view docs/scripts/txt/MergeTextFilesWithSD.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

NAME
    MergeTextFilesWithSD.pl - Merge CSV or TSV TextFile(s) into SDFile

SYNOPSIS
    MergeTextFilesWithSD.pl SDFile TextFile(s)...

    MergeTextFilesWithSD.pl [-h, --help] [--indelim comma | semicolon] [-c,
    --columns colnum,...;... | collabel,...;...] [-k, --keys colkeynum;... |
    colkeylabel;...] [-m, --mode colnum | collabel] [-o, --overwrite] [-r,
    --root rootname] [-s, --sdkey sdfieldname] [-w, --workingdir dirname]
    SDFile TextFile(s)...

DESCRIPTION
    Merge multiple CSV or TSV *TextFile(s)* into *SDFile*. Unless -k --keys
    option is used, data rows from all *TextFile(s)* are added to *SDFile*
    in a sequential order, and the number of compounds in *SDFile* is used
    to determine how many rows of data are added from *TextFile(s)*.

    Multiple *TextFile(s)* names are separated by spaces. 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
    -h, --help
        Print this help message.

    --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.

    -c, --columns *colnum,...;... | collabel,...;...*
        This value is mode specific. It is a list of columns to merge into
        *SDFile* specified by column numbers or labels for each text file
        delimited by ";". All *TextFile(s)* are merged into *SDFile*.

        Default value: *all;all;...*. By default, all columns from
        TextFile(s) are merged into *SDFile*.

        For *colnum* mode, input value format is:
        *colnum,...;colnum,...;...*. Example:

            "1,2;1,3,4;7,8,9"

        For *collabel* mode, input value format is:
        *collabel,...;collabel,...;...*. Example:

            "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg"

    -k, --keys *colkeynum;... | colkeylabel;...*
        This value is mode specific. It specifies column keys to use for
        merging *TextFile(s)* into *SDFile*. The column keys, delimited by
        ";", are specified by column numbers or labels for *TextFile(s)*.

        By default, data rows from *TextFile(s)* are merged into *SDFile* in
        the order they appear.

        For *colnum* mode, input value format is:*colkeynum, colkeynum;...*.
        Example:

            "1;3;7"

        For *collabel* mode, input value format is:*colkeylabel,
        colkeylabel;...*. Example:

            "Mol_Id;Mol_Id;Cmpd_Id"

    -m, --mode *colnum | collabel*
        Specify how to merge *TextFile(s)* into *SDFile*: using column
        numbers or column labels. Possible values: *colnum or collabel*.
        Default value: *colnum*.

    -o, --overwrite
        Overwrite existing files.

    -r, --root *rootname*
        New SD file name is generated using the root: <Root>.sdf. Default
        file name:
        <InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf.

    -s, --sdkey *sdfieldname*
        *SDFile* data field name used as a key to merge data from
        TextFile(s). By default, data rows from *TextFile(s)* are merged
        into *SDFile* in the order they appear.

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

EXAMPLES
    To merge Sample1.csv and Sample2.csv into Sample.sdf and generate
    NewSample.sdf, type:

        % MergeTextFileswithSD.pl -r NewSample -o Sample.sdf
          Sample1.csv Sample2.csv

    To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf
    file, type:

        % MergeTextFilesWithSD.pl -r NewSample -o Sample.sdf
          Sample*.tsv

    To merge column numbers "1,2" and "3,4,5" from Sample2.csv and
    Sample3.csv into Sample.sdf and to generate NewSample.sdf, type:

        % MergeTextFilesWithSD.pl -r NewSample -m colnum -c "1,2;3,4,5"
          -o Sample.sdf Sample1.csv Sample2.csv

    To merge column "Mol_ID,Formula,MolWeight" and "Mol_ID,ChemBankID,NAME"
    from Sample1.csv and Sample2.csv into Sample.sdf using "Mol_ID" as SD
    and column keys to generate NewSample.sdf, type:

        % MergeTextFilesWithSD.pl -r NewSample -s Mol_ID -k "Mol_ID;Mol_ID"
          -m collabel -c "Mol_ID,Formula,MolWeight;Mol_ID,ChemBankID,NAME"
          -o Sample1.sdf Sample1.csv Sample2.csv

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    ExtractFromSDFiles.pl, FilterSDFiles.pl, InfoSDFiles.pl, JoinSDFiles.pl,
    JoinTextFiles.pl, MergeTextFiles.pl, ModifyTextFilesFormat.pl,
    SplitSDFiles.pl, SplitTextFiles.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.