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diff mayachemtools/docs/scripts/man1/MergeTextFilesWithSD.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/MergeTextFilesWithSD.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,272 @@ +.\" 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" +MergeTextFilesWithSD.pl \- Merge CSV or TSV TextFile(s) into SDFile +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +MergeTextFilesWithSD.pl SDFile TextFile(s)... +.PP +MergeTextFilesWithSD.pl [\fB\-h, \-\-help\fR] [\fB\-\-indelim\fR comma | semicolon] +[\fB\-c, \-\-columns\fR colnum,...;... | collabel,...;...] [\fB\-k, \-\-keys\fR colkeynum;... | colkeylabel;...] +[\fB\-m, \-\-mode\fR colnum | collabel] [\fB\-o, \-\-overwrite\fR] [\fB\-r, \-\-root\fR rootname] +[\fB\-s, \-\-sdkey\fR sdfieldname] [\fB\-w, \-\-workingdir\fR dirname] SDFile TextFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Merge multiple \s-1CSV\s0 or \s-1TSV\s0 \fITextFile(s)\fR into \fISDFile\fR. Unless \fB\-k \-\-keys\fR +option is used, data rows from all \fITextFile(s)\fR are added to \fISDFile\fR in a +sequential order, and the number of compounds in \fISDFile\fR is used to determine +how many rows of data are added from \fITextFile(s)\fR. +.PP +Multiple \fITextFile(s)\fR names are separated by spaces. 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\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.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\-c, \-\-columns\fR \fIcolnum,...;... | collabel,...;...\fR" 4 +.IX Item "-c, --columns colnum,...;... | collabel,...;..." +This value is mode specific. It is a list of columns to merge into \fISDFile\fR +specified by column numbers or labels for each text file delimited by \*(L";\*(R". +All \fITextFile(s)\fR are merged into \fISDFile\fR. +.Sp +Default value: \fIall;all;...\fR. By default, all columns from TextFile(s) are +merged into \fISDFile\fR. +.Sp +For \fIcolnum\fR mode, input value format is: \fIcolnum,...;colnum,...;...\fR. Example: +.Sp +.Vb 1 +\& "1,2;1,3,4;7,8,9" +.Ve +.Sp +For \fIcollabel\fR mode, input value format is: \fIcollabel,...;collabel,...;...\fR. Example: +.Sp +.Vb 1 +\& "MW,SumNO;SumNHOH,ClogP,PSA;MolName,Mol_Id,Extreg" +.Ve +.IP "\fB\-k, \-\-keys\fR \fIcolkeynum;... | colkeylabel;...\fR" 4 +.IX Item "-k, --keys colkeynum;... | colkeylabel;..." +This value is mode specific. It specifies column keys to use for merging +\&\fITextFile(s)\fR into \fISDFile\fR. The column keys, delimited by \*(L";\*(R", are specified by column +numbers or labels for \fITextFile(s)\fR. +.Sp +By default, data rows from \fITextFile(s)\fR are merged into \fISDFile\fR in the order they appear. +.Sp +For \fIcolnum\fR mode, input value format is:\fIcolkeynum, colkeynum;...\fR. Example: +.Sp +.Vb 1 +\& "1;3;7" +.Ve +.Sp +For \fIcollabel\fR mode, input value format is:\fIcolkeylabel, colkeylabel;...\fR. Example: +.Sp +.Vb 1 +\& "Mol_Id;Mol_Id;Cmpd_Id" +.Ve +.IP "\fB\-m, \-\-mode\fR \fIcolnum | collabel\fR" 4 +.IX Item "-m, --mode colnum | collabel" +Specify how to merge \fITextFile(s)\fR into \fISDFile\fR: using column numbers or column labels. +Possible values: \fIcolnum or collabel\fR. Default value: \fIcolnum\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New \s-1SD\s0 file name is generated using the root: <Root>.sdf. Default file name: +<InitialSDFileName>MergedWith<FirstTextFileName>1To<Count>.sdf. +.IP "\fB\-s, \-\-sdkey\fR \fIsdfieldname\fR" 4 +.IX Item "-s, --sdkey sdfieldname" +\&\fISDFile\fR data field name used as a key to merge data from TextFile(s). By default, +data rows from \fITextFile(s)\fR are merged into \fISDFile\fR in the order they appear. +.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 merge Sample1.csv and Sample2.csv into Sample.sdf and generate +NewSample.sdf, type: +.PP +.Vb 2 +\& % MergeTextFileswithSD.pl \-r NewSample \-o Sample.sdf +\& Sample1.csv Sample2.csv +.Ve +.PP +To merge all Sample*.tsv into Sample.sdf and generate NewSample.sdf file, type: +.PP +.Vb 2 +\& % MergeTextFilesWithSD.pl \-r NewSample \-o Sample.sdf +\& Sample*.tsv +.Ve +.PP +To merge column numbers \*(L"1,2\*(R" and \*(L"3,4,5\*(R" from Sample2.csv and Sample3.csv +into Sample.sdf and to generate NewSample.sdf, type: +.PP +.Vb 2 +\& % MergeTextFilesWithSD.pl \-r NewSample \-m colnum \-c "1,2;3,4,5" +\& \-o Sample.sdf Sample1.csv Sample2.csv +.Ve +.PP +To merge column \*(L"Mol_ID,Formula,MolWeight\*(R" and \*(L"Mol_ID,ChemBankID,NAME\*(R" +from Sample1.csv and Sample2.csv into Sample.sdf using \*(L"Mol_ID\*(R" as \s-1SD\s0 and column keys +to generate NewSample.sdf, type: +.PP +.Vb 3 +\& % 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 +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +ExtractFromSDFiles.pl, FilterSDFiles.pl, InfoSDFiles.pl, JoinSDFiles.pl, JoinTextFiles.pl, +MergeTextFiles.pl, ModifyTextFilesFormat.pl, SplitSDFiles.pl, SplitTextFiles.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.