NAME
Bio::BPWrapper::AlnManipulations - Functions for bioaln
SYNOPSIS
use Bio::BPWrapper::AlnManipulations;
# Set options hash ...
initialize(\%opts);
write_out(\%opts);SUBROUTINES
initialize()
Sets up most of the actions to be performed on an alignment.
Call this right after setting up an options hash.
Sets package variables: $in_format, $binary, $out_format, and $out.
write_out_paml()
Writes output in PAML format.
write_out()
Performs the bulk of the alignment actions actions set via initialize(\%opts) and calls $AlignIO->write_aln() or write_out_paml().
Call this after calling #initialize(\%opts).
print_avpid
Print the average percent identity of an alignment.
Wraps Bio::SimpleAlign->average_percentage_identity().
boostrap()
Produce a bootstrapped alignment. Bio::Align::Utilities->bootstrap().
draw_codon_view()
Print a CLUSTALW-like alignment, but separated by codons. Intended for use with DNA sequences. Block-final position numbers are printed at the end of every alignment block at the point of wrapping, and block-initial counts appear over first nucleotide in a block.
del_seqs
Delete sequences based on their id. Option takes a comma-separated list of ids. The list of sequences to delete is in $opts{"delete"} which is set via #initilize(\%opts)
remove_gaps()
Remove gaps (and returns an de-gapped alignment). Wraps Bio::SimpleAlign->remove_gaps().
print_length()
Print alignment length. Wraps Bio::SimpleAlign->length().
print_match()
Go through all columns and change residues identical to the reference sequence to be the match character, '.' Wraps Bio::SimpleAlign->match().
print_num_seq()
Print number of sequences in alignment.
pick_seqs()
Pick sequences based on their id. Option takes a comma-separated list of ids. The sequences to pick set in $opts{"pick"} which is set via #initilize(\%opts).
change_ref()
Change the reference sequence to be what is in $opts{"refseq"} which is set via #initilize(\%opts). Wraps Bio::SimpleAlign->set_new_reference().
aln_slice()
Get a slice of the alignment. The slice is specifiedn $opts{"slice"} which is set via #initilize(\%opts).
Wraps Bio::SimpleAlign->slice() with improvements.
get_unique()
Extract the alignment of unique sequences. Wraps Bio::SimpleAlign->uniq_seq().
variable_sites
Extracts variable sites.
avg_id_by_win()
Calculate pairwise average sequence difference by windows (overlapping windows with fixed step of 1). The window size is set in $opts{"window"} which is set via #initilize(\%opts).
dna_to_protein()
Align CDS sequences according to their corresponding protein alignment. Wraps Bio::Align::Utilities->aa_to_dna_aln().
list_ids()
List all sequence ids.
SEE ALSO
bioaln: command-line tool for using this
CONTRIBUTORS
William McCaig <wmccaig at gmail dot com>
Girish Ramrattan <gramratt at gmail dot com>
Che Martin <che dot l dot martin at gmail dot com>
Yözen Hernández yzhernand at gmail dot com
Levy Vargas <levy dot vargas at gmail dot com>
Weigang Qiu (Maintainer)
Rocky Bernstein