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NAME

ExtractFromTextFiles.pl - Extract specific data from TextFile(s)

SYNOPSIS

ExtractFromTextFiles.pl TextFile(s)...

ExtractFromTextFiles.pl [-c, --colmode colnum | collabel] [--categorycol number | string] [--columns "colnum,[colnum]..." | "collabel,[collabel]..."] [-h, --help] [--indelim comma | semicolon] [-m, --mode columns | rows | categories] [-o, --overwrite] [--outdelim comma | tab | semicolon] [-q, --quote yes | no] [--rows "colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"] [ --rowsmode rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange] [-r, --root rootname] [-w, --workingdir dirname] TextFile(s)...

DESCRIPTION

Extract column(s)/row(s) data from TextFile(s) identified by column numbers or labels. Or categorize data using a specified column category. During categorization, a summary text file is generated containing category name and count; an additional text file, containing data for for each category, is also generated. The file names are separated by space. 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.

--categorycol number | string

Column used to categorize data. Default value: First column.

For colnum value of -c, --colmode option, input value is a column number. Example: 1.

For collabel value of -c, --colmode option, input value is a column label. Example: Mol_ID.

--columns "colnum,[colnum]..." | "collabel,[collabel]..."

List of comma delimited columns to extract. Default value: First column.

For colnum value of -c, --colmode option, input values format is: colnum,colnum,.... Example: 1,3,5

For collabel value of -c, --colmode option, input values format is: collabel,collabel,... Example: Mol_ID,MolWeight

-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.

-m, --mode columns | rows | categories

Specify what to extract from TextFile(s). Possible values: columns, rows, or categories. Default value: columns.

For columns mode, data for appropriate columns specified by --columns option is extracted from TextFile(s) and placed into new text files.

For rows mode, appropriate rows specified in conjuction with --rowsmode and rows options are extracted from TextFile(s) and placed into new text files.

For categories mode, coulmn specified by --categorycol is used to categorize data, and a summary text file is generated containing category name and count; an additional text file, containing data for for each category, is also generated.

-o, --overwrite

Overwrite existing files.

--outdelim comma | tab | semicolon.

Output text file delimiter. Possible values: comma, tab, or semicolon. Default value: comma

-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 file name is generated using the root: <Root>.<Ext>. Default for new file names: <TextFile>CategoriesSummary.<Ext>, <TextFile>ExtractedColumns.<Ext>, and <TextFile>ExtractedRows.<Ext> for categories, columns, and rows mode respectively. And <TextFile>Category<CategoryName>.<Ext> for each category retrieved from each text file. The output file type determines <Ext> value: csv and tsv for CSV, and TSV files respectively.

This option is ignored for multiple input files.

--rows "colid,value,criteria..." | "colid,value..." | "colid,mincolvalue,maxcolvalue" | "rownum,rownum,..." | colid | "minrownum,maxrownum"

This value is --rowsmode specific. In general, it's a list of comma separated column ids and associated mode specific value. Based on Column ids specification, column label or number, is controlled by -c, --colmode option.

First line containing column labels is always written out. And value comparisons assume numerical column data.

For rowsbycolvalue mode, input value format contains these triplets: colid,value, criteria.... Possible values for criteria: le, ge or eq. Examples:

MolWt,450,le
MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le

For rowsbycolvaluelist mode, input value format is: colid,value.... Examples:

Mol_ID,20
Mol_ID,20,1002,1115

For rowsbycolvaluerange mode, input value format is: colid,mincolvalue,maxcolvalue. Examples:

MolWt,100,450

For rowbymincolvalue, rowbymaxcolvalue modes, input value format is: colid.

For rownum mode, input value format is: rownum. Default value: 2.

For rownumrange mode, input value format is: minrownum, maxrownum. Examples:

10,40
--rowsmode rowsbycolvalue | rowsbycolvaluelist | rowsbycolvaluerange | rowbymincolvalue | rowbymaxcolvalue | rownums | rownumrange

Specify how to extract rows from TextFile(s). Possible values: rowsbycolvalue, rowsbycolvaluelist, rowsbycolvaluerange, rowbymincolvalue, rowbymaxcolvalue, rownum, rownumrange. Default value: rownum.

Use --rows option to list rows criterion used for extraction of rows from TextFile(s).

-w, --workingdir dirname

Location of working directory. Default: current directory.

EXAMPLES

To extract first column from a text file and generate a new CSV text file NewSample1.csv, type:

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

To extract columns Mol_ID, MolWeight, and NAME from Sample1.csv and generate a new textfile NewSample1.tsv with no quotes, type:

% ExtractFromTextFiles.pl -m columns -c collabel --columns "Mol_ID, MolWeight,NAME" --outdelim tab --quote no -r NewSample1 -o Sample1.csv

To extract rows containing values for MolWeight column of less than 450 from Sample1.csv and generate a new textfile NewSample1.csv, type:

% ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvalue -c collabel --rows MolWeight,450,le -r NewSample1 -o Sample1.csv

To extract rows containing values for MolWeight column between 400 and 500 from Sample1.csv and generate a new textfile NewSample1.csv, type:

% ExtractFromTextFiles.pl -m rows --rowsmode rowsbycolvaluerange -c collabel --rows MolWeight,450,500 -r NewSample1 -o Sample1.csv

To extract a row containing minimum value for column MolWeight from Sample1.csv and generate a new textfile NewSample1.csv, type:

% ExtractFromTextFiles.pl -m rows --rowsmode rowbymincolvalue -c collabel --rows MolWeight -r NewSample1 -o Sample1.csv

AUTHOR

Manish Sud

SEE ALSO

JoinTextFiles.plMergeTextFilesWithSD.plModifyTextFilesFormat.plSplitTextFiles.pl

COPYRIGHT

Copyright (C) 2017 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.

 

 

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