#!/bin/sh
# the next line restarts using wish \
    exec wish "$0" "$@"
set waitlimit 2000
exec clear
puts {
  // \\          // \\  // \\          // \\  // \\
  ': | \\      // | :,\\': | \\      // | :,\\': | \\
  \\ | | \\  // | | //  \\ | | \\  // | | //  \\ | |
    \\ | :,\\': | //      \\ | :,\\': | //      \\ |
      \\ //  \\ //          \\ //  \\ //          \\

  Biowish is a C-extension for the Tcl/Tk scripting language. 
  It consists of one main library which can be loaded dynamically
  into a running Tcl/Tk interpreter. Biowish adds additional 
  molecular biology related Tcl commands like basic nucleotide
  sequence editing/analysing and for Tk a sequence editing widget.

  // \\          // \\  // \\          // \\  // \\
  ': | \\      // | :,\\': | \\      // | :,\\': | \\
  \\ | | \\  // | | //  \\ | | \\  // | | //  \\ | |
    \\ | :,\\': | //      \\ | :,\\': | //      \\ |
      \\ //  \\ //          \\ //  \\ //          \\

  ... This is a testing script for Biowish ....
}
wm withdraw .
after $waitlimit
puts "loading biowish .."
load ./biowish.so

puts "wait [ expr $waitlimit/1000] seconds until next command ..."
set file testseq.embl
# seq is the target array for the sequence
puts "reading $file ..."
biowish::readseq $file seq
puts "array names:\n [array names seq]"
after $waitlimit

# sequence information
puts "Seqinfo: [ biowish::seqinfo $seq(sequence)]"
after $waitlimit
# G+C% 
puts "G+C%: [biowish::gc $seq(sequence)]"
after $waitlimit
# subsequence
biowish::subseq seq 0 100
# subsequence now in seq(subseq,name) and seq(subseq)
puts "Subsequence: [array names seq]"
after $waitlimit

set sseq(sequence) $seq(subseq)
set sseq(name) $seq(subseq,name)
set sseq(length) $seq(subseq,length)

# Reverse, Complement and Antiparallel
puts -nonewline "checking reverse, complement and antiparallel ..."
set rev [ biowish::reverse $sseq(sequence) ]
set com [ biowish::complement $sseq(sequence)]
set anti [ biowish::antiparallel $sseq(sequence)]
set rev_com [ biowish::complement $rev]
if {$anti!=$rev_com} {
    puts stderr "Ooooppps new_s != original sequence"
} else { puts "ok !!! " }
after $waitlimit

set s $sseq(sequence)
# Translation frames
puts "\n\n\n6 frames: [ biowish::6frame $s]"
after $waitlimit
puts "\n\n\n3 frames: [ biowish::3frame $s]"
after $waitlimit
puts "\n\n\n2 frames [ biowish::1frame $s]"
after $waitlimit
puts "\n\n\nall frames [ biowish::all_frames $s]"
after $waitlimit

# single frame translation
for { set i 1} {$i<4} {incr i} {
    set frame($i) [biowish::translate $i $s]
    puts "\n\n\nFrame $i: $frame($i)"
    after $waitlimit
} 
for { set i -1} {$i>-4} {incr i -1} {
    set frame($i) [biowish::translate $i $s]
    puts "\n\n\nFrame $i: $frame($i)"
    after $waitlimit
}
# Mutate sequence 100 times
puts  "mutating 100 times \n [biowish::mutate $s 35 35 15 15 100]"
after $waitlimit
# DNA increment
set nt a
puts "DNA increment ..."
for { set i 0} {$i<50} {incr i} { 
    biowish::dna_incr nt
    puts -nonewline "$nt "
    after 100
    flush stdout
} 
puts -nonewline "\n"
after $waitlimit

# converting sequences to ..
# fasta embl genbank gcg pir raw ig stanford gb nbrf uwgcg dnastrider
# strider fitch pearson zuker olsen phylip phylip3.2 phylip3.3 phylip3.4
# phylip-interleaved phylip-sequential plain codata asn.1 msf paup nexus

puts "\n\n\nconverting sequence\n\t [ biowish::convertseq sseq gcg ]"
after $waitlimit
# write sequence to file
# biowish::writeseq outfile sseq fasta


# TK only ...

# a sequence editor
puts -nonewline "starting sequence editor ...";flush stdout
biowish::xbbtools .xb
update
after $waitlimit
 destroy .xb
puts "ok"
# a sequence editor with file on startup
puts -nonewline "starting sequence editor with file...";flush stdout
biowish::xbbtools_file .xb $file
update
after $waitlimit
 destroy .xb
puts "ok"

# a sequence editor with part of the file on startup
puts -nonewline "starting sequence editor with subsequence ...";flush stdout
biowish::xbbtools_subfile .xb $file 100 200
update
after $waitlimit
 destroy .xb
puts "ok"

# a sequence editor with open reading frames
puts -nonewline "starting sequence editor with open reading frames ...(this may take a while).."
flush stdout
biowish::xbbtools_file .xb $file
set id [biowish::xbb::orfs .xb]
update
lower .xb
puts "ok"
puts -nonewline "zooming 20% ..."
flush stdout
biowish::orfs::zoom $id 0.2
puts "ok"
puts -nonewline "reading features ..."
flush stdout
biowish::orfs::parse_features $id test.features
puts "ok"
update
after [ expr 3*$waitlimit]
destroy .xb

exit