Bio::ToolBox - merge_datasets

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merge_datasets.pl

A program to merge columns of two or more data files.

SYNOPSIS

merge_datasets.pl [–options…] <file1> <file2> …

Merge options:
-l --lookup                      lookup rows by specific value
-a --auto                        automatically select unique columns
-m --manual                      manually select lookup and each data column
-x --index <number,letter,range> specify columns: 1st file numbers, 2nd letters 
-n --lookupname <text>           name of lookup column
-c --coordinate                  use coordinate string as lookup

General options:
-o --out <filename>              default first file
-z --gz                          compress output
-v --version                     print version and exit
-h --help                        show full documentation

OPTIONS

The command line flags and descriptions:

Merge options

• –lookup

  Force the program to merge data by using lookup values in each file. Enable this option if the data rows are not sorted identically. This will be done automatically if the number of data rows are not equal between the files.

• –auto

  Execute in automatic mode, where all columns from the first data file are retained, and only uniquely named or Score columns from subsequent data files are merged. If lookup is enabled, then an appropriate lookup column will be chosen.

• –manual

  Execute in full manual mode, where columns for lookup and merge are chosen interactively from lists.

• –index <number,letter,range>

  For advanced users, provide the list of indices to merge from both datasets. The format is the same as in the interactive mode. Column indices from the first file are represented by numbers, the second file by letters. Values are comma-delimited, and ranges may be provided as “start-stop”. To indicate indices from subsequent files, provide separate –index options for each subsequent file. The default is to run the program interactively.

• –lookupname <text>

• –lun <text>

  Provide an alternate column name to identify the columns automatically in the input files containing the lookup values when performing the lookup. Each file should have the same lookup column name. Default values include ‘Name’, ‘ID’, ‘Transcript’, or ‘Gene’.

• –coordinate

  Use genomic coordinates when performing a lookup. Both 1-base and 0-base coordinate files can be safely and effectively matched. The generated coordinates column is temporary. This is automatically enabled when working with coordinate files, such as BED and GFF. This may be disabled by specifying –nocoordinate, or simply specifying a column lookup name.

General options

• –out <filename>

  Specify the output filename. By default it uses the first file name. Required in automatic mode.

• –gz

  Specify whether (or not) the output file should be compressed with gzip.

• –version

  Print the version number.

• –help

  Display this POD documentation.

DESCRIPTION

This program will merge two or more tab-delimited data files into one file. Datasets or columns from each file are merged together into an output file. Columns are appended to the end (after the rightmost column).

The columns may be specified using one of three methods. By default, the program is run in an interactive mode allowing the columns to be chosen from a presented list for each input file provided. Second, the columns may be specified manually on the command line using one or more –index options. Third, the program may be executed in full automatic mode, where uniquely named datasets from subsequent files are automatically appended to the first file. Score columns from specific formatted files (BED, BedGraph, GFF) are also automatically taken.

The program blindly assumes that rows (features) are equivalent and in the same order for all of the datasets. However, if there are an unequal number of data rows, or the user forces by using the –lookup option, then dataset values are looked up first using specified lookup values before merging (compare with Excel VLOOKUP function). In this case, the dataset lookup indices from each file are identified automatically. Potential lookup columns include ‘Name’, ‘ID’, ‘Transcript’, ‘Gene’, or any user provided name (using the –lookupname option). Files with genomic coordinates, including GFF and BED, may use a temporary coordinate string derived from the features coordinates. If a lookup column can not be identified automatically, then they are chosen interactively.

When a lookup is performed, the first index in the order determines which file is dominant, meaning that all rows from that file are included, and only the rows that match by the lookup value are included from the second file. Null values are recorded when no match is found in the second file.

After merging in interactive mode only, an opportunity for interactively renaming the dataset names is presented.

AUTHOR

Timothy J. Parnell, PhD
Howard Hughes Medical Institute
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.