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comparison docs/scripts/txt/ModifySDFilesDataFields.txt @ 0:4816e4a8ae95 draft default tip
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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 ModifySDFilesDataFields.pl - Modify data fields in SDFile(s) | |
3 | |
4 SYNOPSIS | |
5 ModifySDFilesDataFields.pl SDFile(s)... | |
6 | |
7 ModifySDFilesDataFields.pl [-d, --detail infolevel] [--datafieldscommon | |
8 newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]] | |
9 [--datafieldsmap newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; | |
10 [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]] | |
11 [--datafieldsmapfile filename] [--datafieldURL URLDataFieldLabel, | |
12 CGIScriptPath, CGIParamName, CmpdIDFieldLabel] [-h, --help] [-k, | |
13 --keepolddatafields all | unmappedonly | none] [-m, --mode molname | | |
14 datafields | both] [--molnamemode datafield | labelprefix] [--molname | |
15 datafieldname or prefixstring] [--molnamereplace always | empty] [-o, | |
16 --overwrite] [-r, --root rootname] [-w, --workingdir dirname] | |
17 SDFile(s)... | |
18 | |
19 DESCRIPTION | |
20 Modify molname line and data fields in *SDFile(s)*. Molname line can be | |
21 replaced by a data field value or assigned a sequential ID prefixed with | |
22 a specific string. For data fields and modification of their values, | |
23 these types of options are supported: replace data field labels by | |
24 another set of labels; combine values of multiple data fields and assign | |
25 a new label; add specific set of data field labels and values to all | |
26 compound records; and others. | |
27 | |
28 The file names are separated by space.The valid file extensions are | |
29 *.sdf* and *.sd*. All other file names are ignored. All the SD files in | |
30 a current directory can be specified either by **.sdf* or the current | |
31 directory name. | |
32 | |
33 OPTIONS | |
34 -d, --detail *infolevel* | |
35 Level of information to print about compound records being ignored. | |
36 Default: *1*. Possible values: *1, 2 or 3*. | |
37 | |
38 --datafieldscommon *newfieldlabel, newfieldvalue, [newfieldlabel, | |
39 newfieldvalue,...]* | |
40 Specify data field labels and values for addition to each compound | |
41 record. It's a comma delimited list of data field label and values | |
42 pair. Default: *none*. | |
43 | |
44 Examples: | |
45 | |
46 DepositionDate,YYYY-MM-DD | |
47 Source,www.domainname.org,ReleaseData,YYYY-MM-DD | |
48 | |
49 --datafieldsmap *newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; | |
50 [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]* | |
51 Specify how various data field labels and values are combined to | |
52 generate a new data field labels and their values. All the comma | |
53 delimited data fields, with in a semicolon delimited set, are mapped | |
54 to the first new data field label along with the data field values | |
55 joined via new line character. Default: *none*. | |
56 | |
57 Examples: | |
58 | |
59 Synonym,Name,SystematicName,Synonym;CmpdID,Extreg | |
60 HBondDonors,SumNHOH | |
61 | |
62 --datafieldsmapfile *filename* | |
63 Filename containing mapping of data fields. Format of data fields | |
64 line in this file corresponds to --datafieldsmap option. Example: | |
65 | |
66 Line 1: Synonym,Name,SystematicName,Synonym;CmpdID,Extreg | |
67 Line 2: HBondDonors,SumNHOH | |
68 | |
69 --datafieldURL *URLDataFieldLabel, CGIScriptPath, CGIParamName, | |
70 CmpdIDFieldLabel* | |
71 Specify how to generate a URL for retrieving compound data from a | |
72 web server and add it to each compound record. *URLDataFieldLabel* | |
73 is used as the data field label for URL value which is created by | |
74 combining *CGIScriptPath,CGIParamName,CmpdIDFieldLabel* values: | |
75 CGIScriptPath?CGIParamName=CmpdIDFieldLabelValue. Default: *none*. | |
76 | |
77 Example: | |
78 | |
79 Source,http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID | |
80 | |
81 -h, --help | |
82 Print this help message. | |
83 | |
84 -k, --keepolddatafields *all | unmappedonly | none* | |
85 Specify how to transfer old data fields from input SDFile(s) to new | |
86 SDFile(s) during *datafields | both* value of -m, --mode option: | |
87 keep all old data fields; write out the ones not mapped to new | |
88 fields as specified by --datafieldsmap or <--datafieldsmapfile> | |
89 options; or ignore all old data field labels. For *molname* -m | |
90 --mode, old datafields are always kept. Possible values: *all | | |
91 unmappedonly | none*. Default: *none*. | |
92 | |
93 -m, --mode *molname | datafields | both* | |
94 Specify how to modify SDFile(s): *molname* - change molname line by | |
95 another datafield or value; *datafield* - modify data field labels | |
96 and values by replacing one label by another, combining multiple | |
97 data field labels and values, adding specific set of data field | |
98 labels and values to all compound, or inserting an URL for compound | |
99 retrieval to each record; *both* - change molname line and | |
100 datafields simultaneously. Possible values: *molname | datafields | | |
101 both*. Default: *molname* | |
102 | |
103 --molnamemode *datafield | labelprefix* | |
104 Specify how to change molname line for -m --mode option values of | |
105 *molname | both*: use a datafield label value or assign a sequential | |
106 ID prefixed with *labelprefix*. Possible values: *datafield | | |
107 labelprefix*. Default: *labelprefix*. | |
108 | |
109 --molname *datafieldname or prefixstring* | |
110 Molname generation method. For *datafield* value of --molnamemode | |
111 option, it corresponds to datafield label name whose value is used | |
112 for molname; otherwise, it's a prefix string used for generating | |
113 compound IDs like labelprefixstring<Number>. Default value, *Cmpd*, | |
114 generates compound IDs like Cmpd<Number> for molname. | |
115 | |
116 --molnamereplace *always | empty* | |
117 Specify when to replace molname line for -m --mode option values of | |
118 *molname | both*: always replace the molname line using --molname | |
119 option or only when it's empty. Possible values: *always | empty*. | |
120 Default: *empty*. | |
121 | |
122 -o, --overwrite | |
123 Overwrite existing files. | |
124 | |
125 -r, --root *rootname* | |
126 New SD file name is generated using the root: <Root>.<Ext>. Default | |
127 new file name: <InitialSDFileName>ModifiedDataFields.<Ext>. This | |
128 option is ignored for multiple input files. | |
129 | |
130 -w, --workingdir *dirname* | |
131 Location of working directory. Default: current directory. | |
132 | |
133 EXAMPLES | |
134 To replace empty molname lines by Cmpd<CmpdNumber> and generate a new SD | |
135 file NewSample1.sdf, type: | |
136 | |
137 % ModifySDFilesDataFields.pl -o -r NewSample1 Sample1.sdf | |
138 | |
139 To replace all molname lines by Mol_ID data field generate a new SD file | |
140 NewSample1.sdf, type: | |
141 | |
142 % ModifySDFilesDataFields.pl --molnamemode datafield | |
143 --molnamereplace always -r NewSample1 -o Sample1.sdf | |
144 | |
145 To replace all molname lines by Mol_ID data field, map Name and | |
146 CompoundName to a new datafield Synonym, and generate a new SD file | |
147 NewSample1.sdf, type: | |
148 | |
149 % ModifySDFilesDataFields.pl --molnamemode datafield | |
150 --molnamereplace always --molname Mol_ID --mode both | |
151 --datafieldsmap "Synonym,Name,CompoundName" -r | |
152 NewSample1 -o Sample1.sdf | |
153 | |
154 To replace all molname lines by Mol_ID data field, map Name and | |
155 CompoundName to a new datafield Synonym, add common fields ReleaseDate | |
156 and Source, and generate a new SD file NewSample1.sdf without keeping | |
157 any old SD data fields, type: | |
158 | |
159 % ModifySDFilesDataFields.pl --molnamemode datafield | |
160 --molnamereplace always --molname Mol_ID --mode both | |
161 --datafieldsmap "Synonym,Name,CompoundName" | |
162 --datafieldscommon "ReleaseDate,yyyy-mm-dd,Source, | |
163 www.mayachemtools.org" --keepolddatafields none -r | |
164 NewSample1 -o Sample1.sdf | |
165 | |
166 Preparing SD files PubChem deposition: | |
167 | |
168 Consider a SD file with these fields: Mol_ID, Name, Synonyms and | |
169 Systematic_Name. And Mol_ID data field uniquely identifies your | |
170 compound. | |
171 | |
172 To prepare a new SD file CmpdDataForPubChem.sdf containing only required | |
173 PUBCHEM_EXT_DATASOURCE_REGID field, type: | |
174 | |
175 % ModifySDFilesDataFields.pl --m datafields | |
176 --datafieldsmap | |
177 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID" | |
178 -r CmpdDataForPubChem -o Sample1.sdf | |
179 | |
180 To prepare a new SD file CmpdDataForPubChem.sdf containing only required | |
181 PUBCHEM_EXT_DATASOURCE_REGID field and replace molname line with Mol_ID, | |
182 type: | |
183 | |
184 % ModifySDFilesDataFields.pl --molnamemode datafield | |
185 --molnamereplace always --molname Mol_ID --mode both | |
186 --datafieldsmap | |
187 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID" | |
188 -r CmpdDataForPubChem -o Sample1.sdf | |
189 | |
190 In addition to required PubChem data field, you can also add optional | |
191 PubChem data fields. | |
192 | |
193 To map your Name, Synonyms and Systematic_Name data fields to optional | |
194 PUBCHEM_SUBSTANCE_SYNONYM data field along with required ID field, type: | |
195 | |
196 % ModifySDFilesDataFields.pl --molnamemode datafield | |
197 --molnamereplace always --molname Mol_ID --mode both | |
198 --datafieldsmap | |
199 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; | |
200 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" | |
201 -r CmpdDataForPubChem -o Sample1.sdf | |
202 | |
203 To add your <domain.org> as PUBCHEM_EXT_SUBSTANCE_URL and link substance | |
204 retrieval to your CGI script | |
205 <http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID> via | |
206 PUBCHEM_EXT_DATASOURCE_REGID field along with optional and required data | |
207 fields, type: | |
208 | |
209 % ModifySDFilesDataFields.pl --molnamemode datafield | |
210 --molnamereplace always --molname Mol_ID --mode both | |
211 --datafieldsmap | |
212 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; | |
213 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" | |
214 --datafieldscommon | |
215 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org" | |
216 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL, | |
217 http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID" | |
218 -r CmpdDataForPubChem -o Sample1.sdf | |
219 | |
220 And to add a publication date and request a release data using | |
221 PUBCHEM_PUBLICATION_DATE and PUBCHEM_DEPOSITOR_RECORD_DATE data fields | |
222 along with all the data fields in earlier examples, type: optional | |
223 fields, type: | |
224 | |
225 % ModifySDFilesDataFields.pl --molnamemode datafield | |
226 --molnamereplace always --molname Mol_ID --mode both | |
227 --datafieldsmap | |
228 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; | |
229 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" | |
230 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL, | |
231 http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID" | |
232 --datafieldscommon | |
233 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org, | |
234 PUBCHEM_PUBLICATION_DATE,YYY-MM-DD, | |
235 PUBCHEM_DEPOSITOR_RECORD_DATE,YYYY-MM-DD" | |
236 -r CmpdDataForPubChem -o Sample1.sdf | |
237 | |
238 AUTHOR | |
239 Manish Sud <msud@san.rr.com> | |
240 | |
241 SEE ALSO | |
242 InfoSDFiles.pl, JoinSDFiles.pl, MergeTextFilesWithSD.pl, | |
243 SplitSDFiles.pl, SDFilesToHTML.pl | |
244 | |
245 COPYRIGHT | |
246 Copyright (C) 2015 Manish Sud. All rights reserved. | |
247 | |
248 This file is part of MayaChemTools. | |
249 | |
250 MayaChemTools is free software; you can redistribute it and/or modify it | |
251 under the terms of the GNU Lesser General Public License as published by | |
252 the Free Software Foundation; either version 3 of the License, or (at | |
253 your option) any later version. | |
254 |