Mercurial > repos > qfab > collector_curve
diff collectorcurve/collectorcurve.sh @ 0:f4d86766f766 draft
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author | qfab |
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date | Fri, 30 May 2014 03:16:03 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/collectorcurve/collectorcurve.sh Fri May 30 03:16:03 2014 -0400 @@ -0,0 +1,73 @@ +#!/bin/bash + +echo $@ + +command='' +filetype=$1 +input=$2 +label=$3 +echo label is $label +if [ $label != 'None' ]; then + labelformatted=${label//,/-} + command+=', 'label=$labelformatted +fi +output=$4 +outputid=$5 +outputpath=$6 +calc=$7 +advanced=$8 +if [ $advanced == True ]; then + cabund=$9 + abund=${10} + if [ $cabund == True ]; then + command+=', 'abund=$abund + fi + csize=${11} + size=${12} + if [ $csize == True ]; then + if [ $size != 0 ]; then + command+=', 'size=$size + fi + fi + cfreq=${13} + freq=${14} + if [ $cfreq == True ]; then + command+=', 'freq=$freq + echo $command + fi +fi + + +echo path: $outputpath id: $outputid +## get filename only remove the extension +file="${input%.*}" +echo `cp $input $file'.'$filetype` +inputfile=$file'.'$filetype +calculator=${calc//,/-} +IFS=',' read -a sum_calc <<< "$calc" +for element in "${sum_calc[@]}" +do + if [[ "$element" != "nseqs" ]] && [[ "$element" != "coverage" ]] && [[ "$element" != "sobs" ]] + then + sum_calculator+='-'$element + fi +done +#echo "collect.single($filetype=$inputfile, calc=$calc)" +## use Mothur collect.single to calculate collector's curve - alpha diversity +#mothur "#summary.single($filetype=$inputfile, calc=$calculator$command)" +mothur "#summary.single($filetype=$inputfile, calc=nseqs-coverage-sobs$sum_calculator$command)" +mothur "#collect.single($filetype=$inputfile, calc=$calculator$command)" +IFS=, read -a calcs <<< "${calc}" +count=0 +##copy summary as main output +echo `cp $file'.summary' $output` +#copy calc files into directory +for i in "${calcs[@]}" +do + #if [ $count == 0 ]; then + # echo `cp $file'.'$i $output` + #else + echo `cp $file'.'$i $outputpath'/primary_'$outputid'_'$i'_visible_tabular'` + #fi + let count+=1 +done