Mercurial > repos > konradpaszkiewicz > oasesoptimiser

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author konradpaszkiewicz
date Tue, 07 Jun 2011 17:09:27 -0400
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d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/bin/bash
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 min_k=$1
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 max_k=$2
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 input=$3
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 args=$#
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 if [$args -gt 3]; then
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8 velvetoptions=$4
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9 oasesoptions=$5
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 else
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 velvetoptions=''
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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12 oasesoptions=''
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 fi
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14
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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15 for i in `seq $min_k 2 $max_k`
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 do
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17 velveth . $i $input
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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18 velvetg . -read_trkg yes
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 oases . $oasesoptions
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 mv transcripts.fa transcripts_$i.fa
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 done
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22
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 velveth . $max_k -long transcripts_*.fa $input
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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24 velvetg . -read_trkg yes $velvetoptions
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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25 oases . -amos_file yes -unused_reads yes $oasesoptions
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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