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.
This repository is a test of bionitio-boot.sh.
This program is released as open source software under the terms of MIT License.
XXX instructions about how to do this needed.
bionitio_testperl5_2.pl depends on BioPerl for parsing FASTA
files, and Log4Perl for logging. Installing these can be done in many ways:
sudo apt-get install bioperl
sudo yum install perl-bioperl
sudo cpan Bio::Perl
sudo cpan Log::Log4perl
Bionitio_testperl5_2 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. Bionitio_testperl5_2 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.
Bionitio_testperl5_2 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 bionitio_testperl5_2 and do not contribute to the computed statistics. By default --minlen is set to zero.
These are the statistics computed by bionitio_testperl5_2, 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 bionitio_testperl5_2 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 bionitio_testperl5_2 acts in the same way as if there are no sequences in the file.
In the examples below, % indicates the command line prompt.
Bionitio_testperl5_2 can display usage information on the command line via the -h or --help argument:
% ./bionitio_testperl5_2 -h
usage: bionitio_testperl5_2 [FASTA_FILES] [--help|-h] [--log] [--version] [--minlen|-m]
Read one or more FASTA files, compute simple stats for each file
optional positional arguments:
FASTA_FILES ? input FASTA files
optional named arguments:
--help, -h ? show this help message and exit
--log LOG_FILE ? record program progress in LOG_FILE
--version VERSION ? Print the program version and then exit
--minlen, -m N ? Minimum length sequence to include in stats
Default: 0
Bionitio_testperl5_2 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, bionitio_testperl5_2 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 bionitio_testperl5_2.
The example below illustrates bionitio_testperl5_2 applied to a single named FASTA file called file1.fa:
% bionitio_testperl5_2 file1.fa
FILENAME NUMSEQ TOTAL MIN AVG MAX
file1.fa 5264 3801855 31 722 53540
The example below illustrates bionitio_testperl5_2 applied to three named FASTA files called file1.fa, file2.fa and file3.fa:
% bionitio_testperl5_2 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
The example below illustrates bionitio_testperl5_2 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 <:
% bionitio_testperl5_2 < 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 bionitio_testperl5_2:
% cat file1.fa | bionitio_testperl5_2
FILENAME NUMSEQ TOTAL MIN AVG MAX
stdin 5264 3801855 31 722 53540
Bionitio_testperl5_2 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 bionitio_testperl5_2 applied to a single FASTA file called file.fawith a--minlenfilter of1000`.
% bionitio_testperl5_2 --minlen 1000 file.fa
FILENAME NUMSEQ TOTAL MIN AVG MAX
file1.fa 4711 2801855 1021 929 53540
If the --log FILE command line argument is specified, bionitio_testperl5_2 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.
% bionitio_testperl5_2 --log bt.log file1.fasta file2.fasta
# normal bionitio_testperl5_2 output appears here
# contents of log file displayed below
% cat bt.log
2017/04/22 19:41:40 INFO program started
2017/04/22 19:41:40 INFO command line arguments: ./bionitio_testperl5_2.pl file1.fasta file2.fasta
2017/04/22 19:41:40 INFO Processing FASTA file from file1.fasta
2017/04/22 19:41:40 INFO Processing FASTA file from file2.fasta
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 bionitio_testperl5_2 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 bionitio_testperl5_2 applied to a single FASTA file called empty.fa which contains zero sequences:
% bionitio_testperl5_2 empty.fa
FILENAME NUMSEQ TOTAL MIN AVG MAX
empty.fa 0 0 - - -
Bionitio_testperl5_2 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 bionitio_testperl5_2 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 bionitio_testperl5_2 will also print a usage message to the standard error device (stderr).
- 3: Input FASTA file is invalid. This can occur if bionitio_testperl5_2 can read an input file but the file format is invalid.
XXX FIXME
% ./bionitio_testperl5_2_test.pl
# the output of the test cases will appear here
A set of sample test input files is provided in the test_data folder.
% bionitio_testperl5_2 two_sequence.fasta
FILENAME TOTAL NUMSEQ MIN AVG MAX
two_sequence.fasta 2 357 120 178 237
Please submit bug reports and feature requests to the issue tracker on GitHub: