Bioutils

BioPerl-based Sequence Utilities

Figure 1. Design and Methods of bioutils

What is bioutils?

bioutils is a suite of Perl scripts that provide convenient command-line access to popular BioPerl methods. Designed as UNIX utilities, these tools aim to circumvent a constant need (and urge) for composing one-off BioPerl scripts for routine manipulations of sequences, alignments and trees.

The initial release of bioutils consists of four utilities (Figure 1):

• bioseq: a wrapper of BioPerl class Bio::Seq (with additional methods)
• bioaln: a wrapper of Bio::SimpleAlign (which inherits Bio::Seq; with additional methods)
• biopop: a wrapper of Bio::PopGen (which can be converted from Bio::SimpleAlign; with additional methods)
• biotree: a wrapper of Bio::tree (with additional methods)

These utilities have been in development since 2002 in the lab of Dr Weigang Qiu at Hunter College of the City University of New York. They are the main code base of the Qiu Lab, which specializes in microbial evolutionary genomics. They proved to be convenient, efficient, and popular among students and researchers passing through the lab. By releasing bioutils as an Open Source tool, we hope to (1) share our experience and (2) invite other developers to join the effort of making BioPerl more accessible.

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Live Demos

Basic Usage

• bioseq

bioseq -l foo.fasta # print seq names and lengths from FASTA (default format) file
bioseq -r foo.fasta # reverse complement
bioseq -t1 foo.fasta # translate in the +1 frame
bioseq -t3 foo.fasta # translate in +1, +2, and +3 frames
bioseq -t6 foo.fasta # translate in all 6 frames
bioseq -p'id:seq_1' foo.fasta # pick a sequence by ID
bioseq -p'order:3' # pick the 3rd sequence
bioseq -p're:Human' foo.fasta # pick all sequences labeled as "Human" (by regular expression)
bioseq -g foo.fasta # remove all gaps
bioseq -z'CP003201' -o'genbank' # retrieve a GenBank file with accession
bioseq -z'CP003201' -o'fasta' # same file in FASTA

• bioaln

bioaln -i'fasta' -o'phylip' foo.fasta # convert a FASTA alignment to PHYLIP
bioaln -l foo.aln # print alignment length of a CLUSTALW (default format) file
bioaln -s'100, 200' foo.aln # obtain an alignment slice
bioaln -m foo.aln # show only variable sites
bioaln -r'seq_2' foo.aln # use "seq_2" as reference (first) sequence
bioaln -g foo.aln # remove gapped sites
bioaln -p'seq_1,seq_3,seq_6' foo.aln # pick a subset of sequences
bioaln -d'seq_1,seq_3,seq_6' foo.aln # delele a subset of sequences

• biotree

• biopop

Power usage

# Pipe with the same utility
bioseq -p'order:5' foo.fasta | bioseq -s'100,200' | bioseq -r | bioseq -t1 # pick, subseq, revcom, and translate
# Pipe among utilities
bioaln -o'fasta' foo.aln | bioseq -g # remove gaps within individual sequences

Creative usage

echo -ne ">lookup\nATG\n" | bioseq -t1 # Lookup a codon product
len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln | bioaln -l); echo "$len-$len_degap" | bc -l # count alignment gaps

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Main contributors

• Yozen Hernandez
• Weigang Qiu
• Pedro Pagan
• Levy Vargas

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