Overview

This program reads one or more input FASTA files. For each file it computes a variety of statistics, and then prints a summary of the statistics as output.

In the examples below, $ indicates the command line prompt.

Licence

This program is released as open source software under the terms of MIT License.

Installing

Clone this repository:

$ git clone https://github.com/d-cameron/biodaniel

Move into the repository directory:

$ cd biodaniel

Biodaniel can be installed using pip in a variety of ways ($ indicates the command line prompt):

1. Inside a virtual environment:

$ python3 -m venv biodaniel_dev
$ source biodaniel_dev/bin/activate
$ pip install -U /path/to/biodaniel

2. Into the global package database for all users:

$ pip install -U /path/to/biodaniel

3. Into the user package database (for the current user only):

$ pip install -U --user /path/to/biodaniel

General behaviour

Biodaniel accepts zero or more FASTA filenames on the command line. If zero filenames are specified it reads a single FASTA file from the standard input device (stdin). Otherwise it reads each named FASTA file in the order specified on the command line. Biodaniel reads each input FASTA file, computes various statistics about the contents of the file, and then displays a tab-delimited summary of the statistics as output. Each input file produces at most one output line of statistics. Each line of output is prefixed by the input filename or by the text "stdin" if the standard input device was used.

Biodaniel processes each FASTA file one sequence at a time. Therefore the memory usage is proportional to the longest sequence in the file.

An optional command line argument --minlen can be supplied. Sequences with length strictly less than the given value will be ignored by biodaniel and do not contribute to the computed statistics. By default --minlen is set to zero.

These are the statistics computed by biodaniel, for all sequences with length greater-than-or-equal-to --minlen:

• NUMSEQ: the number of sequences in the file satisfying the minimum length requirement.
• TOTAL: the total length of all the counted sequences.
• MIN: the minimum length of the counted sequences.
• AVERAGE: the average length of the counted sequences rounded down to an integer.
• MAX: the maximum length of the counted sequences.

If there are zero sequences counted in a file, the values of MIN, AVERAGE and MAX cannot be computed. In that case biodaniel will print a dash (-) in the place of the numerical value. Note that when --minlen is set to a value greater than zero it is possible that an input FASTA file does not contain any sequences with length greater-than-or-equal-to the specified value. If this situation arises biodaniel acts in the same way as if there are no sequences in the file.

Help message

Biodaniel can display usage information on the command line via the -h or --help argument:

$ biodaniel -h
usage: biodaniel [-h] [--minlen N] [--version] [--log LOG_FILE]
                  [FASTA_FILE [FASTA_FILE ...]]

Print fasta stats

positional arguments:
  FASTA_FILE      Input FASTA files

optional arguments:
  -h, --help      show this help message and exit
  --minlen N      Minimum length sequence to include in stats (default 0)
  --version       show program's version number and exit
  --log LOG_FILE  record program progress in LOG_FILE

Reading FASTA files named on the command line

Biodaniel accepts zero or more named FASTA files on the command line. These must be specified following all other command line arguments. If zero files are named, biodaniel will read a single FASTA file from the standard input device (stdin).

There are no restrictions on the name of the FASTA files. Often FASTA filenames end in .fa or .fasta, but that is merely a convention, which is not enforced by biodaniel.

The example below illustrates biodaniel applied to a single named FASTA file called file1.fa:

$ biodaniel file1.fa
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
file1.fa	5264	3801855	31	722	53540

The example below illustrates biodaniel applied to three named FASTA files called file1.fa, file2.fa and file3.fa:

$ biodaniel file1.fa file2.fa file3.fa
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
file1.fa	5264	3801855	31	722	53540
file2.fa	5264	3801855	31	722	53540
file3.fa	5264	3801855	31	722	53540

Reading a single FASTA file from standard input

The example below illustrates biodaniel reading a FASTA file from standard input. In this example we have redirected the contents of a file called file1.fa into the standard input using the shell redirection operator <:

$ biodaniel < file1.fa
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
stdin	5264	3801855	31	722	53540

Equivalently, you could achieve the same result by piping a FASTA file into biodaniel:

$ cat file1.fa | biodaniel
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
stdin	5264	3801855	31	722	53540

Filtering sequences by length

Biodaniel provides an optional command line argument --minlen which causes it to ignore (not count) any sequences in the input FASTA files with length strictly less than the supplied value.

The example below illustrates biodaniel applied to a single FASTA file called file.fawith a--minlenfilter of1000`.

$ biodaniel --minlen 1000 file.fa
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
file1.fa	4711	2801855	1021	929	53540

Logging

If the --log FILE command line argument is specified, biodaniel will output a log file containing information about program progress. The log file includes the command line used to execute the program, and a note indicating which files have been processes so far. Events in the log file are annotated with their date and time of occurrence.

$ biodaniel --log bt.log file1.fasta file2.fasta 
# normal biodaniel output appears here
# contents of log file displayed below

$ cat bt.log
12/04/2016 19:14:47 program started
12/04/2016 19:14:47 command line: /usr/local/bin/biodaniel --log bt.log file1.fasta file2.fasta
12/04/2016 19:14:47 Processing FASTA file from file1.fasta
12/04/2016 19:14:47 Processing FASTA file from file2.fasta

Empty files

It is possible that the input FASTA file contains zero sequences, or, when the --minlen command line argument is used, it is possible that the file contains no sequences of length greater-than-or-equal-to the supplied value. In both of those cases biodaniel will not be able to compute minimum, maximum or average sequence lengths, and instead it shows output in the following way:

The example below illustrates biodaniel applied to a single FASTA file called empty.fa which contains zero sequences:

$ biodaniel empty.fa
FILENAME	NUMSEQ	TOTAL	MIN	AVG	MAX
empty.fa	0	0	-	-	-

Exit status values

Biodaniel returns the following exit status values:

• 0: The program completed successfully.
• 1: File I/O error. This can occur if at least one of the input FASTA files cannot be opened for reading. This can occur because the file does not exist at the specified path, or biodaniel does not have permission to read from the file.
• 2: A command line error occurred. This can happen if the user specifies an incorrect command line argument. In this circumstance biodaniel will also print a usage message to the standard error device (stderr).
• 3: Input FASTA file is invalid. This can occur if biodaniel can read an input file but the file format is invalid.

Testing

Unit tests

$ cd biodaniel/python/biodaniel
$ python -m unittest -v biodaniel_test

Test suite

A set of sample test input files is provided in the test_data folder.

$ biodaniel two_sequence.fasta
FILENAME        TOTAL   NUMSEQ  MIN     AVG     MAX
two_sequence.fasta      2       357     120     178     237

Bug reporting and feature requests

Please submit bug reports and feature requests to the issue tracker on GitHub:

biodaniel issue tracker