This program reads a FASTA file and displays statistics on the number of proteins and number of residues. It also verifies that the protein names, descriptions, and sequences are in the correct format.
This is a command line program. For a graphical (GUI) program, see the Protein Digestion Simulator which includes a FASTA file validation window. The executable for Protein Digestion Simulator is available on AppVeyor or on GitHub
The latest version of the application may be available on the AppVeyor CI server,
but builds are deleted after 6 months.
Otherwise, see the GitHub release page
The program can optionally create a new, fixed version of the FASTA file where proteins with duplicate sequences have been consolidated, and proteins with duplicate names have been renamed.
To remove duplicates from huge fasta files (over 1 GB in size), first create the ProteinHashes.txt file by calling this program with:
ValidateFastaFile.exe Proteins.fasta /B /SkipDupeSeqCheck /SkipDupeNameCheck
Next call the program again, providing the name of the ProteinHashes file:
ValidateFastaFile.exe Proteins.fasta /HashFile:Proteins_ProteinHashes.txt
- Download Validate-Fasta-File.zip from AppVeyor
- Alternatively, download from the GitHub release page
- Extract the files
- Run ValidateFastaFile.exe from the the command prompt
ValidateFastaFile.exe
/I:InputFilePath.fasta [/O:OutputDirectoryPath]
[/P:ParameterFilePath] [/C]
[/F] [/R] [/D] [/L] [/V] [/KeepSameName]
[/AllowDash] [/AllowAsterisk]
[/SkipDupeNameCheck] [/SkipDupeSeqCheck]
[/B] [/HashFile]
[/X] [/S:[MaxLevel]] [/Q]
The input file path can contain the wildcard character * and should point to a fasta file
The output directory path is optional, and will be used if /C, /F, or /B is used
- If omitted, the output stats file will be created in the directory containing the .Exe file.
The parameter file path is optional
- If included, it should point to a valid XML parameter file.
Use /C to specify that an output file should be created, rather than displaying the results on the screen.
Use /F to generate a new, fixed .Fasta file (long protein names will be auto-shortened)
- At the same time, a file with protein names and hash values for each unique protein sequences will be generated (_UniqueProteinSeqs.txt)
- This file will also list the other proteins that have duplicate sequences as the first protein mapped to each sequence
- If duplicate sequences are found, an easily parseable mapping file will also be created (_UniqueProteinSeqDuplicates.txt)
Use /R to rename proteins with duplicate names when using /F to generate a fixed fasta file
Use /D to consolidate proteins with duplicate protein sequences when using /F to generate a fixed fasta file.
Use /L to ignore I/L (isoleucine vs. leucine) differences when consolidating
proteins with duplicate protein sequences while generating a fixed fasta file
Use /V to remove invalid residues (non-letter characters, including an asterisk) when using /F to generate a fixed fasta file
Use /KeepSameName to keep proteins with the same name but differing sequences
when using /F to generate a fixed fasta file (if they have the same name and
same sequence, will only retain one entry)
- Ignored if
/Ror/Dis used
Use /AllowDash to allow a - in residues
use /AllowAsterisk to allow * in residues
When parsing large fasta files, you can reduce the memory used by disabling the checking for duplicates
/SkipDupeSeqCheckdisables duplicate sequence checking (which can require a large amount of memory)/SkipDupeNameCheckdisables duplicate name checking (which typically requires less memory)
Use /B to save a hash info file (even if not consolidating duplicates)
- This is useful for parsing a large fasta file to obtain the sequence hash for each protein, since hash values are not cached in memory, thus very little memory is required
Use /HashFile to specify a pre-computed hash file to use for determining which proteins to keep when generating a fixed fasta file
- Use of
/HashFileautomatically enables/Fand automatically disables/D,/R, and/B
Use /X to specify that a model XML parameter file should be created
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
The optional /Q switch will suppress all error messages.
Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
Licensed under the Apache License, Version 2.0; you may not use this program except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0