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.\" ========================================================================
.\"
.IX Title "ELEMENTALANALYSISTEXTFILES 1"
.TH ELEMENTALANALYSISTEXTFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  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 <[e-mail]>
.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.