These scripts are written in the Ruby programming language. You can view more information here.
You must have the Ruby programming language installed to use these scripts. Type
ruby -vMany of these scripts also require the BioRuby gem to be installed. You can find information about installing the BioRuby gem, view the documentation here.
Splits a fasta file into smaller fasta files.
Usage: split-fasta.rb [options] file1 file2 ...
-v, --verbose Print more info
-l, --log Log information to file
-r, --records [NUM] Number of records to get (defaults: all)
-n, --per-file [NUM] Number of records per file (default: 100)
-o, --offset [NUM] Number of records to skip (default: 0)
-d, --dir [DIR] Output dir (default: out)
-p, --print Print reads
-t, --test Test file lengths afterward
-c, --deep-test Test file contents afterward
-h, --help Display this screen
Example:
split-fasta.rb -n 1000 -d sample_split my_fasta_file.fastaThis example splits the fasta file into a series of fasta files containing 1000 reads each. The files will be in the directory 'sample_split'.
Use this script to submit multiple blast jobs to the PBS system.
Usage: multi-blast.rb [options]
-v, --verbose Print more info
-i, --input-dir [NAME] Input directory
-o, --output-dir [NAME] Output directory
--output-script Output script rather than submitting it
-e, --extension [NAME] Extension of fasta files [default: fna]
-p, --prefix [NAME] PBS job prefix [default: kartchner]
-g, --group [NAME] Queue to use [default: standard]
-q, --queue [NAME] Number of CPUs to use [default: rmaier]
-n, --num-cpus [NUM] Number of CPUs to use [default: 12]
-r, --ram [NUM] Amount of RAM to use [default: 23gb]
-c, --cpu-time [NUM] Amount of CPU time to use [default: 50:0:0]
-w, --wall-time [NUM] Amount of Wall time to use [default: 7:0:0]
-s, --start [NUM] Start Index [default: 0]
-z, --end [NUM] End index [default: 50]
-d, --db-path [PATH] BLAST Database path [default: /genome/nr]
-b, --base-name [NAME] Base name of FASTA files
--blast-path [PATH] Path of blast executable
-t, --test-only Test instead of submitting jobs
Example:
multi-blast.rb -i /gsfs1/xdisk/bmf/datasets/main -o /gsfs1/xdisk/bmf/results -b my_fasta_file_ -q windfall {0..9}This example submits a series of blast jobs to the PBS system. This script should be used with files created with the split-fasta.rb script. The 'base name' (my_fasta_file_) is found by looking at your fasta files. Take everything up to the number part of the filename, and that is the base name. E.g., if you have my_fasta_file_1, my_fasta_file_2, ..., your base name is 'my_fasta_file_'.
Used to combine multiple blast output files into one file.
Usage: combine-blast.rb [options] file1 file2 ...
-v, --verbose Print more info
-l, --log Log information to file
-f, --output-file [FILE] Number of records to skip (default: 0)
-d, --dir [DIR] Output dir (default: out)
-h, --help Display this screen
Example:
combine-blast.rb -f output.blastx *.blastxThis example will copy all blastx files in the current directory into a single new file called 'output.blastx'. Make sure you have enough space to contain both the original and new copies of the data.
Reads in a fasta file and then rewrites the file
Usage: fasta-rewrite.rb [options]
-v, --verbose Print more info
-l, --log Log information to file
-o, --out-file [FILE] Output file
-d, --dir [DIR] Output dir (default: out)
-i, --in-file [FILE] Input file
-h, --help Display this screen
Example:
fasta-rewrite.rb -i input.fasta -o output.fastaThis example reads in a fasta file and writes each read to a new file. If your fasta file seems to contain errors, try using this script to remove them.
Counts the reads in a fasta file
Usage: fasta-stat.rb [options] file1 file2 ...
-v, --verbose Print more info
-c, --count Count reads in file
-h, --help Display this screen
Example:
fasta-stat.rb -c my_fasta_file.fastaThis example counts the reads in a fasta file.
Calculates Mean, Median, Mode, and Standard Deviation for FASTQ data
Usage: fastq-stat.rb [options] file1 file2 ...
-v, --verbose Print more info
-n, --num-records [NUM] Number of records to get (defaults: all)
-h, --help Display this screen
Example:
fastq-stat.rb my_fastq_data.fastqThis example generates statistics for the file 'my_fastq_data.fastq'.
Use this to submit a job to the PBS system without creating a separate script
Important: You must use absolute paths in your command when using this script. If you use relative paths, the PBS system may not be able to find your files.
Usage: qsub.rb [options] command
-v, --verbose Print more info
-o, --output-script Output script to file and do not submit
-n, --num-cpus [NUM] Number of CPUs to use
-r, --ram [NUM] Amount of RAM to use
-c, --cpu-time [NUM] Amount of CPU time to use
-w, --wall-time [NUM] Amount of Wall time to use
-t, --test-only Test and print script to stdout
Example:
qsub.rb -v -n 12 /bin/blastx -num_threads 8 -db /genome/nr -query /datasets/main/organism.fnaSubmits the blastx command as a PBS job using 12 CPUs and printing verbose information regarding the operation of the script.
Filters FASTA data and provides detailed information about the process.
Usage: quality-filter.rb [options] file
-v, --verbose Print more info
-p, --print Print out sequence data in FastQ format
-l, --log Log the output
-b, --output-bad-seqs Output bad sequences
-d, --output-dir [DIR] Select output dir (default: out)
-o, --output [FILE] Select output file (default: output.fasta)
-r, --num-records [NUM] Number of records to get (default: all)
-h, --help Display this screen
Example:
quality-filter.rb -b -d output_dir -o quality-filtered.fastaIn this example, the -b switch causes the script to output the sequences that are excluded by the quality filter rather than discard them. The -d switch chooses the output directory, and the -o switch chooses the output file.