Mercurial > repos > ulfschaefer > phephenix

comparison vcfs2fasta.sh @ 7:29a682a7dd16 draft

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Uploaded
author ulfschaefer
date Thu, 16 Jun 2016 06:40:02 -0400
parents cb29f95c7b88
children f7494340ae7f
comparison
equal deleted inserted replaced
6:74f595df6e51 7:29a682a7dd16
6 shift 6 shift
7 WITHMIXTURES=$1 7 WITHMIXTURES=$1
8 shift 8 shift
9 COLUMNNS=$1 9 COLUMNNS=$1
10 shift 10 shift
11 COLUMNGAPS=$1
12 shift
11 SAMPLENS=$1 13 SAMPLENS=$1
14 shift
15 SAMPLEGAPS=$1
12 shift 16 shift
13 REFERENCE=$1 17 REFERENCE=$1
14 shift 18 shift
15 INCLUDE=$1 19 INCLUDE=$1
16 shift 20 shift
17 EXCLUDE=$1 21 EXCLUDE=$1
22 shift
23 STATS=$1
18 shift 24 shift
19 INPUT=$@ 25 INPUT=$@
20 26
21 CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT" 27 CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT"
22 28
26 32
27 if [ $COLUMNNS != "NOTTHERE" ]; then 33 if [ $COLUMNNS != "NOTTHERE" ]; then
28 CMD="$CMD --column-Ns $COLUMNNS" 34 CMD="$CMD --column-Ns $COLUMNNS"
29 fi 35 fi
30 36
37 if [ $COLUMNGAPS != "NOTTHERE" ]; then
38 CMD="$CMD --column-gaps $COLUMNGAPS"
39 fi
40
31 if [ $SAMPLENS != "NOTTHERE" ]; then 41 if [ $SAMPLENS != "NOTTHERE" ]; then
32 CMD="$CMD --sample-Ns $SAMPLENS" 42 CMD="$CMD --sample-Ns $SAMPLENS"
43 fi
44
45 if [ $SAMPLEGAPS != "NOTTHERE" ]; then
46 CMD="$CMD --sample-gaps $SAMPLEGAPS"
33 fi 47 fi
34 48
35 if [ $REFERENCE != "NOTTHERE" ]; then 49 if [ $REFERENCE != "NOTTHERE" ]; then
36 CMD="$CMD --reference $REFERENCE" 50 CMD="$CMD --reference $REFERENCE"
37 fi 51 fi
38 52
39 if [ $INCLUDE != "NOTTHERE" ]; then 53 if [ $INCLUDE != "NOTTHERE" ]; then
40 CMD="$CMD --include INCLUDE" 54 CMD="$CMD --include $INCLUDE"
41 fi 55 fi
42 56
43 if [ $EXCLUDE != "NOTTHERE" ]; then 57 if [ $EXCLUDE != "NOTTHERE" ]; then
44 CMD="$CMD --exclude EXCLUDE" 58 CMD="$CMD --exclude $EXCLUDE"
45 fi 59 fi
46 60
47 echo $CMD 61 echo $CMD
48 eval $CMD 62 eval $CMD