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|
##################################################
#
# README splice_sites
#
# This README runs as a shell script.
# Here you can find the commands
# we used to produce all the figures for:
#
# ""
#
# USAGE: bash README > .log 2>&1
#
# $Id: README,v 1.2 2003/03/04 19:06:09 jabril Exp $
#
##################################################
#
SECONDS=0 ;
#
#
# Original Files
#
# KCRB.AG.hs.gff KCRB.AG.mm.gff KCRB.AG.hs-mm.gff_tmp
# KCRB.GT.hs.gff KCRB.GT.mm.gff KCRB.GT.hs-mm.gff
#
# Fixing GFF input files
#
# gawk '{$6=sprintf("%.2f",$6);
# $9=$6;
# print $0}' KCRB.AG.hs-mm.gff_tmp > KCRB.AG.hs-mm.gff
# cp KCRB.AG.hs.gff KCRB.hs.gff~
# cp KCRB.AG.mm.gff KCRB.mm.gff~
#
# sort +3n -4 KCRB.hs.gff~ KCRB.hs_utr.gff > KCRB.hs.gff
# sort +3n -4 KCRB.mm.gff~ KCRB.mm_utr.gff > KCRB.mm.gff
#
echo "# Getting the PostScripts with GFF2APLOT" ;
#
echo "# -> GT - DONORS" ;
# GT - DONORS
$BIN/gff2aplot.pl -v -t "DONOR SITES" \
-- KCRB.hs.gff \
KCRB.mm.gff \
KCRB.GT.hs-mm.gff \
> KCRB.GT.hs-mm.ps \
2> KCRB.GT.hs-mm.log;
#
echo "# -> AG - ACCEPTORS" ;
# AG - ACCEPTORS
$BIN/gff2aplot.pl -v -t "ACCEPTOR SITES" \
-- KCRB.hs.gff \
KCRB.mm.gff \
KCRB.AG.hs-mm.gff \
> KCRB.AG.hs-mm.ps \
2> KCRB.AG.hs-mm.log;
#
echo "# -> GT + AG" ;
# GT + AG
$BIN/gff2aplot.pl -v -t "DONOR + ACCEPTOR SITES" \
-- KCRB.hs.gff \
KCRB.mm.gff \
KCRB.GT.hs-mm.gff \
KCRB.AG.hs-mm.gff \
> KCRB.GT-AG.hs-mm.ps \
2> KCRB.GT-AG.hs-mm.log;
# Extra customization
cat > GT-AG.rc <<'+++EOF+++'
#
# L #
# percent_box_label=SIMILARITY
# percent_box_label_fontsize=10pt
show_percent_box=on
percent_box_score_range=0.0..1.0
major_tickmark_score=0.25
minor_tickmark_score=0.05
x_label=Homo sapiens
x_label_font=helvetica-boldoblique
y_label=Mus musculus
y_label_font=helvetica-boldoblique
ribbon_color_merge=on
color_merge_factor=0.5
aplot_score_range=0..1
#
# G #
*::group_shape=arrow
#
# F #
utr::feature_color=lightgrey
exon::feature_color=darkorange
exon::show_ribbons=on
utr::show_ribbons=on
exon::ribbon_style=both
utr::ribbon_style=ribbons
exon::ribbon_color=lightyellow
utr::ribbon_color=palegrey
# GT - Donors
alignGT::alignment_color=darkred
# AG - Acceptors
alignAG::alignment_color=darkblue
*::alignment_scale_color=on
+++EOF+++
#
echo "# -> GT + AG ... CUSTOMIZED" ;
# GT + AG
$BIN/gff2aplot.pl -v -t "DONOR + ACCEPTOR SITES (Color Version)" \
--x-sequence-coords 0..4200 \
--y-sequence-coords 0..4600 \
--custom-filename GT-AG.rc \
-- KCRB.hs.gff \
KCRB.mm.gff \
KCRB.GT.hs-mm.gff \
KCRB.AG.hs-mm.gff \
> KCRB.GT-AG.hs-mm.color.ps \
2> KCRB.GT-AG.hs-mm.color.log;
# Extra customization
cat > GT-AG_sm.rc <<'+++EOF+++'
# L #
color_merge_factor=1
+++EOF+++
#
echo "# -> GT + AG ... MORE CUSTOMIZED" ;
# GT + AG
$BIN/gff2aplot.pl -v -t "DONOR + ACCEPTOR SITES (Color Version)" \
--x-sequence-coords 0..4200 \
--y-sequence-coords 0..4600 \
--custom-filename GT-AG.rc \
--custom-filename GT-AG_sm.rc \
-- KCRB.hs.gff \
KCRB.mm.gff \
KCRB.GT.hs-mm.gff \
KCRB.AG.hs-mm.gff \
> KCRB.GT-AG.hs-mm.color_small.ps \
2> KCRB.GT-AG.hs-mm.color_small.log;
#
# Preparing web images
#
filenames () {
cat << 'EOF';
EOF
};
#
# echo "# Using \"ghostscript\" to obtain JPEG images from PS files" ;
echo "# Using \"ghostscript\" to obtain PNG images from PS files" ;
#
GS=`which gs || echo "gs"`;
MG=`which mogrify || echo "mogrify"`;
CV=`which convert || echo "convert"`;
#
filenames | while read n ;
do {
echo "# -> $n" ;
$GS -dBATCH -dNOPAUSE -r300 \
-sPAPERSIZE=a4 -sDEVICE=png16m \
-sOutputFile=$n.png $n.ps ;
cp -v $n.png $n.s.png ;
# mogrify is a ImageMagick tool that allow us to transform images on batch,
# large high-resolution jpeg files are scaled down to thumbnail resolution (2479x3508=>123x175)
# it overwrites original file (so that we previously get a renamed copy for each jpeg to process).
$MG -verbose -geometry 5% $n.s.png ;
#
# $GS -dBATCH -dNOPAUSE -r300 \
# -sPAPERSIZE=a4 -sDEVICE=jpeg \
# -sOutputFile=$n.jpg $n.ps ;
# png large version is pretty smaller than jpeg
# cp -v $n.jpg $n.s.jpg ;
# $MG -verbose -geometry 5% $n.s.jpg ;
};
done ;
$CV 'vid:*.s.png' splicesites.summary.png
#
echo "# Using \"ghostscript\" to obtain PDF documents from PS files" ;
#
filenames | while read n ;
do {
echo "# -> $n" ;
$GS -dBATCH -dNOPAUSE -r300 \
-sPAPERSIZE=a4 -sDEVICE=pdfwrite \
-sOutputFile=$n.pdf $n.ps ;
};
done ;
#
#
# echo "# LaTeXing all figures together..." ;
#
# latex splicesites.tex;
# dvips splicesites.dvi -o splicesites.ps;
#
#
echo "###" ;
echo "### TOTAL TIME: $SECONDS seconds..." ;
#
#
# That's all folks... ;^D
#
# >> Copyleft (C) 2002/2003 - Josep F. Abril <<
#
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