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diff mayachemtools/docs/scripts/man1/ElementalAnalysisTextFiles.1 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/man1/ElementalAnalysisTextFiles.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,284 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ElementalAnalysisTextFiles.pl \- Perform elemental analysis using formula column in TextFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ElementalAnalysisTextFiles.pl TextFile(s)... +.PP +ElementalAnalysisTextFiles.pl [\fB\-c, \-\-colmode\fR colnum | collabel] [\fB\-d, \-\-detail\fR infolevel] [\fB\-f, \-\-fast\fR] +[\fB\-f, \-\-formulacol\fR colnum | collabel] [\fB\-h, \-\-help\fR] [\fB\-\-indelim\fR comma | semicolon] +[\fB\-m, \-\-mode\fR All | \*(L"ElementalAnysis, [MolecularWeight, ExactMass]\*(R"] [\fB\-o, \-\-overwrite\fR] +[\fB\-\-outdelim\fR comma | tab | semicolon] [\fB\-p, \-\-precision\fR number] [\fB\-q, \-\-quote\fR yes | no] +[\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-startcol\fR colnum | collabel] [\fB\-\-startcolmode\fR before | after] +\&\fB\-v \-\-valuecollabels\fR [Name, Label, [Name, Label,...]] [\fB\-w, \-\-workingdir\fR dirname] TextFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Perform elemental analysis using molecular formula column specified by a column number or label in +\&\fITextFile(s)\fR. +.PP +In addition to straightforward molecular formulas \- H2O, HCl, C3H7O2N \- +other supported variations are: Ca3(\s-1PO4\s0)2, [PCl4]+, [Fe(\s-1CN\s0)6]4\-, C37H42N2O6+2, Na2CO3.10H2O, +8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including +D and T, are not supported. +.PP +The valid file extensions are \fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab delimited +text files respectively. All other file names are ignored. All the text files in a +current directory can be specified by \fI*.csv\fR, \fI*.tsv\fR, or the current directory +name. The \fB\-\-indelim\fR option determines the format of \fITextFile(s)\fR. Any file +which doesn't correspond to the format indicated by \fB\-\-indelim\fR option is ignored. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-c, \-\-colmode\fR \fIcolnum | collabel\fR" 4 +.IX Item "-c, --colmode colnum | collabel" +Specify how columns are identified in \fITextFile(s)\fR: using column number or column +label. Possible values: \fIcolnum or collabel\fR. Default value: \fIcolnum\fR. +.IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4 +.IX Item "-d, --detail infolevel" +Level of information to print about lines being ignored. Default: \fI1\fR. Possible values: +\&\fI1, 2 or 3\fR. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-\-fast\fR" 4 +.IX Item "--fast" +In this mode, the formula column specified using \fB\-f, \-\-formulacol\fR option is assumed +to contain valid molecular formula data and initial formula validation check is skipped. +.IP "\fB\-f, \-\-formulacol\fR \fIcol number | col name\fR" 4 +.IX Item "-f, --formulacol col number | col name" +This value is mode specific. It specifies molecular formula column to use for performing +elemental analysis on \fITextFile(s)\fR. Possible values: \fIcol number or col label\fR. +Default value: \fIfirst column containing the word formula in its column label\fR. +.ie n .IP "\fB\-m, \-\-mode\fR \fIAll | ""ElementalAnalysis,[MolecularWeight,ExactMass]""\fR" 4 +.el .IP "\fB\-m, \-\-mode\fR \fIAll | ``ElementalAnalysis,[MolecularWeight,ExactMass]''\fR" 4 +.IX Item "-m, --mode All | ElementalAnalysis,[MolecularWeight,ExactMass]" +Specify what values to calculate using molecular formula in \fITextFile(s)\fR: calculate all supported +values or specify a comma delimited list of values. Possible values: \fIAll | \*(L"ElementalAnalysis, +[MolecularWeight, ExactMass]\*(R"\fR. Default: \fIAll\fR +.IP "\fB\-\-indelim\fR \fIcomma | semicolon\fR" 4 +.IX Item "--indelim comma | semicolon" +Input delimiter for \s-1CSV\s0 \fITextFile(s)\fR. Possible values: \fIcomma or semicolon\fR. +Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored and \fItab\fR is used as a +delimiter. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--outdelim comma | tab | semicolon" +Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR. +.IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4 +.IX Item "-p, --precision number" +Precision of calculated values in the output file. Default: up to \fI2\fR decimal places. +Valid values: positive integers. +.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4 +.IX Item "-q, --quote yes | no" +Put quotes around column values in output text file. Possible values: \fIyes or +no\fR. Default value: \fIyes\fR. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New text file name is generated using the root: <Root>.<Ext>. Default new file +name: <InitialTextFileName>ElementalAnalysis.<Ext>. The csv, and tsv +<Ext> values are used for comma/semicolon, and tab delimited text files +respectively. This option is ignored for multiple input files. +.IP "\fB\-s, \-\-startcol\fR \fIcolnum | collabel\fR" 4 +.IX Item "-s, --startcol colnum | collabel" +This value is mode specific. It specifies the column in text files which is +used for start adding calculated column values. For \fIcolnum\fR mode, specify +column number and for \fIcollabel\fR mode, specify column label. +.Sp +Default value: \fIlast\fR. Start merge after the last column. +.IP "\fB\-\-startcolmode\fR \fIbefore | after\fR" 4 +.IX Item "--startcolmode before | after" +Start adding calculated column values after the \fB\-s, \-\-startcol\fR value. Possible values: \fIbefore or after\fR. +Default value: \fIafter\fR. +.IP "\fB\-v \-\-valuecollabels\fR \fIName,Label,[Name,Label,...]\fR" 4 +.IX Item "-v --valuecollabels Name,Label,[Name,Label,...]" +Specify column labels to use for calculated values. In general, it's a comma delimited +list of value name and column label pairs. Supported value names: \fIElementalAnalysis, +MolecularWeight, and ExactMass\fR. Default labels: \fIElementalAnalysis, MolecularWeight, +and ExactMass\fR. +.IP "\fB\-w, \-\-workingdir\fR \fIdirname\fR" 4 +.IX Item "-w, --workingdir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To perform elemental analysis, calculate molecular weight and exact mass using formulas +in a column with the word Formula in its column label and generate a new \s-1CSV\s0 text +file NewSample1.csv, type: +.PP +.Vb 1 +\& % ElementalAnalysisTextFiles.pl \-o \-r NewSample1 Sample1.csv +.Ve +.PP +To perform elemental analysis using formulas in column number two, use column label +Analysis for calculated data, and generate a new \s-1CSV\s0 text file NewSample1.csv, type: +.PP +.Vb 3 +\& % ElementalAnalysisTextFiles.pl \-\-m ElementalAnalysis \-\-formulacol 2 +\& \-\-valuecollabels "ElementalAnalysis,Analysis" \-o \-r NewSample1 +\& Sample1.csv +.Ve +.PP +To calculate molecular weight using formula in column label Formula with four decimal +precision and generate a new \s-1CSV\s0 text file NewSample1.csv, type +.PP +.Vb 2 +\& % ElementalAnalysisTextFiles.pl \-\-m MolecularWeight \-\-colmode collabel +\& \-\-formulacol Formula \-\-precision 4 \-o \-r NewSample1 Sample1.csv +.Ve +.PP +To calculate exact mass using formula in column label Formula with four decimal +precision, adding column for exact mass right after Formula column, and generate a +new \s-1CSV\s0 text file NewSample1.csv, type +.PP +.Vb 3 +\& % ElementalAnalysisTextFiles.pl \-\-m ExactMass \-\-colmode collabel +\& \-\-formulacol Formula \-\-precision 4 \-\-startcolmode after +\& \-\-startcol Formula \-o \-r NewSample1 Sample1.csv +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.