
|
|
|
188 Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide\fR.
|
|
|
189 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
190 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
191 Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
192 Default value: \fIcomma\fR.
|
|
|
193 .IP "\fB\-\-output\fR \fI\s-1STDOUT\s0 | File\fR" 4
|
|
|
194 .IX Item "--output STDOUT | File"
|
|
|
195 List information at \s-1STDOUT\s0 or write it to a file. Possible values: \fI\s-1STDOUT\s0 or File\fR. Default:
|
|
|
196 \&\fI\s-1STDOUT\s0\fR. \fB\-r, \-\-root\fR option is used to generate output file name.
|
|
|
197 .IP "\fB\-\-OutputStyle\fR \fINucleicAcidBlock | NucleicAcidRows\fR" 4
|
|
|
198 .IX Item "--OutputStyle NucleicAcidBlock | NucleicAcidRows"
|
|
|
199 Specify how to list nucleic acid information: add a new line for each property and present it as a block
|
|
|
200 for each nucleic acid; or include all properties in one line and show it as a single line.
|
|
|
201 .Sp
|
|
|
202 Possible values: \fINucleicAcidBlock | NucleicAcidRows\fR. Default: \fINucleicAcidBlock\fR
|
|
|
203 .Sp
|
|
|
204 An example for \fINucleicAcidBlock\fR output style:
|
|
|
205 .Sp
|
|
|
206 .Vb 7
|
|
|
207 \& Code: Ado
|
|
|
208 \& OtherCodes: A
|
|
|
209 \& Name: Adenosine
|
|
|
210 \& Type: Nucleoside
|
|
|
211 \& MolecularFormula: C10H13O4N5
|
|
|
212 \& MolecularWeight: 267.2413
|
|
|
213 \& ... ...
|
|
|
214 .Ve
|
|
|
215 .Sp
|
|
|
216 An example for \fINucleicAcidRows\fR output style:
|
|
|
217 .Sp
|
|
|
218 .Vb 1
|
|
|
219 \& Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight
|
|
|
220 .Ve
|
|
|
221 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
222 .IX Item "-o, --overwrite"
|
|
|
223 Overwrite existing files.
|
|
|
224 .IP "\fB\-\-precision\fR \fInumber\fR" 4
|
|
|
225 .IX Item "--precision number"
|
|
|
226 Precision for listing numerical values. Default: up to \fI4\fR decimal places.
|
|
|
227 Valid values: positive integers.
|
|
|
228 .IP "\fB\-\-PropertiesMode\fR \fICategories | Names | All\fR" 4
|
|
|
229 .IX Item "--PropertiesMode Categories | Names | All"
|
|
|
230 Specify how property names are specified: use category names; explicit list of property names; or
|
|
|
231 use all available properties. Possible values: \fICategories, Names, or All\fR. Default: \fICategories\fR.
|
|
|
232 .Sp
|
|
|
233 This option is used in conjunction with \fB\-p, \-\-properties\fR option to specify properties of
|
|
|
234 interest.
|
|
|
235 .IP "\fB\-p, \-\-properties\fR \fICategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]\fR" 4
|
|
|
236 .IX Item "-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]"
|
|
|
237 This option is \fB\-\-propertiesmode\fR specific. In general, it's a list of comma separated category or
|
|
|
238 property names.
|
|
|
239 .Sp
|
|
|
240 Specify which nucleic acid properties information to list for the nucleic acid IDs specified using
|
|
|
241 command line parameters: list basic information; list all available information; or specify a comma
|
|
|
242 separated list of nucleic acid property names.
|
|
|
243 .Sp
|
|
|
244 Possible values: \fIBasic | BasicPlus | PropertyName,[PropertyName,...]\fR.
|
|
|
245 Default: \fIBasic\fR.
|
|
|
246 .Sp
|
|
|
247 \&\fIBasic\fR includes: \fICode, OtherCodes, Name, Type, MolecularFormula, MolecularWeight\fR
|
|
|
248 .Sp
|
|
|
249 \&\fIBasicPlus\fR includes: \fICode, OtherCodes, Name, Type, MolecularFormula, MolecularWeight, ExactMass,
|
|
|
250 ElementalComposition\fR
|
|
|
251 .Sp
|
|
|
252 Here is a complete list of available properties: \fICode, OtherCodes, BasePair, Name, Type, MolecularFormula,
|
|
|
253 MolecularFormulaAtpH7.5, MolecularWeight, ExactMass, ElementalComposition\fR.
|
|
|
254 .IP "\fB\-\-PropertiesListing\fR \fIByGroup | Alphabetical\fR" 4
|
|
|
255 .IX Item "--PropertiesListing ByGroup | Alphabetical"
|
|
|
256 Specify how to list properties for nucleic acids: group by category or an alphabetical by
|
|
|
257 property names. Possible values: \fIByGroup or Alphabetical\fR. Default: \fIByGroup\fR
|
|
|
258 .IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4
|
|
|
259 .IX Item "-q, --quote yes | no"
|
|
|
260 Put quotes around column values in output text file. Possible values: \fIyes or
|
|
|
261 no\fR. Default value: \fIyes\fR.
|
|
|
262 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
|
|
|
263 .IX Item "-r, --root rootname"
|
|
|
264 New text file name is generated using the root: <Root>.<Ext>. File name is only
|
|
|
265 used during \fIFile\fR value of \fB\-o, \-\-output\fR option.
|
|
|
266 .Sp
|
|
|
267 Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv
|
|
|
268 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
|
|
|
269 .IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
|
|
|
270 .IX Item "-w, --WorkingDir dirname"
|
|
|
271 Location of working directory. Default: current directory.
|
|
|
272 .SH "EXAMPLES"
|
|
|
273 .IX Header "EXAMPLES"
|
|
|
274 To list basic properties information for nucleoside A, type:
|
|
|
275 .PP
|
|
|
276 .Vb 1
|
|
|
277 \& % InfoNucleicAcids.pl
|
|
|
278 .Ve
|
|
|
279 .PP
|
|
|
280 To list all available properties information for nucleoside A, type:
|
|
|
281 .PP
|
|
|
282 .Vb 1
|
|
|
283 \& % InfoNucleicAcids.pl \-\-propertiesmode all A
|
|
|
284 .Ve
|
|
|
285 .PP
|
|
|
286 To list all available information for all available nucleic acids, type:
|
|
|
287 .PP
|
|
|
288 .Vb 1
|
|
|
289 \& % InfoNucleicAcids.pl \-\-propertiesmode All All
|
|
|
290 .Ve
|
|
|
291 .PP
|
|
|
292 To list basic properties information for all nucleobases, type:
|
|
|
293 .PP
|
|
|
294 .Vb 1
|
|
|
295 \& % InfoNucleicAcids.pl \-m NucleicAcidType Nucleoside
|
|
|
296 .Ve
|
|
|
297 .PP
|
|
|
298 To list basic properties information for all nucleotides and deoxynulceotides, type:
|
|
|
299 .PP
|
|
|
300 .Vb 1
|
|
|
301 \& % InfoNucleicAcids.pl \-m NucleicAcidType Nucleotide Deoxynucleotide
|
|
|
302 .Ve
|
|
|
303 .PP
|
|
|
304 To list basic properties information for variety of nucleic acids, type:
|
|
|
305 .PP
|
|
|
306 .Vb 1
|
|
|
307 \& % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5\*(Aq\-dATP"
|
|
|
308 .Ve
|
|
|
309 .PP
|
|
|
310 To list code and molecular weights for nucleosides A, G, C and T, type:
|
|
|
311 .PP
|
|
|
312 .Vb 2
|
|
|
313 \& % InfoNucleicAcids.pl \-\-PropertiesMode Names \-\-properties
|
|
|
314 \& Code,MolecularWeight A G C T
|
|
|
315 .Ve
|
|
|
316 .PP
|
|
|
317 To alphabetically list all the available properties for nucleotides dAMP, dGMP,
|
|
|
318 dCMP, and dTMP in rows instead of nucleic acid blocks with quotes around the values, type:
|
|
|
319 .PP
|
|
|
320 .Vb 3
|
|
|
321 \& % InfoNucleicAcids.pl \-\-PropertiesMode All \-\-PropertiesListing
|
|
|
322 \& Alphabetical \-\-OutputStyle NucleicAcidRows \-q yes dAMP dGMP
|
|
|
323 \& dCMP dTMP
|
|
|
324 .Ve
|
|
|
325 .PP
|
|
|
326 To alphabetically list all the available properties for all available nucleic acids to
|
|
|
327 a file names NucleicAcidsProperties.csv with quotes around the values, type
|
|
|
328 .PP
|
|
|
329 .Vb 3
|
|
|
330 \& % InfoNucleicAcids.pl \-\-PropertiesMode All \-\-PropertiesListing
|
|
|
331 \& Alphabetical \-\-output File \-\-OutputStyle NucleicAcidRows \-r
|
|
|
332 \& NucleicAcidsProperties \-o \-q Yes All
|
|
|
333 .Ve
|
|
|
334 .SH "AUTHOR"
|
|
|
335 .IX Header "AUTHOR"
|
|
|
336 Manish Sud <msud@san.rr.com>
|
|
|
337 .SH "SEE ALSO"
|
|
|
338 .IX Header "SEE ALSO"
|
|
|
339 InfoAminoAcids.pl, InfoPeriodicTableElements.pl
|
|
|
340 .SH "COPYRIGHT"
|
|
|
341 .IX Header "COPYRIGHT"
|
|
|
342 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
343 .PP
|
|
|
344 This file is part of MayaChemTools.
|
|
|
345 .PP
|
|
|
346 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
347 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
348 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
349 any later version.
|
