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1
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1 NAME
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2 MergeTextFilesWithSD.pl - Merge CSV or TSV TextFile(s) into SDFile
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3
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4 SYNOPSIS
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5 MergeTextFilesWithSD.pl SDFile TextFile(s)...
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6
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7 MergeTextFilesWithSD.pl [-h, --help] [--indelim comma | semicolon] [-c,
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8 --columns colnum,...;... | collabel,...;...] [-k, --keys colkeynum;... |
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9 colkeylabel;...] [-m, --mode colnum | collabel] [-o, --overwrite] [-r,
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10 --root rootname] [-s, --sdkey sdfieldname] [-w, --workingdir dirname]
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11 SDFile TextFile(s)...
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12
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13 DESCRIPTION
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14 Merge multiple CSV or TSV *TextFile(s)* into *SDFile*. Unless -k --keys
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15 option is used, data rows from all *TextFile(s)* are added to *SDFile*
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16 in a sequential order, and the number of compounds in *SDFile* is used
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17 to determine how many rows of data are added from *TextFile(s)*.
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18
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19 Multiple *TextFile(s)* names are separated by spaces. The valid file
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20 extensions are *.csv* and *.tsv* for comma/semicolon and tab delimited
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21 text files respectively. All other file names are ignored. All the text
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22 files in a current directory can be specified by **.csv*, **.tsv*, or
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23 the current directory name. The --indelim option determines the format
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24 of *TextFile(s)*. Any file which doesn't correspond to the format
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25 indicated by --indelim option is ignored.
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26
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27 OPTIONS
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28 -h, --help
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29 Print this help message.
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30
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31 --indelim *comma | semicolon*
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32 Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
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33 semicolon*. Default value: *comma*. For TSV files, this option is
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34 ignored and *tab* is used as a delimiter.
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35
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36 -c, --columns *colnum,...;... | collabel,...;...*
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37 This value is mode specific. It is a list of columns to merge into
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38 *SDFile* specified by column numbers or labels for each text file
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39 delimited by ";". All *TextFile(s)* are merged into *SDFile*.
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40
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41 Default value: *all;all;...*. By default, all columns from
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42 TextFile(s) are merged into *SDFile*.
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43
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44 For *colnum* mode, input value format is:
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45 *colnum,...;colnum,...;...*. Example:
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46
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47 "1,2;1,3,4;7,8,9"
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48
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49 For *collabel* mode, input value format is:
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50 *collabel,...;collabel,...;...*. Example:
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51
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52 "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg"
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53
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54 -k, --keys *colkeynum;... | colkeylabel;...*
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55 This value is mode specific. It specifies column keys to use for
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56 merging *TextFile(s)* into *SDFile*. The column keys, delimited by
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57 ";", are specified by column numbers or labels for *TextFile(s)*.
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58
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59 By default, data rows from *TextFile(s)* are merged into *SDFile* in
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60 the order they appear.
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61
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62 For *colnum* mode, input value format is:*colkeynum, colkeynum;...*.
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63 Example:
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64
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65 "1;3;7"
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66
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67 For *collabel* mode, input value format is:*colkeylabel,
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68 colkeylabel;...*. Example:
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69
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70 "Mol_Id;Mol_Id;Cmpd_Id"
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71
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72 -m, --mode *colnum | collabel*
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73 Specify how to merge *TextFile(s)* into *SDFile*: using column
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74 numbers or column labels. Possible values: *colnum or collabel*.
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75 Default value: *colnum*.
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76
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77 -o, --overwrite
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78 Overwrite existing files.
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79
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80 -r, --root *rootname*
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81 New SD file name is generated using the root: <Root>.sdf. Default
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82 file name:
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83 <InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf.
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84
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85 -s, --sdkey *sdfieldname*
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86 *SDFile* data field name used as a key to merge data from
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87 TextFile(s). By default, data rows from *TextFile(s)* are merged
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88 into *SDFile* in the order they appear.
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89
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90 -w, --workingdir *dirname*
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91 Location of working directory. Default: current directory.
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92
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93 EXAMPLES
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94 To merge Sample1.csv and Sample2.csv into Sample.sdf and generate
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95 NewSample.sdf, type:
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96
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97 % MergeTextFileswithSD.pl -r NewSample -o Sample.sdf
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98 Sample1.csv Sample2.csv
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99
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100 To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf
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101 file, type:
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102
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103 % MergeTextFilesWithSD.pl -r NewSample -o Sample.sdf
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104 Sample*.tsv
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105
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106 To merge column numbers "1,2" and "3,4,5" from Sample2.csv and
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107 Sample3.csv into Sample.sdf and to generate NewSample.sdf, type:
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108
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109 % MergeTextFilesWithSD.pl -r NewSample -m colnum -c "1,2;3,4,5"
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110 -o Sample.sdf Sample1.csv Sample2.csv
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111
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112 To merge column "Mol_ID,Formula,MolWeight" and "Mol_ID,ChemBankID,NAME"
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113 from Sample1.csv and Sample2.csv into Sample.sdf using "Mol_ID" as SD
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114 and column keys to generate NewSample.sdf, type:
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115
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116 % MergeTextFilesWithSD.pl -r NewSample -s Mol_ID -k "Mol_ID;Mol_ID"
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117 -m collabel -c "Mol_ID,Formula,MolWeight;Mol_ID,ChemBankID,NAME"
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118 -o Sample1.sdf Sample1.csv Sample2.csv
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119
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120 AUTHOR
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121 Manish Sud <msud@san.rr.com>
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122
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123 SEE ALSO
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124 ExtractFromSDFiles.pl, FilterSDFiles.pl, InfoSDFiles.pl, JoinSDFiles.pl,
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125 JoinTextFiles.pl, MergeTextFiles.pl, ModifyTextFilesFormat.pl,
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126 SplitSDFiles.pl, SplitTextFiles.pl
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127
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128 COPYRIGHT
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129 Copyright (C) 2015 Manish Sud. All rights reserved.
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130
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131 This file is part of MayaChemTools.
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132
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133 MayaChemTools is free software; you can redistribute it and/or modify it
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134 under the terms of the GNU Lesser General Public License as published by
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135 the Free Software Foundation; either version 3 of the License, or (at
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136 your option) any later version.
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137
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