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Bio-BPWrapper-1.13
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/ bioseq

NAME

bioseq - Manipulation of FASTA sequences based on BioPerl

SYNOPSIS

bioseq [options] input_file

bioseq [-h | --help | -V | --version | --man]

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

FASTA filters

Multiple FASTA-file output

bioseq -r fasta_file            # [r]everse-complement sequences
bioseq -p 'order:3' fasta_file  # pick the 3rd sequences
bioseq -p 're:B31' fasta_file   # pick sequences with regex
bioseq -d 'order:3' fasta_file  # delete the 3rd sequences
bioseq -d 're:B31' fasta_file   # delete sequences with regex
bioseq -t 1 dna_fasta           # translate in 1st reading frame
bioseq -t 3 dna_fasta           # translate in 3 reading frames
bioseq -t 6 dna_fasta           # translate in 6 reading frames
bioseq -g fasta_file            # remove gaps

Single FASTA-file output

bioseq -s '1,10' fasta_file         # sub-sequence from positions 1-10
bioseq --reloop '10' contig_fasta   # re-circularize a genome at position 10

Less common usages

bioseq --linearize fasta_file                # Linearize FASTA: one sequence per line
bioseq --break fasta_file                    # Break into single-seq files
bioseq --count-codons cds_fasta              # Codon counts (for coding sequences)
bioseq --hydroB pep_fasta                    # Hydrophobicity score (for protein seq)
bioseq --input 'genbank' --feat2fas file.gb  # extract genbank features to FASTA
bioseq --restrict 'EcoRI' dna_fasta          # Fragments from restriction digest

Serialize 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 & subseq

DESCRIPTION

bioseq is a command-line utility for common, routine sequence manipulations based on BioPerl modules including 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 chaining (by UNIX pipes) of serial bioseq runs.

Methods that are currently not wrappers should ideally be factored into individual Bio::Perl modules, which are better tested and handle exceptions better than stand-alone codes in the Bio::BPWrapper package. As a design principle, command-line scripts here should consist of only wrapper calls.

OPTIONS

--anonymize, -A 'number'

This options was designed for legacy programs (e.g., PHLIP suites) that takes only 10 character-long sequence IDs.

Replace sequence IDs with serial IDs n characters long. The sequence is prefaced with a leading 'S'. For example using option --anonymize '5' the first ID will be S0001.

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. A message containing the sed filename is written to STDERR.

--break, -B

Break into individual sequences, writing a FASTA file for each sequence.

--codon-info <CUTG file>

Calculate codon bias of a CDS using Shannon information, as deviation from the genome-wide codon usage (in CUTG GCG format). (Reference: <to be added>)

--codon-sim <CUTG file>

(Temporarily disabled)

Output a CDS with the same AA sequence with each AA replaced by a synonymous codon randomly chosen from a genome codon pool (specified by CUTG GCG file; see test-files/BbB31.cutg). Only the 1st sequence used if multiple sequences are supplied.

For testing the signficcance of codon-bias information, it is necessary to run this repeatedly to generate at least 100 simulated CDSs, e.g., for i in {1..10}; do bioseq --codon-sim test-files/BbB31.cutg test-files/test-bioseq.cds; done

Two non-BioPerl module dependencies: Algorithm::Numerical::Sample; Math::Random.

--codon-table

Interface to Bio::Tools::CodonTable. Methods include: translate a codon to AA & reverse list codons for an AA. Currently only takes a 3-letter DNA-base codon or a 1-letter uppercase IUPAC aa code

--codon-table 'ACG'
--codon-table 'L'
--composition, -c

Base or AA composition.

--count-codons, -C

Count codons for coding sequences (e.g., a genome file consisting of CDS sequences).

--delete, -d 'tag:value'

Delete a sequence or a comma-separated list of sequences, e.g.,

--delete id:foo	 # by id
--delete order:2	 # by order
--delete length:n     # by min length, where 'n' is length
--delete ambig:x	 # by max number of x ambiguous bases (non-ATCGs), e.g., if x=20, delete seqs w/ 20 or mroe N's
--delete id:foo,bar   # list by id
--delete re:REGEX     # using a regular expression (only one regex is expected)
--delete file:name    # by file, one id per line
--feat2fas | -F

Extract gene sequences in FASTA from a GenBank file of bacterial genome. Won't work for a eukaryote genbank file. For example:

bioseq -i'genbank' -F <genbank_file.gb> (throws error if not genbank file)
--fetch, -f <genbank_accession>

Retrieves a sequence from GenBank using the provided accession number, e.g., bioseq -f 'NC_003078' -o 'genbank'

--hydroB, -H

Return the mean Kyte-Doolittle hydropathicity for protein sequences.

--iep

Return iso-electric point for a protein sequences as well as charges at a series of pH values. Depends on Bio::Tools::pICalculator.

--input, -i

Input file format. By default, this is 'fasta'. For Genbank format, use 'genbank'. For EMBL format, use 'embl'. For FASTQ, use 'fastq'

[We tried to guess the format using Bio::Tools::GuessSeqFormat, but it didn't work for pipe. Guess format will be delayed until this issue is fixed]

--lead-gaps | -G

Count and return the number of leading gaps in each sequence.

--length, -l

Print all sequence lengths.

--linearize, -L

Linearize FASTA, one sequence per line.

--longest-orf, -z

Find and return the longest ORF (return the original if no error for -t1, i.e., no internal stop at the 1st reading frame). This is useful for fixing out-of-frame seqs. Turn on -Z (no revcom to search only in the given strand)

--mol-wt

Print lower and upper bound of molecular weight

--no-gaps, -g

Remove gaps

--num-seq, -n

Print number of sequences.

--output, -o 'format'

Output file format. By default, this is 'fasta'. For Genbank format, use 'genbank'. For EMBL format, use 'embl'.

--pick, -p 'tag:value'

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
--pick 'file:name'     id list in file, one id per line
--reloop, -R 'number'

Re-circularize a bacterial genome by starting at a specified position. For example, for sequence "ABCDE", bioseq -R'2' would generate "BCDEA".

--rename, -N 'file'

Append sequence names specified by a file (two tab-separated columns: old_name, new_name)

--remove-stop, -X

Remove stop codons (e.g., for PAML input)

--restrict, -x 'RE'

Predicted fragments from digestion by a specified restriction enzyme.

--restrict-coord 'RE'

Predicted fragments from digestion by a specified restriction enzyme. Outputs cooridnates of overhangs in BED format.

--revcom | -r

Reverse complement.

--sort 'id|length'

Sort by id or length (Contributor: Jeffery Rosario; Fall 2017)

--split-cdhit 'cdhit .clstr file'

Parse cdhit output .clstr file and generate a FASTA file for each CDHIT family.

--subseq | -s 'beginning_index,ending_index'

Select substring (of the 1st sequence).

--translate | -t [1|3|6]

Translate in 1, 3, or 6 frames. e.g., -t1, -t3, or -t6.

Common Options

--help, -h

Print a brief help message and exit.

--man (but not "-m")

Print the manual page and exit.

--version, -V

Print current release version of this command and exit.

SEE ALSO

CONTRIBUTORS

  • Yözen Hernández <yzhernand at gmail dot com> (Initial desgin and implementation)

  • Girish Ramrattan <gramratt at gmail dot com> (developer)

  • Levy Vargas <levy dot vargas at gmail dot com> (developer)

  • Weigang Qiu (Maintainer)

  • Rocky Bernstein (testing and release)

  • Filipe G. Vieira (developer of --restrict; --restrict-coord methods)

TO DO

  • Add bioperl scripts ("bp_xxx.pl") functions?

TO CITE

  • Hernandez, Bernstein, Qiu, et al (2017). "BpWrappers: Command-line utilities for manipulation of sequences, alignments, and phylogenetic trees based on BioPerl". (In prep).

  • Stajich et al (2002). "The BioPerl Toolkit: Perl Modules for the Life Sciences". Genome Research 12(10):1611-1618.