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README.md

A Pedantic FASTA Parser and Tool Set

pfasta is a tool set for handling FASTA files and also comes with a pedantic parser.

Compilation and Installation

Compilation is simple.

git clone https://github.com/kloetzl/pfasta.git
cd pfasta
make
sudo make install

For increased error handling compile with libbsd support make WITH_LIBBSD=1. To change the installation directory use make DESTDIR=/usr/local install.

Tool Set

After compilation the main directory will contain a set of tools. They are designed to behave well on the commandline.

  • acgt: Reduce residues to the four canonical bases.
  • aln2dist: Convert an alignment to a distance matrix.
  • aln2maf: Convert an alignment to MAF.
  • cchar: Count the number of nucleotides.
  • concat: Concatenate sequences.
  • fancy_info: Print a fancy report.
  • format: Format sequences.
  • gc_content: Determine the GC content.
  • n50: Compute the N50.
  • revcomp: Compute the reverse complement.
  • shuffle: Shuffle a set of sequences.
  • sim: Simulate a set of genetic sequences.
  • split: Split a FASTA file into multiple files on a sequence basis.
  • validate: Check if a file conforms to the grammar given below.

Therein is also a wrapper program pfasta which bundles all of the tools at installation. Use the following command

pfasta format file.fasta

to format a file.

Parser

Even though FASTA is probably one of the simplest data formats ever created, a surprising amount of things can do wrong when trying to parse a FASTA file in C. pfasta was designed with pedantic error handling: It detects a lot of errors and also makes it easy to print useful warnings.

Grammar

A FASTA file contains one or more sequences. Each sequence consists of a header line with a name and an optional comment. Then follow multiple lines with the data. Here is a regex explaining what sequences are considered valid.

>[^[:space:]]+([^\n]*)\n
([-*a-zA-Z][^[:space:]]*[[:space:]]*)+

[:space:] refers to the character class defined by the respective C function isspace(3).

API Usage

To use the parser in your own tools, install the library and #include <pfasta.h>. You then have access to a number of simple functions to setup a parser and use it on files. For a complete example on their usage see tools/gc_content.c. Don't forget to link with -lpfasta.

struct pfasta_parser {
    const char *errstr;
    int done;
    /* internal data */
};

This structure holds a number of members to represent the state of the FASTA parser. Please make sure, that it is properly initialized before usage. Always free this structure when the parser is done.

struct pfasta_record {
    char *name, *comment, *sequence;
    size_t name_length, comment_length, sequence_length;
};

There is no magic to this structure. Its just a container of three strings. Feel free to duplicate or move them. But don't forget to free the data after usage!

struct pfasta_parser pfasta_parse(int);

This function initializes a pfasta_parser struct with a parser bound to a specific file descriptor. Iff an error occurred errstr is set to contain a suitable message. Otherwise you can read data from it as long as done isn't set. The parser should be freed after usage.

Please note that the user is responsible for opening the file descriptor as readable and closing after usage.

struct pfasta_record pfasta_read( struct pfasta_parser *);

Using a properly initialized parser, this function can read FASTA sequences. These are stored in the simple structure and returned. On error, the errstr property of the parser is set.

void pfasta_free( struct pfasta_parser *);
void pfasta_record_free( struct pfasta_record *);

These two functions free the resources allocated by the structures above.

If the preprocessor macro PFASTA_NO_THREADS is defined, the parser is not fully thread safe. It probably also is not thread safe with older compilers.

const char *pfasta_version(void);

Get a string defining the version of the pfasta library.

Releases

The tool set is not released as tarballs. Instead, versioning is done via git tags.

License

This code is open source software released under the permissive ISC license. See the LICENSE file for details.

Links

  • A good alternative to pfasta that also parses FASTQ files is kseq.h.
  • Another tool set written in Go is seqkit.
  • Please submit bugs at GitHub