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1 #!/usr/bin/perl -w
2 #
3 # $RCSfile: InfoNucleicAcids.pl,v $
4 # $Date: 2015/02/28 20:46:20 $
5 # $Revision: 1.26 $
6 #
7 # Author: Manish Sud <msud@san.rr.com>
8 #
9 # Copyright (C) 2015 Manish Sud. All rights reserved.
10 #
11 # This file is part of MayaChemTools.
12 #
13 # MayaChemTools is free software; you can redistribute it and/or modify it under
14 # the terms of the GNU Lesser General Public License as published by the Free
15 # Software Foundation; either version 3 of the License, or (at your option) any
16 # later version.
17 #
18 # MayaChemTools is distributed in the hope that it will be useful, but without
19 # any warranty; without even the implied warranty of merchantability of fitness
20 # for a particular purpose. See the GNU Lesser General Public License for more
21 # details.
22 #
23 # You should have received a copy of the GNU Lesser General Public License
24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
26 # Boston, MA, 02111-1307, USA.
27 #
28
29 use strict;
30 use FindBin; use lib "$FindBin::Bin/../lib";
31 use Getopt::Long;
32 use File::Basename;
33 use Text::ParseWords;
34 use Benchmark;
35 use FileUtil;
36 use TextUtil;
37 use NucleicAcids;
38
39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
40
41 # Autoflush STDOUT
42 $| = 1;
43
44 # Starting message...
45 $ScriptName = basename($0);
46 print "\n$ScriptName: Starting...\n\n";
47 $StartTime = new Benchmark;
48
49 # Get the options and setup script...
50 SetupScriptUsage();
51 if ($Options{help}) {
52 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
53 }
54
55 print "Processing options...\n";
56 my(%OptionsInfo);
57 ProcessOptions();
58
59 ListNucleicAcidProperties();
60 print "\n$ScriptName:Done...\n\n";
61
62 $EndTime = new Benchmark;
63 $TotalTime = timediff ($EndTime, $StartTime);
64 print "Total time: ", timestr($TotalTime), "\n";
65
66 ###############################################################################
67
68 # List data for an nucleic acid...
69 sub ListNucleicAcidData {
70 my($DataLabelRef, $DataValueRef) = @_;
71 my($Index, $Line, $Value);
72
73 if ($OptionsInfo{NucleicAcidRowsOutput}) {
74 $Line = '';
75 # Format data...
76 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) {
77 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
78 }
79 else {
80 # Always quote values containing commas...
81 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0];
82 for $Index (1 .. $#{$DataValueRef} ) {
83 $Value = $DataValueRef->[$Index];
84 if ($Value =~ /\,/) {
85 $Value = qq("$Value");
86 }
87 $Line .= $OptionsInfo{OutDelim} . $Value;
88 }
89 }
90 if ($OptionsInfo{FileOutput}) {
91 print OUTFILE "$Line\n";
92 }
93 else {
94 print "$Line\n";
95 }
96 }
97 else {
98 # Format and list data...
99 $Line = '';
100 for $Index (0 .. $#{$DataLabelRef} ) {
101 $Line = $DataLabelRef->[$Index] . ' ' . $DataValueRef->[$Index];
102 if ($OptionsInfo{FileOutput}) {
103 print OUTFILE "$Line\n";
104 }
105 else {
106 print "$Line\n";
107 }
108 }
109 }
110 }
111
112 # List data for an nucleic acid...
113 sub ListHeaderRowData {
114 my($DataLabelRef) = @_;
115 my($Line);
116
117 # Format data...
118 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
119 $Line =~ s/\://g;
120 # List data...
121 if ($OptionsInfo{FileOutput}) {
122 print OUTFILE "$Line\n";
123 }
124 else {
125 print "$Line\n";
126 }
127 }
128
129 # List properties for nucleic acids...
130 sub ListNucleicAcidProperties {
131 my($NucleicAcidID, $NucleicAcidDataRef, $PropertyName, $PropertyValue, @PropertyLabels, @PropertyValues);
132
133 print "Listing information for nucleic acid(s)...\n";
134
135 if ($OptionsInfo{FileOutput}) {
136 print "Generating file $OptionsInfo{OutFileName}...\n";
137 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
138 }
139
140 # Setup property labels...
141 @PropertyLabels = ();
142 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
143 push @PropertyLabels, ("$PropertyName:");
144 }
145
146 if ($OptionsInfo{NucleicAcidRowsOutput}) {
147 ListHeaderRowData(\@PropertyLabels);
148 }
149
150 # Go over specified properties...
151 for $NucleicAcidID (@{$OptionsInfo{SpecifiedNucleicAcidIDs}}) {
152 $NucleicAcidDataRef = NucleicAcids::GetNucleicAcidPropertiesData($NucleicAcidID);
153
154 if (!$OptionsInfo{NucleicAcidRowsOutput}) {
155 if ($OptionsInfo{FileOutput}) {
156 print OUTFILE "\nListing properties for nucleic acid $NucleicAcidID...\n\n";
157 }
158 else {
159 print "\nListing properties for nucleic acid $NucleicAcidID...\n\n";
160 }
161 }
162
163 # Collect data..
164 @PropertyValues = ();
165 for $PropertyName (@{$OptionsInfo{SpecifiedProperies}}) {
166 $PropertyValue = $NucleicAcidDataRef->{$PropertyName};
167 if (IsFloat($PropertyValue)) {
168 $PropertyValue = sprintf("%.$OptionsInfo{Precision}f", $PropertyValue) + 0;
169 }
170 push @PropertyValues, $PropertyValue;
171 }
172 # List data...
173 ListNucleicAcidData(\@PropertyLabels, \@PropertyValues);
174 }
175 if ($OptionsInfo{FileOutput}) {
176 close OUTFILE;
177 }
178 print "\n";
179 }
180
181 # Get propery names from categories...
182 sub GetPropertyNamesFromCategories {
183 my($CategoryName) = @_;
184 my(@PropertyNames);
185
186 @PropertyNames = ();
187 if ($CategoryName =~ /^Basic$/i) {
188 @PropertyNames = ('Code', 'OtherCodes', 'Name', 'Type', 'MolecularFormula', 'MolecularWeight');
189 } elsif ($CategoryName =~ /^BasicPlus$/i) {
190 @PropertyNames = ('Code', 'OtherCodes', 'Name', 'Type', 'MolecularFormula', 'MolecularWeight', 'ExactMass', 'ElementalComposition');
191 }
192
193 return @PropertyNames;
194 }
195
196 # Process option values...
197 sub ProcessOptions {
198 %OptionsInfo = ();
199
200 $OptionsInfo{Mode} = $Options{mode};
201
202 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
203 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
204
205 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
206 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
207
208 $OptionsInfo{Output} = $Options{output};
209 $OptionsInfo{OutputStyle} = $Options{outputstyle};
210
211 $OptionsInfo{NucleicAcidRowsOutput} = ($Options{outputstyle} =~ /^NucleicAcidRows$/i) ? 1 : 0;
212 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
213
214 $OptionsInfo{Precision} = $Options{precision};
215
216 my($NucleicAcidID, @NucleicAcidIDs);
217
218 @{$OptionsInfo{SpecifiedNucleicAcidIDs}} = ();
219
220 # Set up Nucleic Acids IDs except for All mode...
221 @NucleicAcidIDs = ();
222
223 if (@ARGV >= 1) {
224 push @NucleicAcidIDs, @ARGV;
225 }
226 else {
227 # Setup mode specified default values...
228 if ($Options{mode} =~ /NucleicAcidID/i) {
229 push @NucleicAcidIDs, 'A';
230 }
231 elsif ($Options{mode} =~ /NucleicAcidType/i) {
232 push @NucleicAcidIDs, 'Nucleoside';
233 }
234 else {
235 push @NucleicAcidIDs, 'A';
236 }
237 }
238
239 # Generate list of nucleic acids...
240 if (@ARGV == 1 && $ARGV[0] =~ /^All$/i) {
241 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, NucleicAcids::GetNucleicAcids();
242 }
243 else {
244 if ($Options{mode} =~ /NucleicAcidID/i) {
245 ID: for $NucleicAcidID (@NucleicAcidIDs) {
246 if (NucleicAcids::IsNucleicAcid($NucleicAcidID)) {
247 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, $NucleicAcidID;
248 }
249 else {
250 warn "Ignoring nucleic acid ID, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid ID...\n";
251 next ID;
252 }
253 }
254 }
255 elsif ($Options{mode} =~ /NucleicAcidType/i) {
256 ID: for $NucleicAcidID (@NucleicAcidIDs) {
257 if (!NucleicAcids::IsNucleicAcidType($NucleicAcidID)) {
258 warn "Ignoring nucleic acid type, $NucleicAcidID, specified using command line parameter option: Unknown nucleic acid type...\n";
259 next ID;
260 }
261 push @{$OptionsInfo{SpecifiedNucleicAcidIDs}}, NucleicAcids::GetNucleicAcidsByType($NucleicAcidID);
262 }
263 }
264 }
265 SetupSpecifiedProperties();
266
267 # Setup output file name...
268 $OptionsInfo{OutFileName} = '';
269 if ($OptionsInfo{FileOutput}) {
270 my($OutFileRoot, $OutFileExt);
271
272 $OutFileRoot = '';
273 $OutFileExt = "csv";
274 if ($Options{outdelim} =~ /^tab$/i) {
275 $OutFileExt = "tsv";
276 }
277 if ($Options{root}) {
278 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
279 if ($RootFileName && $RootFileExt) {
280 $OutFileRoot = $RootFileName;
281 }
282 else {
283 $OutFileRoot = $Options{root};
284 }
285 }
286 else {
287 $OutFileRoot = 'NucleicAcidsInfo';
288 }
289 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt;
290 if (!$Options{overwrite}) {
291 if (-e $OptionsInfo{OutFileName}) {
292 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n";
293 }
294 }
295 }
296 }
297
298 # Setup properties to list...
299 sub SetupSpecifiedProperties {
300
301 $OptionsInfo{Properties} = defined $Options{properties} ? $Options{properties} : undef;
302
303 $OptionsInfo{PropertiesMode} = $Options{propertiesmode};
304 $OptionsInfo{PropertiesListing} = $Options{propertieslisting};
305
306 # Make sure appropriate properties/category names are specified...
307 @{$OptionsInfo{SpecifiedProperies}} = ();
308 if ($Options{properties} && ($Options{propertiesmode} =~ /^All$/i) ) {
309 warn "Warning: Ignoring values specifed by \"-p --properties\" option: Not valid for All value of \"--propertiesmode\" option...\n";
310 }
311 if ($Options{propertiesmode} =~ /^All$/i) {
312 if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
313 push @{$OptionsInfo{SpecifiedProperies}}, NucleicAcids::GetNucleicAcidPropertiesNames('Alphabetical');
314 }
315 else {
316 push @{$OptionsInfo{SpecifiedProperies}}, NucleicAcids::GetNucleicAcidPropertiesNames();
317 }
318 }
319 else {
320 if ($Options{properties}) {
321 if ($Options{propertiesmode} =~ /^Categories$/i) {
322 # Check category name...
323 if ($Options{properties} !~ /^(Basic|BasicPlus)$/i) {
324 die "Error: The value specified, $Options{properties}, for option \"-p --properties\" in conjunction with \"Categories\" value for option \"--propertiesmode\" is not valid. Allowed values: Basic and BasicPlus\n";
325 }
326 # Set propertynames...
327 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories($Options{properties});
328 }
329 else {
330 # Check property names..
331 my($Name, $PropertyName, @Names);
332 @Names = split /\,/, $Options{properties};
333 NAME: for $Name (@Names) {
334 $PropertyName = RemoveLeadingAndTrailingWhiteSpaces($Name);
335 if (NucleicAcids::IsNucleicAcidProperty($PropertyName)) {
336 push @{$OptionsInfo{SpecifiedProperies}}, $PropertyName;
337 }
338 else {
339 warn "Warning: Ignoring value, $Name, specifed by \"-p --properties\" option: Unknown property name...\n";
340 }
341 }
342 if ($Options{propertieslisting} =~ /^Alphabetical$/i) {
343 # Code, OtherCodes and Name are always listed first...
344 my($CodePresent, $OtherCodesPresent, $NamePresent, @AlphabeticalProperties, %PropertiesMap);
345 %PropertiesMap = ();
346 @AlphabeticalProperties = ();
347 $CodePresent = 0; $OtherCodesPresent = 0; $NamePresent = 0;
348 NAME: for $Name (@{$OptionsInfo{SpecifiedProperies}}) {
349 if ($Name =~ /^Code$/i) {
350 $CodePresent = 1;
351 next NAME;
352 }
353 if ($Name =~ /^OtherCodes$/i) {
354 $OtherCodesPresent = 1;
355 next NAME;
356 }
357 if ($Name =~ /^Name$/i) {
358 $NamePresent = 1;
359 next NAME;
360 }
361 $PropertiesMap{$Name} = $Name;
362 }
363 # Setup the alphabetical list...
364 if ($CodePresent) {
365 push @AlphabeticalProperties, 'Code';
366 }
367 if ($OtherCodesPresent) {
368 push @AlphabeticalProperties, 'OtherCodesPresent';
369 }
370 if ($NamePresent) {
371 push @AlphabeticalProperties, 'Name';
372 }
373 for $Name (sort keys %PropertiesMap) {
374 push @AlphabeticalProperties, $Name;
375 }
376 @{$OptionsInfo{SpecifiedProperies}} = ();
377 push @{$OptionsInfo{SpecifiedProperies}}, @AlphabeticalProperties;
378 }
379 }
380 }
381 else {
382 # Set default value...
383 push @{$OptionsInfo{SpecifiedProperies}}, GetPropertyNamesFromCategories('Basic');
384 }
385 }
386 }
387
388 # Setup script usage and retrieve command line arguments specified using various options...
389 sub SetupScriptUsage {
390
391 # Retrieve all the options...
392 %Options = ();
393 $Options{mode} = "NucleicAcidID";
394 $Options{outdelim} = "comma";
395 $Options{output} = "STDOUT";
396 $Options{outputstyle} = "NucleicAcidBlock";
397 $Options{precision} = 4;
398 $Options{propertiesmode} = "Categories";
399 $Options{propertieslisting} = "ByGroup";
400 $Options{quote} = "yes";
401
402 if (!GetOptions(\%Options, "help|h", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "properties|p=s", "propertieslisting=s", "propertiesmode=s", "quote|q=s", "root|r=s", "workingdir|w=s")) {
403 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
404 }
405 if ($Options{workingdir}) {
406 if (! -d $Options{workingdir}) {
407 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
408 }
409 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
410 }
411 if ($Options{mode} !~ /^(NucleicAcidID|NucleicAcidType)$/i) {
412 die "Error: The value specified, $Options{mode}, for option \"--mode\" is not valid. Allowed values: NucleicAcidID or NucleicAcidType\n";
413 }
414 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
415 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
416 }
417 if ($Options{output} !~ /^(STDOUT|File)$/i) {
418 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n";
419 }
420 if ($Options{outputstyle} !~ /^(NucleicAcidBlock|NucleicAcidRows)$/i) {
421 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: NucleicAcidBlock or NucleicAcidRows\n";
422 }
423 if (!IsPositiveInteger($Options{precision})) {
424 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
425 }
426 if ($Options{propertiesmode} !~ /^(Categories|Names|All)$/i) {
427 die "Error: The value specified, $Options{propertiesmode}, for option \"--propertiesmode\" is not valid. Allowed values: Categories, Names, or All\n";
428 }
429 if ($Options{propertieslisting} !~ /^(ByGroup|Alphabetical)$/i) {
430 die "Error: The value specified, $Options{propertieslisting}, for option \"--propertieslisting\" is not valid. Allowed values: ByGroup, or Alphabetical\n";
431 }
432 if ($Options{quote} !~ /^(yes|no)$/i) {
433 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
434 }
435 }
436
437 __END__
438
439 =head1 NAME
440
441 InfoNucleicAcids.pl - List properties of nucleic acids
442
443 =head1 SYNOPSIS
444
445 InfoNucleicAcids.pl NucleicAcidIDs...
446
447 InfoNucleicAcids.pl [B<-h, --help>] [B<-m, --mode> NucleicAcidID | NucleicAcidType]
448 [B<--OutDelim> comma | tab | semicolon]
449 [B<--output> STDOUT | File] [B<--OutputStyle> NucleicAcidBlock | NucleicAcidRows]
450 [B<-o, --overwrite>] [B<--precision> number] [B<--PropertiesMode> Categories | Names | All]
451 [B<-p, --properties> CategoryName, [CategoryName,...] | PropertyName, [PropertyName,...]]
452 [B<--PropertiesListing> ByGroup | Alphabetical] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
453 [B<-w, --WorkingDir> dirname] NucleicAcidIDs...
454
455 =head1 DESCRIPTION
456
457 List nucleic acid properties. Nucleic acids identification supports two types of IDs: code
458 or name. Nucleic acid properties data, in addition to basic information about nucleic acids - code,
459 name, type, chemical formula and molecular weight - include information about exact mass and
460 elemental composition.
461
462 =head1 PARAMETERS
463
464 =over 4
465
466 =item B<NucleicAcidIDs> I<Code [NucleicAcidName...] | NucleicAcidType [NucleicAcidType...]>
467
468 I<NucleicAcidIDs> is a space delimited list of values to identify nucleic acids.
469
470 For I<NucleicAcidID> mode, input value format is: I<Code [NucleicAcidName...]>. Default: I<A>.
471 Examples:
472
473 A
474 dG AMP
475 Cytidine T UDP dpppA "5'-dATP"
476
477 For I<NucleicAcidType> mode, input value format is: I<NucleicAcidType [NucleicAcidType...]>.
478 Default: I<A>. Possible values are: I<Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide,
479 Deoxynucleotide>. Default: I<Nucleoside>.
480 Examples:
481
482 Deoxynucleoside
483 Nucleobase Nucleotide
484
485 =back
486
487 =head1 OPTIONS
488
489 =over 4
490
491 =item B<-h, --help>
492
493 Print this help message.
494
495 =item B<-m, --mode> I<NucleicAcidID | NucleicAcidType>
496
497 Specify nucleic acids for listing properties using one of these methods: nucleic acid
498 code and/or names or nucleic acid type.
499
500 Possible values: I<NucleicAcidID or NucleicAcidType>. Default: I<NucleicAcidID>
501
502 For I<NucleicAcidType>, command line parameters support these type: I<Nucleobase,
503 Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide>.
504
505 =item B<--OutDelim> I<comma | tab | semicolon>
506
507 Output text file delimiter. Possible values: I<comma, tab, or semicolon>
508 Default value: I<comma>.
509
510 =item B<--output> I<STDOUT | File>
511
512 List information at STDOUT or write it to a file. Possible values: I<STDOUT or File>. Default:
513 I<STDOUT>. B<-r, --root> option is used to generate output file name.
514
515 =item B<--OutputStyle> I<NucleicAcidBlock | NucleicAcidRows>
516
517 Specify how to list nucleic acid information: add a new line for each property and present it as a block
518 for each nucleic acid; or include all properties in one line and show it as a single line.
519
520 Possible values: I<NucleicAcidBlock | NucleicAcidRows>. Default: I<NucleicAcidBlock>
521
522 An example for I<NucleicAcidBlock> output style:
523
524 Code: Ado
525 OtherCodes: A
526 Name: Adenosine
527 Type: Nucleoside
528 MolecularFormula: C10H13O4N5
529 MolecularWeight: 267.2413
530 ... ...
531
532 An example for I<NucleicAcidRows> output style:
533
534 Code,OtherCodes,Name,Type,MolecularFormula,MolecularWeight
535
536 =item B<-o, --overwrite>
537
538 Overwrite existing files.
539
540 =item B<--precision> I<number>
541
542 Precision for listing numerical values. Default: up to I<4> decimal places.
543 Valid values: positive integers.
544
545 =item B<--PropertiesMode> I<Categories | Names | All>
546
547 Specify how property names are specified: use category names; explicit list of property names; or
548 use all available properties. Possible values: I<Categories, Names, or All>. Default: I<Categories>.
549
550 This option is used in conjunction with B<-p, --properties> option to specify properties of
551 interest.
552
553 =item B<-p, --properties> I<CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]>
554
555 This option is B<--propertiesmode> specific. In general, it's a list of comma separated category or
556 property names.
557
558 Specify which nucleic acid properties information to list for the nucleic acid IDs specified using
559 command line parameters: list basic information; list all available information; or specify a comma
560 separated list of nucleic acid property names.
561
562 Possible values: I<Basic | BasicPlus | PropertyName,[PropertyName,...]>.
563 Default: I<Basic>.
564
565 I<Basic> includes: I<Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight>
566
567 I<BasicPlus> includes: I<Code, OtherCodes, Name, Type, MolecularFormula, MolecularWeight, ExactMass,
568 ElementalComposition>
569
570 Here is a complete list of available properties: I<Code, OtherCodes, BasePair, Name, Type, MolecularFormula,
571 MolecularFormulaAtpH7.5, MolecularWeight, ExactMass, ElementalComposition>.
572
573 =item B<--PropertiesListing> I<ByGroup | Alphabetical>
574
575 Specify how to list properties for nucleic acids: group by category or an alphabetical by
576 property names. Possible values: I<ByGroup or Alphabetical>. Default: I<ByGroup>
577
578 =item B<-q, --quote> I<yes | no>
579
580 Put quotes around column values in output text file. Possible values: I<yes or
581 no>. Default value: I<yes>.
582
583 =item B<-r, --root> I<rootname>
584
585 New text file name is generated using the root: <Root>.<Ext>. File name is only
586 used during I<File> value of B<-o, --output> option.
587
588 Default file name: NucleicAcidInfo<mode>.<Ext>. The csv, and tsv
589 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
590
591 =item B<-w, --WorkingDir> I<dirname>
592
593 Location of working directory. Default: current directory.
594
595 =back
596
597 =head1 EXAMPLES
598
599 To list basic properties information for nucleoside A, type:
600
601 % InfoNucleicAcids.pl
602
603 To list all available properties information for nucleoside A, type:
604
605 % InfoNucleicAcids.pl --propertiesmode all A
606
607 To list all available information for all available nucleic acids, type:
608
609 % InfoNucleicAcids.pl --propertiesmode All All
610
611 To list basic properties information for all nucleobases, type:
612
613 % InfoNucleicAcids.pl -m NucleicAcidType Nucleoside
614
615 To list basic properties information for all nucleotides and deoxynulceotides, type:
616
617 % InfoNucleicAcids.pl -m NucleicAcidType Nucleotide Deoxynucleotide
618
619 To list basic properties information for variety of nucleic acids, type:
620
621 % InfoNucleicAcids.pl A dG AMP Cytidine T UDP "5'-dATP"
622
623 To list code and molecular weights for nucleosides A, G, C and T, type:
624
625 % InfoNucleicAcids.pl --PropertiesMode Names --properties
626 Code,MolecularWeight A G C T
627
628 To alphabetically list all the available properties for nucleotides dAMP, dGMP,
629 dCMP, and dTMP in rows instead of nucleic acid blocks with quotes around the values, type:
630
631 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
632 Alphabetical --OutputStyle NucleicAcidRows -q yes dAMP dGMP
633 dCMP dTMP
634
635 To alphabetically list all the available properties for all available nucleic acids to
636 a file names NucleicAcidsProperties.csv with quotes around the values, type
637
638 % InfoNucleicAcids.pl --PropertiesMode All --PropertiesListing
639 Alphabetical --output File --OutputStyle NucleicAcidRows -r
640 NucleicAcidsProperties -o -q Yes All
641
642 =head1 AUTHOR
643
644 Manish Sud <msud@san.rr.com>
645
646 =head1 SEE ALSO
647
648 InfoAminoAcids.pl, InfoPeriodicTableElements.pl
649
650 =head1 COPYRIGHT
651
652 Copyright (C) 2015 Manish Sud. All rights reserved.
653
654 This file is part of MayaChemTools.
655
656 MayaChemTools is free software; you can redistribute it and/or modify it under
657 the terms of the GNU Lesser General Public License as published by the Free
658 Software Foundation; either version 3 of the License, or (at your option)
659 any later version.
660
661 =cut