[BioRuby] Help using EMBOSS in Bioruby...

[Toshiaki Katayama]

Sharvari,

Sorry, I missed your previous mails.

On 2008/01/03, at 4:53, Sharvari Gujja wrote:

> Hi,
>
> I was wondering how to use water and needle emboss tools in Bioruby. I am aware that the class Bio::EMBOSS exists with methods:
>
> *entret*(arg) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000989.html>
> *new*(cmd_line) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000990.html>
>
> *seqret*(arg) src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000988.html>
>
>
> *exec*() src <http://bioruby-doc.org/rdoc/classes/Bio/EMBOSS.src/M000991.html>
>
> I would like to know how to use water and needle tools.I really appreciate your help.
>
> Thanks
> Sharvari


On 2008/01/08, at 5:47, Sharvari Gujja wrote:

> Hello Mr.Toshiaki,
>
> First off, I'd like to thank you for all your help.
>
> I have just one more question for you. I am trying to see how to use Smith-Waterman / Needleman Wunch alignment in Bioruby.
> I really appreciate any input from you.
>
> Thanks
> Sharvari


There are several ways to do it. Simplest version would be

  result = `water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse' -stdout -auto`

and usage of the Bio::EMBOSS class is well documented in the source code.

  http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby//lib/bio/appl/emboss.rb?rev=1.8&cvsroot=bioruby


bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec
########################################
# Program: water
# Rundate: Wed  9 Jan 2008 11:22:59
# Commandline: water
#    -asequence swissprot:slpi_human
#    -bsequence swissprot:slpi_mouse
#    -stdout
#    -auto
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: SLPI_HUMAN
# 2: SLPI_MOUSE
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 132
# Identity:      79/132 (59.8%)
# Similarity:    96/132 (72.7%)
# Gaps:           3/132 ( 2.3%)
# Score: 464.5
# 
#
#=======================================

SLPI_HUMAN         1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK     48
                     |||.||.||.||||||.||||.||| ||  :.|.|.||.||.||||:.:|
SLPI_MOUSE         1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK     49

SLPI_HUMAN        49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM     98
                     |:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:|
SLPI_MOUSE        50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM     99

SLPI_HUMAN        99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV    130
                     |||||.|:.||||....|||.|:|||.|:.|:
SLPI_MOUSE       100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM    131


#---------------------------------------
#---------------------------------------
  ==> nil