#!/bin/sh
now="$(date +%s)"

clear
printf "Current directory is:  \n\n";
pwd
echo  "\nEnter input file name: \c"
read  input

echo  "\nHow are your groups delimited?  \nFor example, \"_\" (underscore), \"-\" (dash), \" \" (space), etc.: \c"
read  delimiter

echo "\nDo you need to cluster sequences into OTUs?  y/n:  \c"
read cd_hit_choice

echo "\nCan you afford to pay for color graphics?  y/n:  \c"
read graphics_color

printf "\nEnter number of seconds to pause between steps... "
read sleep

if [ $cd_hit_choice = "y" ] ; then 

#---run cdhit---
#printf "\n\nRunning CD-HIT for 0.01 cutoff...\n\n"
#cdhit-est -i $input -o output_file_99 -c 0.99 -n 9 -g 1
#clear
printf "\n\nRunning CD-HIT for 0.03 cutoff...\n\n"
cdhit-est -i $input -o output_file_97 -c 0.97 -n 9 -g 1
clear
printf "\n\nRunning CD-HIT for 0.05 cutoff...\n\n"
cdhit-est -i $input -o output_file_95 -c 0.95 -n 8 -g 1
clear
printf "\n\nRunning CD-HIT for 0.1 cutoff...\n\n"
cdhit-est -i $input -o output_file_90 -c 0.90 -n 7 -g 1
clear
#printf "\n\nRunning CD-HIT for 0.15 cutoff...\n\n"
#cdhit-est -i $input -o output_file_85 -c 0.85 -n 6 -g 1
#clear



fi

#---print number of clusters to screen---
printf "\nNumber of clusters in each file is:\n\n"
grep -c ">Clus" *_??.clstr
printf "\n\n"

#---pause---
sleep $sleep

#---Making summary data table for downstream R scripts---
printf "\nReformatting cd-hit output into single data table for downstream analyses...\n"
sleep $sleep
my_cluster_cleaner.pl -d $delimiter

#---Converting cd-hit output to mothur---
printf "\nDone.\n\nReformatting cd-hit output files into mothur format...\n"
sleep $sleep
my_cd-hit_to_mothur_converter.pl


#---Generating group file for mothur---
printf "\nGenerating group file for mothur...\n"
sleep $sleep
my_group_file_maker.pl -i $input -d $delimiter

#---Call mothur for venn diagrams and tree file---
mothur "#read.otu(list=mothur_converter_output.list, group=group_file.groups); venn(); tree.shared()"
sleep $sleep

#======Make graphics and stats output with R=======
clear
printf "\nRunning R scripts to make graphics and perform stats:\n"
printf "\nContact brian.oakley at arsdotusdadotgov if any questions...\n"
printf "\n--------------------------------------------------------\n\n";

printf "\nMaking rarefaction curves for each cutoff...."
if [ $graphics_color = "y" ]; then
R CMD BATCH ~/shell_scripts/make_rarefaction_curves_color.r
fi
if [ $graphics_color = "n" ]; then
R CMD BATCH ~/shell_scripts/make_rarefaction_curves_bw.r
fi

printf "Done.\n\n\nMaking OTU distributions for each cutoff...."
R CMD BATCH ~/shell_scripts/make_OTU_distributions.r

printf "Done.\n\n\nMaking OTU frequency distributions for each cutoff ...."
R CMD BATCH ~/shell_scripts/make_freq_dists_w_constant_clusters.r

printf "Done.\n\n\nRunning cca for each cutoff...."
R CMD BATCH ~/shell_scripts/make_cca_plots.r

printf "Done.\n\n\nCalculating richness and diversity stats for each cutoff...."
R CMD BATCH ~/shell_scripts/make_richness_diversity_stats.r
printf "Done!\n\n\n"

#=======Done with graphics=========


later="$(date +%s)"
elapsed_seconds="$(expr $later - $now)"
printf "Done!\n\n\n\nElapsed time: $elapsed_seconds seconds\n\n\n\n"