Fasta File Splitter

Overview

This program reads a protein FASTA file and splits it apart into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.

Use the /N switch to the define the number of files to create.

Alternatively, use the /MB switch to specify the size of each file.

Examples: FastaFileSplitter.exe H_sapiens_IPI_2008-02-07.fasta /N:25 FastaFileSplitter.exe H_sapiens_IPI_2008-02-07.fasta /MB:50

Syntax

FastaFileSplitter.exe /I:SourceFastaFile [/O:OutputDirectoryPath]
 [/N:SplitCount] [/MB:TargetSizeMB] [/P:ParameterFilePath]
 [/S:[MaxLevel]] [/A:AlternateOutputDirectoryPath] [/R] [/L]

The input file path can contain the wildcard character * and should point to a FASTA file. The output directory switch is optional. If omitted, the output file will be created in the same directory as the input file.

Use /N to define the number of parts to split the input file into.

• For example, /N:10 will split the input FASTA file into 10 parts

Alternatively, use /MB to specify the size of the split FASTA files, in MB (minimum 5 MB)

• For example, /MB:100 will create separate FASTA files that are each ~100 MB in size
• If both /N and /MB are specified, /N will be ignored

The parameter file path is optional.

• If included, it should point to a valid XML parameter file.

Use /S to process all valid files in the input directory and subdirectories. Include a number after /S (like /S:2) to limit the level of subdirectories to examine.

• When using /S, you can redirect the output of the results using /A
• When using /S, you can use /R to re-create the input directory hierarchy in the alternate output directory (if defined)

Use /L to log messages to a file.

Contacts

Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://omics.pnl.gov/ or https://panomics.pnnl.gov/

License

The FASTA File Splitter is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2021 Battelle Memorial Institute