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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ELEMENTALANALYSISTEXTFILES 1"
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127 .TH ELEMENTALANALYSISTEXTFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 ElementalAnalysisTextFiles.pl \- Perform elemental analysis using formula column in TextFile(s)
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ElementalAnalysisTextFiles.pl TextFile(s)...
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137 .PP
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138 ElementalAnalysisTextFiles.pl [\fB\-c, \-\-colmode\fR colnum | collabel] [\fB\-d, \-\-detail\fR infolevel] [\fB\-f, \-\-fast\fR]
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139 [\fB\-f, \-\-formulacol\fR colnum | collabel] [\fB\-h, \-\-help\fR] [\fB\-\-indelim\fR comma | semicolon]
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140 [\fB\-m, \-\-mode\fR All | \*(L"ElementalAnysis, [MolecularWeight, ExactMass]\*(R"] [\fB\-o, \-\-overwrite\fR]
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141 [\fB\-\-outdelim\fR comma | tab | semicolon] [\fB\-p, \-\-precision\fR number] [\fB\-q, \-\-quote\fR yes | no]
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142 [\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-startcol\fR colnum | collabel] [\fB\-\-startcolmode\fR before | after]
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143 \&\fB\-v \-\-valuecollabels\fR [Name, Label, [Name, Label,...]] [\fB\-w, \-\-workingdir\fR dirname] TextFile(s)...
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144 .SH "DESCRIPTION"
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145 .IX Header "DESCRIPTION"
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146 Perform elemental analysis using molecular formula column specified by a column number or label in
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147 \&\fITextFile(s)\fR.
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148 .PP
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149 In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \-
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150 other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)6]4\-, C37H42N2O6+2, Na2CO3.10H2O,
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151 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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152 D and T, are not supported.
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153 .PP
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154 The valid file extensions are \fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab delimited
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155 text files respectively. All other file names are ignored. All the text files in a
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156 current directory can be specified by \fI*.csv\fR, \fI*.tsv\fR, or the current directory
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157 name. The \fB\-\-indelim\fR option determines the format of \fITextFile(s)\fR. Any file
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158 which doesn't correspond to the format indicated by \fB\-\-indelim\fR option is ignored.
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159 .SH "OPTIONS"
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160 .IX Header "OPTIONS"
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161 .IP "\fB\-c, \-\-colmode\fR \fIcolnum | collabel\fR" 4
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162 .IX Item "-c, --colmode colnum | collabel"
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163 Specify how columns are identified in \fITextFile(s)\fR: using column number or column
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164 label. Possible values: \fIcolnum or collabel\fR. Default value: \fIcolnum\fR.
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165 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
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166 .IX Item "-d, --detail infolevel"
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167 Level of information to print about lines being ignored. Default: \fI1\fR. Possible values:
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168 \&\fI1, 2 or 3\fR.
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169 .IP "\fB\-h, \-\-help\fR" 4
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170 .IX Item "-h, --help"
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171 Print this help message.
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172 .IP "\fB\-\-fast\fR" 4
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173 .IX Item "--fast"
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174 In this mode, the formula column specified using \fB\-f, \-\-formulacol\fR option is assumed
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175 to contain valid molecular formula data and initial formula validation check is skipped.
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176 .IP "\fB\-f, \-\-formulacol\fR \fIcol number | col name\fR" 4
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177 .IX Item "-f, --formulacol col number | col name"
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178 This value is mode specific. It specifies molecular formula column to use for performing
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179 elemental analysis on \fITextFile(s)\fR. Possible values: \fIcol number or col label\fR.
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180 Default value: \fIfirst column containing the word formula in its column label\fR.
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181 .ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4
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182 .el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4
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183 .IX Item "-m, --mode All | ElementalAnalysis,[MolecularWeight,ExactMass]"
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184 Specify what values to calculate using molecular formula in \fITextFile(s)\fR: calculate all supported
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185 values or specify a comma delimited list of values. Possible values: \fIAll | \*(L"ElementalAnalysis,
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186 [MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR
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187 .IP "\fB\-\-indelim\fR \fIcomma | semicolon\fR" 4
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188 .IX Item "--indelim comma | semicolon"
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189 Input delimiter for \s-1CSV\s0 \fITextFile(s)\fR. Possible values: \fIcomma or semicolon\fR.
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190 Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored and \fItab\fR is used as a
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191 delimiter.
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192 .IP "\fB\-o, \-\-overwrite\fR" 4
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193 .IX Item "-o, --overwrite"
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194 Overwrite existing files.
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195 .IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4
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196 .IX Item "--outdelim comma | tab | semicolon"
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197 Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR
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198 Default value: \fIcomma\fR.
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199 .IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4
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200 .IX Item "-p, --precision number"
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201 Precision of calculated values in the output file. Default: up to \fI2\fR decimal places.
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202 Valid values: positive integers.
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203 .IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4
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204 .IX Item "-q, --quote yes | no"
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205 Put quotes around column values in output text file. Possible values: \fIyes or
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206 no\fR. Default value: \fIyes\fR.
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207 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4
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208 .IX Item "-r, --root rootname"
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209 New text file name is generated using the root: <Root>.<Ext>. Default new file
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210 name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv
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211 <Ext> values are used for comma/semicolon, and tab delimited text files
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212 respectively. This option is ignored for multiple input files.
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213 .IP "\fB\-s, \-\-startcol\fR \fIcolnum | collabel\fR" 4
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214 .IX Item "-s, --startcol colnum | collabel"
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215 This value is mode specific. It specifies the column in text files which is
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216 used for start adding calculated column values. For \fIcolnum\fR mode, specify
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217 column number and for \fIcollabel\fR mode, specify column label.
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218 .Sp
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219 Default value: \fIlast\fR. Start merge after the last column.
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220 .IP "\fB\-\-startcolmode\fR \fIbefore | after\fR" 4
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221 .IX Item "--startcolmode before | after"
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222 Start adding calculated column values after the \fB\-s, \-\-startcol\fR value. Possible values: \fIbefore or after\fR.
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223 Default value: \fIafter\fR.
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224 .IP "\fB\-v \-\-valuecollabels\fR \fIName,Label,[Name,Label,...]\fR" 4
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225 .IX Item "-v --valuecollabels Name,Label,[Name,Label,...]"
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226 Specify column labels to use for calculated values. In general, it's a comma delimited
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227 list of value name and column label pairs. Supported value names: \fIElementalAnalysis,
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228 MolecularWeight, and ExactMass\fR. Default labels: \fIElementalAnalysis, MolecularWeight,
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229 and ExactMass\fR.
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230 .IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4
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231 .IX Item "-w, --workingdir dirname"
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232 Location of working directory. Default: current directory.
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233 .SH "EXAMPLES"
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234 .IX Header "EXAMPLES"
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235 To perform elemental analysis, calculate molecular weight and exact mass using formulas
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236 in a column with the word Formula in its column label and generate a new \s-1CSV\s0 text
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237 file NewSample1.csv, type:
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238 .PP
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239 .Vb 1
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240 \& % ElementalAnalysisTextFiles.pl \-o \-r NewSample1 Sample1.csv
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241 .Ve
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242 .PP
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243 To perform elemental analysis using formulas in column number two, use column label
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244 Analysis for calculated data, and generate a new \s-1CSV\s0 text file NewSample1.csv, type:
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245 .PP
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246 .Vb 3
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247 \& % ElementalAnalysisTextFiles.pl \-\-m ElementalAnalysis \-\-formulacol 2
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248 \& \-\-valuecollabels "ElementalAnalysis,Analysis" \-o \-r NewSample1
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249 \& Sample1.csv
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250 .Ve
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251 .PP
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252 To calculate molecular weight using formula in column label Formula with four decimal
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253 precision and generate a new \s-1CSV\s0 text file NewSample1.csv, type
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254 .PP
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255 .Vb 2
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256 \& % ElementalAnalysisTextFiles.pl \-\-m MolecularWeight \-\-colmode collabel
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257 \& \-\-formulacol Formula \-\-precision 4 \-o \-r NewSample1 Sample1.csv
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258 .Ve
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259 .PP
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260 To calculate exact mass using formula in column label Formula with four decimal
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261 precision, adding column for exact mass right after Formula column, and generate a
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262 new \s-1CSV\s0 text file NewSample1.csv, type
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263 .PP
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264 .Vb 3
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265 \& % ElementalAnalysisTextFiles.pl \-\-m ExactMass \-\-colmode collabel
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266 \& \-\-formulacol Formula \-\-precision 4 \-\-startcolmode after
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267 \& \-\-startcol Formula \-o \-r NewSample1 Sample1.csv
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268 .Ve
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269 .SH "AUTHOR"
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270 .IX Header "AUTHOR"
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271 Manish Sud <msud@san.rr.com>
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272 .SH "SEE ALSO"
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273 .IX Header "SEE ALSO"
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274 AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl
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275 .SH "COPYRIGHT"
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276 .IX Header "COPYRIGHT"
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277 Copyright (C) 2015 Manish Sud. All rights reserved.
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278 .PP
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279 This file is part of MayaChemTools.
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280 .PP
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281 MayaChemTools is free software; you can redistribute it and/or modify it under
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282 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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283 Software Foundation; either version 3 of the License, or (at your option)
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284 any later version.
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