Mercurial > repos > rmarenco > multi_fasta_glimmer_hmm

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planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
author rmarenco
date Thu, 18 Aug 2016 18:50:00 -0400
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0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
rmarenco
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1 #!/bin/sh
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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2 set -e
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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3
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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4 reference_fasta=$1
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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5 trained_dir=$2
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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6 output=$3
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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7 temp="temp_contig_file"
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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8
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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9 # Write the glimmerhmm, with the comments
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
rmarenco
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10 glimmerHMM_first () {
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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11 glimmerhmm $1 ${trained_dir} -o ${output} -g
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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12 }
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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13
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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14 # Write the glimmerhmm output without the comments
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
rmarenco
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15 glimmerHMM_without_comments () {
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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16 glimmerhmm $1 ${trained_dir} -g | tail -n +2 >> ${output}
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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17 }
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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18
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19 count=1
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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20 # Loop through the contigs to run glimmer on each
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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21 while read line
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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22 do
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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23 # Get the content of actual contig
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
rmarenco
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24 #samtools_faidx_show_contig ${reference_fasta} ${contig} > contig_content
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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25 first_char=$(echo ${line} | cut -c1-1)
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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26
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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27 if [ ${first_char} = '>' ]
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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28 then
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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29 # If true, it means we have finished reading at least the first contig
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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30 if [ -f ${temp} ]
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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31 then
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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32 if [ ${count} -eq 1 ]
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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33 then
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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34 glimmerHMM_first ${temp};
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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35 count=$((count+1))
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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36 else
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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37 glimmerHMM_without_comments ${temp};
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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38 fi
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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39 fi
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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40 echo ${line} > ${temp}
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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41 else
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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42 echo ${line} >> ${temp}
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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43 fi
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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44 done < "${reference_fasta}"
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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45
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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46 # Still last contig to process
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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47 glimmerHMM_without_comments ${temp};
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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48
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49 # Delete the temp_contig_file
0ddb5ee32ff6 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 28bd73b26b50165eded1d9ba995979acdf005ad1-dirty
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50 rm ${temp}