[BioRuby-cvs] bioruby/doc Tutorial.rd,1.15,1.16
Pjotr Prins
pjotr at dev.open-bio.org
Sat Feb 2 14:15:19 UTC 2008
Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31326
Modified Files:
Tutorial.rd
Log Message:
Modified tutorial
Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Tutorial.rd 2 Feb 2008 14:01:54 -0000 1.15
--- Tutorial.rd 2 Feb 2008 14:15:08 -0000 1.16
***************
*** 115,120 ****
puts seq.complement.translate # translation of complemental strand
! counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
! p randomseq = Bio::Sequence::NA.randomize(counts) # reshuffle sequence with same freq.
The p, print and puts methods are standard Ruby ways of outputting to
--- 115,122 ----
puts seq.complement.translate # translation of complemental strand
! # reshuffle sequence with same frequencies:
! counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),
! 'g'=>seq.count('g'),'t'=>seq.count('t')}
! p randomseq = Bio::Sequence::NA.randomize(counts)
The p, print and puts methods are standard Ruby ways of outputting to
***************
*** 265,269 ****
print ">#{gb.accession} " # Accession
puts gb.definition # Definition
! puts gb.naseq # Nucleic acid sequence (Bio::Sequence::NA object)
end
--- 267,272 ----
print ">#{gb.accession} " # Accession
puts gb.definition # Definition
! puts gb.naseq # Nucleic acid sequence
! # (Bio::Sequence::NA object)
end
***************
*** 387,391 ****
aaseq.splicing('21..119')
- (EDITOR's NOTE: why use STRINGs here?)
=== More databases
--- 390,393 ----
***************
*** 494,498 ****
and cut a sequence with an enzyme follow up with:
! res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, {:view_ranges => true})
if res.kind_of? Symbol #error
err = Err.find_by_code(res.to_s)
--- 496,501 ----
and cut a sequence with an enzyme follow up with:
! res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0},
! {:view_ranges => true})
if res.kind_of? Symbol #error
err = Err.find_by_code(res.to_s)
***************
*** 529,534 ****
fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep. (TRANSLATOR'S NOTE: I think
! we should provide sample data to readers.)
#!/usr/bin/env ruby
--- 532,536 ----
fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep.
#!/usr/bin/env ruby
***************
*** 536,547 ****
require 'bio'
! # Creates FASTA factory object ("ssearch" instead of "fasta34" can also work)
factory = Bio::Fasta.local('fasta34', ARGV.pop)
(EDITOR's NOTE: not consistent pop command)
- # Reads FASTA-formatted files (TRANSLATOR'S NOTE: something wrong in Japanese text)
ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
! # Iterates over each entry. the variable "entry" is a Bio::FastaFormat object.
ff.each do |entry|
# shows definition line (begins with '>') to the standard error output
--- 538,550 ----
require 'bio'
! # Creates FASTA factory object ("ssearch" instead of
! # "fasta34" can also work)
factory = Bio::Fasta.local('fasta34', ARGV.pop)
(EDITOR's NOTE: not consistent pop command)
ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
! # Iterates over each entry. the variable "entry" is a
! # Bio::FastaFormat object:
ff.each do |entry|
# shows definition line (begins with '>') to the standard error output
***************
*** 555,559 ****
# If E-value is smaller than 0.0001
if hit.evalue < 0.0001
! # shows identifier of query and hit, E-value, start and end positions of homologous region (TRANSLATOR'S NOTE: should I change Japanese document?)
print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
p hit.lap_at
--- 558,563 ----
# If E-value is smaller than 0.0001
if hit.evalue < 0.0001
! # shows identifier of query and hit, E-value, start and
! # end positions of homologous region
print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
p hit.lap_at
***************
*** 569,573 ****
FASTA many times easily. Instead of using Fasta#query method,
Bio::Sequence#fasta method can be used.
- (TRANSLATOR'S NOTE: Bio::Sequence#fasta are not so frequently used.)
seq = ">test seq\nYQVLEEIGRGSFGSVRKVIHIPTKKLLVRKDIKYGHMNSKE"
--- 573,576 ----
***************
*** 585,589 ****
with the Report object. For example, getting information for hits:
-
report.each do |hit|
puts hit.evalue # E-value
--- 588,591 ----
***************
*** 594,606 ****
puts hit.query_def # definition(comment line) of query sequence
puts hit.query_len # length of query sequence
! puts hit.query_seq # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
puts hit.target_id # identifier of hit sequence
puts hit.target_def # definition(comment line) of hit sequence
puts hit.target_len # length of hit sequence
! puts hit.target_seq # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of hit sequence)
! puts hit.query_start # start position of homologous region in query sequence
! puts hit.query_end # end position of homologous region in query sequence
! puts hit.target_start # start posiotion of homologous region in hit(target) sequence
! puts hit.target_end # end position of homologous region in hit(target) sequence
puts hit.lap_at # array of above four numbers
end
--- 596,612 ----
puts hit.query_def # definition(comment line) of query sequence
puts hit.query_len # length of query sequence
! puts hit.query_seq # sequence of homologous region
puts hit.target_id # identifier of hit sequence
puts hit.target_def # definition(comment line) of hit sequence
puts hit.target_len # length of hit sequence
! puts hit.target_seq # hit of homologous region of hit sequence
! puts hit.query_start # start position of homologous
! # region in query sequence
! puts hit.query_end # end position of homologous region
! # in query sequence
! puts hit.target_start # start posiotion of homologous region
! # in hit(target) sequence
! puts hit.target_end # end position of homologous region
! # in hit(target) sequence
puts hit.lap_at # array of above four numbers
end
***************
*** 695,717 ****
report.each do |hit|
! puts hit.bit_score # bit score (*)
! puts hit.query_seq # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
! puts hit.midline # middle line string of alignment of homologous region (*)
! puts hit.target_seq # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
! puts hit.evalue # E-value
! puts hit.identity # % identity
! puts hit.overlap # length of overlapping region
! puts hit.query_id # identifier of query sequence
! puts hit.query_def # definition(comment line) of query sequence
! puts hit.query_len # length of query sequence
! puts hit.target_id # identifier of hit sequence
! puts hit.target_def # definition(comment line) of hit sequence
! puts hit.target_len # length of hit sequence
! puts hit.query_start # start position of homologous region in query sequence
! puts hit.query_end # end position of homologous region in query sequence
! puts hit.target_start # start position of homologous region in hit(target) sequence
! puts hit.target_end # end position of homologous region in hit(target) sequence
! puts hit.lap_at # array of above four numbers
end
--- 701,723 ----
report.each do |hit|
! puts hit.bit_score
! puts hit.query_seq
! puts hit.midline
! puts hit.target_seq
! puts hit.evalue
! puts hit.identity
! puts hit.overlap
! puts hit.query_id
! puts hit.query_def
! puts hit.query_len
! puts hit.target_id
! puts hit.target_def
! puts hit.target_len
! puts hit.query_start
! puts hit.query_end
! puts hit.target_start
! puts hit.target_end
! puts hit.lap_at
end
***************
*** 1171,1175 ****
== KEGG API
! Please refer to KEGG_API.rd.ja (TRANSLATOR'S NOTE: English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
* ((<URL:http://www.genome.jp/kegg/soap/>))
--- 1177,1181 ----
== KEGG API
! Please refer to KEGG_API.rd.ja (English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
* ((<URL:http://www.genome.jp/kegg/soap/>))
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