py_fasta_validator

A Python extension of the fasta validator

This is a Python C-extension to validate a fasta file. It only checks a few things, and by default only sets its response via the return code, so you will need to check that in your Python code. See the examples provided.

The simple rules that we adhere to are:

1. Each header line starts with a >. The header preceedes the sequence.
2. Every other line is considered a sequence line
3. Sequence lines may not contain whitespace, numbers, or non-sequence characters. In other words, they must only contain the characters [A-Z] and [a-z]
4. Sequence lines can end with a new line or return depending on whether you have edited this file on a mac, pc, or linux machine.
5. Sequence lines can be empty.
6. The sequence identifier is the string of characters in the header line following the > and upto the first whitespace. Everything after the first whitespace is descriptive, and can be as long as you like
7. Each sequence identifier must be unique within the fasta file.

We will exit with the following return codes:

• 0 this is a valid fasta file
• 1 the first line does not start with a > (rule 1 violated).
• 2 there are duplicate sequence identifiers in the file (rule 7 violated)
• 4 there are characters in a sequence line other than [A-Za-z]

Other exit codes (e.g. 255, 254, etc) indicate internal errors in the program.

Prerequisites

fasta validator is written in ANSI C but you will also need the Python developers toolkit (e.g. python-3.x-dev installed on your machine to provide Python.h)

Installation

Everyone

Install with pip:

pip3 install pyfastavalidator

Advanced

To clone the code from GitHub use:

git clone https://github.com/linsalrob/fasta_validator.git
cd fasta_validator

To build the code, use:

make

This should compile the source into an executable in the current working directory.

Please note, if you get an error like this:

gcc  -Wall -o fasta_validate ./fasta_validate.c -I/usr/include/python3.8 -I/usr/include/x86_64-linux-gnu/python3.8
/usr/bin/ld: /tmp/ccgvrFaq.o: in function `python_input':
fasta_validate.c:(.text+0x481): undefined reference to `PyArg_ParseTuple'
/usr/bin/ld: fasta_validate.c:(.text+0x48c): undefined reference to `PyExc_RuntimeError'
/usr/bin/ld: fasta_validate.c:(.text+0x49b): undefined reference to `PyErr_SetString'
/usr/bin/ld: fasta_validate.c:(.text+0x4c3): undefined reference to `PyLong_FromLong'
/usr/bin/ld: /tmp/ccgvrFaq.o: in function `PyInit_fastaValidator':
fasta_validate.c:(.text+0x4f2): undefined reference to `PyModule_Create2'
collect2: error: ld returned 1 exit status
make: *** [Makefile:9: all] Error 1

Then we need to append the version of python to the make command. I am (currently) running python3.8 and the command to compile without error is:

make CFLAGS=-lpython3.8

I don't know the exact cause of this error, but pkg-config --libs python3 is not reporting anything when it should report -lpython3.8

To install this code as root (sudo) you can use:

make install

and this will copy the executable to /usr/local/bin.

to install it as a user, just copy the compiled binary fasta_validate to somewhere on your path.

Testing

To test the code you can use the example provided.

python3 example_validations.py -f test/good.fasta

or you can run that example on all the tests:

for F in test/*; do
	python3 example_validations.py -f $F;
done

Citation

Please cite this as

Edwards, R.A. 2019. fasta_validate: a fast and efficient fasta validator written in pure C. DOI: 10.5281/zenodo.2532044

What is the difference between this and fasta_validator?

Not very much!

The original C code was written for the Search SRA project as we wanted to validate fasta files uploaded by users. That code is written in C, and does not require any additional libraries to install.

This version adds the Python hooks, and so it requires the Python development library to be installed. Therefore, we kept them as two separate projects, although you'll notice the C code is essentially the same!

License

This software is released using the MIT License