NAME
    ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula
    column in TextFile(s)

SYNOPSIS
    ElementalAnalysisTextFiles.pl TextFile(s)...

    ElementalAnalysisTextFiles.pl [-c, --colmode colnum | collabel] [-d,
    --detail infolevel] [-f, --fast] [-f, --formulacol colnum | collabel]
    [-h, --help] [--indelim comma | semicolon] [-m, --mode All |
    "ElementalAnysis, [MolecularWeight, ExactMass]"] [-o, --overwrite]
    [--outdelim comma | tab | semicolon] [-p, --precision number] [-q,
    --quote yes | no] [-r, --root rootname] [-s, --startcol colnum |
    collabel] [--startcolmode before | after] -v --valuecollabels [Name,
    Label, [Name, Label,...]] [-w, --workingdir dirname] TextFile(s)...

DESCRIPTION
    Perform elemental analysis using molecular formula column specified by a
    column number or label in *TextFile(s)*.

    In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
    other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)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.

    The valid file extensions are *.csv* and *.tsv* 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 **.csv*,
    **.tsv*, or the current directory name. The --indelim option determines
    the format of *TextFile(s)*. Any file which doesn't correspond to the
    format indicated by --indelim option is ignored.

OPTIONS
    -c, --colmode *colnum | collabel*
        Specify how columns are identified in *TextFile(s)*: using column
        number or column label. Possible values: *colnum or collabel*.
        Default value: *colnum*.

    -d, --detail *infolevel*
        Level of information to print about lines being ignored. Default:
        *1*. Possible values: *1, 2 or 3*.

    -h, --help
        Print this help message.

    --fast
        In this mode, the formula column specified using -f, --formulacol
        option is assumed to contain valid molecular formula data and
        initial formula validation check is skipped.

    -f, --formulacol *col number | col name*
        This value is mode specific. It specifies molecular formula column
        to use for performing elemental analysis on *TextFile(s)*. Possible
        values: *col number or col label*. Default value: *first column
        containing the word formula in its column label*.

    -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
        Specify what values to calculate using molecular formula in
        *TextFile(s)*: calculate all supported values or specify a comma
        delimited list of values. Possible values: *All |
        "ElementalAnalysis, [MolecularWeight, ExactMass]"*. Default: *All*

    --indelim *comma | semicolon*
        Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
        semicolon*. Default value: *comma*. For TSV files, this option is
        ignored and *tab* is used as a delimiter.

    -o, --overwrite
        Overwrite existing files.

    --outdelim *comma | tab | semicolon*
        Output text file delimiter. Possible values: *comma, tab, or
        semicolon* Default value: *comma*.

    -p, --precision *number*
        Precision of calculated values in the output file. Default: up to
        *2* decimal places. Valid values: positive integers.

    -q, --quote *yes | no*
        Put quotes around column values in output text file. Possible
        values: *yes or no*. Default value: *yes*.

    -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.

    -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
        *colnum* mode, specify column number and for *collabel* mode,
        specify column label.

        Default value: *last*. Start merge after the last column.

    --startcolmode *before | after*
        Start adding calculated column values after the -s, --startcol
        value. Possible values: *before or after*. Default value: *after*.

    -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: *ElementalAnalysis, MolecularWeight, and
        ExactMass*. Default labels: *ElementalAnalysis, MolecularWeight, and
        ExactMass*.

    -w, --workingdir *dirname*
        Location of working directory. Default: current directory.

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 CSV text file NewSample1.csv, type:

        % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv

    To perform elemental analysis using formulas in column number two, use
    column label Analysis for calculated data, and generate a new CSV text
    file NewSample1.csv, type:

        % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2
          --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1
          Sample1.csv

    To calculate molecular weight using formula in column label Formula with
    four decimal precision and generate a new CSV text file NewSample1.csv,
    type

        % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel
          --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv

    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 CSV text file NewSample1.csv, type

        % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel
          --formulacol Formula --precision 4 --startcolmode after
          --startcol Formula -o -r NewSample1 Sample1.csv

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

