Entering edit mode
7.9 years ago
kapil.joshi036
▴
80
Hello all , I want to extract the all 4 nucleotide signal values A T G C , I gone through this post and tried whatever maintained there.When i used following commend
abiview -graph data -outseq myseq.fa myseq.ab1
it generating the 4 files but i m not getting the peak values at each position here is the one output file
##
##Title abiview of Seq_D12_RAJASHEKAR_MITO5_F_008
##Graphs 4
##Number 1
##Points 43
##XminA 801.000000 XmaxA 805.000000 YminA 0.000000 YmaxA 2399.000000
##Xmin 0.000000 Xmax 0.000000 Ymin 0.000000 Ymax 0.000000
##ScaleXmin 801.000000 ScaleXmax 805.000000 ScaleYmin 0.000000 ScaleYmax 2399.000000
##Maintitle
##Subtitle
##Xtitle
##Ytitle
801.090881 22.000000
801.181824 22.000000
801.272705 22.000000
801.363647 23.000000
801.454529 25.000000
801.545471 27.000000
801.636353 28.000000
801.727295 29.000000
801.818176 29.000000
801.909119 29.000000
802.000000 28.000000
802.083313 27.000000
802.166687 26.000000
802.250000 26.000000
802.333313 27.000000
802.416687 27.000000
802.500000 28.000000
802.583313 30.000000
802.666687 31.000000
802.750000 33.000000
802.833313 34.000000
802.916687 35.000000
803.000000 35.000000
803.090881 34.000000
803.181824 32.000000
803.272705 30.000000
803.363647 29.000000
803.454529 29.000000
803.545471 31.000000
803.636353 33.000000
803.727295 36.000000
803.818176 38.000000
803.909119 37.000000
804.000000 35.000000
804.111084 31.000000
804.222229 26.000000
804.333313 22.000000
804.444458 19.000000
804.555542 18.000000
804.666687 19.000000
804.777771 20.000000
804.888916 21.000000
805.000000 20.000000
##DataObjects
##Number 0
##GraphObjects
##Number 4
Textline x1 801.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
Textline x1 802.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
Textline x1 803.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
Textline x1 804.000000 y1 2349.000000 x2 0.000000 y2 0.000000 colour 1 size 1.0 T
but my sequence length is around 800 bp its not showing the values for the 450 bp in the sequence when i use perl
eperl -MBio::Trace::ABIF -MArray::Transpose -e 'BEGIN{$abif=Bio::Trace::ABIF->new($_); $,="\t",$\="\n"}; $abif- >open_abif(@ARGV) or die "can not open"; print @$_ foreach transpose ([map {[$_,$abif->raw_trace($_)]} qw(A T G C)])' my.ab1 > my_ab1_trace.tab
its giving me around 16000 rows so can any1 please tell me how to extract details of each signal values
P.S Need to be compatible with linux terminal