# FASTA descriptors: bioseq -l fasta_file # [l]engths of sequences bioseq -n fasta_file # [n]umber of sequences bioseq -c fasta_file # base or aa [c]omposition of sequences # FASTA filters (FASTA in FASTA out) - one or more sequences: bioseq -r fasta_file # [r]everse-complement sequences bioseq -p'order:3' fasta_file # [p]ick the 3rd sequences bioseq -p're:B31' fasta_file # [p]ick sequences with regex bioseq -d'order:3' fasta_file # [d]elete the 3rd sequences bioseq -d're:B31' fasta_file # [d]elete sequences with regex bioseq -t1 dna_fasta # [t]ranslate in 1st reading frame bioseq -t3 dna_fasta # [t]ranslate in 3 reading frames bioseq -t6 dna_fasta # [t]ranslate in 6 reading frames bioseq -g fasta_file # remove [g]aps bioseq -A fasta_file # [A]nonymize sequence IDs # FASTA filters (FASTA in FASTA out) - single sequence: bioseq -s'1,10' fasta_file # [s]ubsequence from positions 1-10 bioseq -R'10' bac_genome_fasta # [R]e-circularize a genome t position 10 # Retrieve sequence from database bioseq -f 'X83553' -o 'genbank' # [f]etch a genbank file by accession bioseq -f 'X83553' -o 'fasta' # [f]etch a genbank file in FASTA # Less common usages (options in CAPs) bioseq -L fasta_file # [L]inearize FASTA: one sequence per line bioseq -B fasta_file # [B]reak into single-seq files bioseq -C cds_fasta # [C]odon counts (for coding sequences) bioseq -H pep_fasta # [H]ydrophobicity score (for protein seq) bioseq -i'genbank' -F file.gb # extract genbank [F]eatures to FASTA bioseq -x 'EcoRI' dna_fasta # Fragments from restriction digest # Chaining with pipes: bioseq -p'id:B31' dna_fasta | bioseq -g | bioseq -t1 # pick a seq, remove gaps, & translate bioseq -p'order:2' dna_fasta | bioseq -r | bioseq -s'10,20' # pick the 2nd seq, rev-com it, & subseq
bioseq is a command-line utility for common, routine sequence manipulations. Most methods are wrappers for BioPerl modules (Bio::Seq, Bio::SeqIO, Bio::SeqUtils, and Bio::Tools::SeqStats). By default, bioseq assumes that both the input and the output files are in FASTA format, to facilitate the chainning (by UNIX pipes) of multiple bioseq runs.
Methods that are currently NOT wrappers should ideally be factored into individual BioPerl modules, which are better tested and handle exceptions better than stand-alone codes in bp-utils. As a design principle, bp-utils should consist of ONLY wrapper calls.
Print a brief help message and exit.
Usage: bioseq -h
Print the manual page and exit.
Usage: bioseq -man
Base or AA composition. A wrapper for Bio::Tools::SeqStats->count_monomers().
Usage: bioseq -c <input_file>
Delete a sequence or a comma-separated list of sequences, eg, -d 'id:foo' by id -d 'order:2' by order -d 'length:n' by min length, where 'n' is length -d 'ambig:x' by min % ambiguous base/aa, where 'x' is the % -d 'id:foo,bar' list by id -d 're:REGEX' using a regular expression (only one regex is expected)
Usage: bioseq -d 'tag:value' <input_file>
Retrieves a sequence from GenBank using the provided accession number. A wrapper for Bio::DB::GenBank->get_Seq_by_acc().
Usage: bioseq -f <genbank_accession>
Remove gaps
Usage: bioseq -g <input_file>
Input file format. By default, this is 'fasta'. For Genbank format, use 'genbank'. For EMBL format, use 'embl'. Wrap Bio::SeqIO.
Usage: bioseq -i 'format' <input_file>
Print all sequence lengths. Wrap Bio::Seq->length().
Usage: bioseq -l <input_file>
Print number of sequences.
Usage: bioseq -n <input_file>
Output file format. By default, this is 'fasta'. For Genbank format, use 'genbank'. For EMBL format, use 'embl'. Wrap Bio::SeqIO.
Usage: bioseq -o 'format' <input_file>
Select a single sequence: --pick 'id:foo' by id --pick 'order:2' by order --pick 're:REGEX' using a regular expression
Select a list of sequences: --pick 'id:foo,bar' list by id --pick 'order:2,3' list by order --pick 'order:2-10' list by range
Usage: bioseq -p 'tag:value' <input_file>
Reverse complement. Wrap Bio::Seq->revcom().
Usage: bioseq -r <input_file>
Select substring (of the 1st sequence). Wrap Bio::Seq->subseq().
Usage: bioseq -s 'beginning_index, ending_index' <input_file>
Example: bioseq -s'20,80' <input_file> (or -s='20,80')
Translate in 1, 3, or 6 frames. eg, -t1, -t3, or -t6. Wrap Bio::Seq->translate(), Bio::SeqUtils->translate_3frames(), and Bio::SeqUtils->translate_6frames().
Usage: bioseq -t [1|3|6] <input_file>
Predicted fragments from digestion by a specified restriction enzyme. An input file with a single sequence is expected. A wrapper of Bio::Restriction::Analysis->cut().
Usage: bioseq -x 'RE' <dna_fasta_file>
Replace sequence IDs with serial IDs 'n' characters long, including a leading 'S' (e.g., -A'5' gives S0001). Produces a sed script file with a '.sed' suffix that may be used with sed's '-f' argument. If the filename is '-', the sed file is named STDOUT.sed instead. The sed filename is specified on STDERR.
Usage: bioseq -A 'number' <input_file>
Break into individual sequences, one sequence per file
Usage: bioseq -B <input_file>
Count codons for coding sequences (e.g., a genome file consisting of CDS sequences). A wrapper of Bio::Tools::SeqStats->count_codons().
Usage: bioseq -C <input_file>
Extract gene sequences in FASTA from a GenBank file of bacterial genome. Won't work for a eukaryote genbank file.
Usage: bioseq -i'genbank' -F <genbank_file>
Count and return the number of leading gaps in each sequence.
Usage: bioseq -G <input_file>
Return the mean Kyte-Doolittle hydropathicity for protein sequences. A wrapper of Bio::Tools::SeqStats->hydrophobicity().
Linearize FASTA, one sequence per line
Usage: bioseq -L <input_file>
Re-circularize a bacterial genome by starting at a specified position, e.g. for sequence "ABCDE", bioseq -R'2' would generate 'BCDEA'.
Usage: bioseq -R 'number' <input_file>
Print current release version of bp-utils.
Usage: bioseq -V
Remove stop codons (e.g., PAML input)
Usage: bioseq -X <input_file>
Perl 5.010, BioPerl
Please see project wiki page https://github.com/bioperl/bp-utils/wiki for documentation and use cases.
Please email weigang@genectr.hunter.cuny.edu.
Yozen Hernandez <yzhernand at gmail dot com> Girish Ramrattan <gramratt at gmail dot com> Levy Vargas <levy dot vargas at gmail dot com> Weigang Qiu <weigang at genectr dot hunter dot cuny dot edu> (Maintainer)
To install Bio::BPWrapper, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::BPWrapper
CPAN shell
perl -MCPAN -e shell install Bio::BPWrapper
For more information on module installation, please visit the detailed CPAN module installation guide.