Mercurial > repos > ziru-zhou > bamedit
comparison split.sh @ 3:e623e9c7bb23 draft
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| author | ziru-zhou |
|---|---|
| date | Tue, 18 Dec 2012 09:20:12 -0500 |
| parents | |
| children |
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| 2:5f4cb6ee3427 | 3:e623e9c7bb23 |
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| 1 #!bin/bash | |
| 2 | |
| 3 #purpose: shell script which performs the split option | |
| 4 #author: Ziru Zhou | |
| 5 #date: October, 2012 | |
| 6 | |
| 7 main() | |
| 8 { | |
| 9 output1="${1}" | |
| 10 output2="${2}" | |
| 11 input="${3}" | |
| 12 | |
| 13 $(samtools view -H ${input} > tmp) | |
| 14 linecount=$(samtools view ${input} | wc -l) | |
| 15 half=$(((${linecount} + 1) / 2)) | |
| 16 samtools view ${input} | shuf | split -d -l ${half} | |
| 17 | |
| 18 $(cat tmp x00 > x00h) | |
| 19 $(cat tmp x01 > x01h) | |
| 20 samtools view -bSo ${output1} x00h | |
| 21 samtools view -bSo ${output2} x01h | |
| 22 | |
| 23 rm tmp x00h x01h x00 x01 | |
| 24 } | |
| 25 main "${@}" |