Mercurial > repos > ulfschaefer > phephenix
comparison vcfs2fasta.sh @ 0:cb29f95c7b88 draft
Uploaded
author | ulfschaefer |
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date | Mon, 09 May 2016 09:27:06 -0400 |
parents | |
children | 29a682a7dd16 |
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-1:000000000000 | 0:cb29f95c7b88 |
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1 #!/bin/bash | |
2 | |
3 echo $@ | |
4 | |
5 OUTPUT=$1 | |
6 shift | |
7 WITHMIXTURES=$1 | |
8 shift | |
9 COLUMNNS=$1 | |
10 shift | |
11 SAMPLENS=$1 | |
12 shift | |
13 REFERENCE=$1 | |
14 shift | |
15 INCLUDE=$1 | |
16 shift | |
17 EXCLUDE=$1 | |
18 shift | |
19 INPUT=$@ | |
20 | |
21 CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT" | |
22 | |
23 if [ $WITHMIXTURES != "NOTTHERE" ]; then | |
24 CMD="$CMD --with-mixtures $WITHMIXTURES" | |
25 fi | |
26 | |
27 if [ $COLUMNNS != "NOTTHERE" ]; then | |
28 CMD="$CMD --column-Ns $COLUMNNS" | |
29 fi | |
30 | |
31 if [ $SAMPLENS != "NOTTHERE" ]; then | |
32 CMD="$CMD --sample-Ns $SAMPLENS" | |
33 fi | |
34 | |
35 if [ $REFERENCE != "NOTTHERE" ]; then | |
36 CMD="$CMD --reference $REFERENCE" | |
37 fi | |
38 | |
39 if [ $INCLUDE != "NOTTHERE" ]; then | |
40 CMD="$CMD --include INCLUDE" | |
41 fi | |
42 | |
43 if [ $EXCLUDE != "NOTTHERE" ]; then | |
44 CMD="$CMD --exclude EXCLUDE" | |
45 fi | |
46 | |
47 echo $CMD | |
48 eval $CMD |