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comparison collectorcurve/collectorcurve.sh @ 0:f4d86766f766 draft

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author qfab
date Fri, 30 May 2014 03:16:03 -0400
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-1:000000000000 0:f4d86766f766
1 #!/bin/bash
2
3 echo $@
4
5 command=''
6 filetype=$1
7 input=$2
8 label=$3
9 echo label is $label
10 if [ $label != 'None' ]; then
11 labelformatted=${label//,/-}
12 command+=', 'label=$labelformatted
13 fi
14 output=$4
15 outputid=$5
16 outputpath=$6
17 calc=$7
18 advanced=$8
19 if [ $advanced == True ]; then
20 cabund=$9
21 abund=${10}
22 if [ $cabund == True ]; then
23 command+=', 'abund=$abund
24 fi
25 csize=${11}
26 size=${12}
27 if [ $csize == True ]; then
28 if [ $size != 0 ]; then
29 command+=', 'size=$size
30 fi
31 fi
32 cfreq=${13}
33 freq=${14}
34 if [ $cfreq == True ]; then
35 command+=', 'freq=$freq
36 echo $command
37 fi
38 fi
39
40
41 echo path: $outputpath id: $outputid
42 ## get filename only remove the extension
43 file="${input%.*}"
44 echo `cp $input $file'.'$filetype`
45 inputfile=$file'.'$filetype
46 calculator=${calc//,/-}
47 IFS=',' read -a sum_calc <<< "$calc"
48 for element in "${sum_calc[@]}"
49 do
50 if [[ "$element" != "nseqs" ]] && [[ "$element" != "coverage" ]] && [[ "$element" != "sobs" ]]
51 then
52 sum_calculator+='-'$element
53 fi
54 done
55 #echo "collect.single($filetype=$inputfile, calc=$calc)"
56 ## use Mothur collect.single to calculate collector's curve - alpha diversity
57 #mothur "#summary.single($filetype=$inputfile, calc=$calculator$command)"
58 mothur "#summary.single($filetype=$inputfile, calc=nseqs-coverage-sobs$sum_calculator$command)"
59 mothur "#collect.single($filetype=$inputfile, calc=$calculator$command)"
60 IFS=, read -a calcs <<< "${calc}"
61 count=0
62 ##copy summary as main output
63 echo `cp $file'.summary' $output`
64 #copy calc files into directory
65 for i in "${calcs[@]}"
66 do
67 #if [ $count == 0 ]; then
68 # echo `cp $file'.'$i $output`
69 #else
70 echo `cp $file'.'$i $outputpath'/primary_'$outputid'_'$i'_visible_tabular'`
71 #fi
72 let count+=1
73 done