Mercurial > repos > rmarenco > multi_fasta_glimmer_hmm
comparison multi_glimmer.sh @ 0:0ddb5ee32ff6 draft default tip
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 |
| parents | |
| children |
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| -1:000000000000 | 0:0ddb5ee32ff6 |
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| 1 #!/bin/sh | |
| 2 set -e | |
| 3 | |
| 4 reference_fasta=$1 | |
| 5 trained_dir=$2 | |
| 6 output=$3 | |
| 7 temp="temp_contig_file" | |
| 8 | |
| 9 # Write the glimmerhmm, with the comments | |
| 10 glimmerHMM_first () { | |
| 11 glimmerhmm $1 ${trained_dir} -o ${output} -g | |
| 12 } | |
| 13 | |
| 14 # Write the glimmerhmm output without the comments | |
| 15 glimmerHMM_without_comments () { | |
| 16 glimmerhmm $1 ${trained_dir} -g | tail -n +2 >> ${output} | |
| 17 } | |
| 18 | |
| 19 count=1 | |
| 20 # Loop through the contigs to run glimmer on each | |
| 21 while read line | |
| 22 do | |
| 23 # Get the content of actual contig | |
| 24 #samtools_faidx_show_contig ${reference_fasta} ${contig} > contig_content | |
| 25 first_char=$(echo ${line} | cut -c1-1) | |
| 26 | |
| 27 if [ ${first_char} = '>' ] | |
| 28 then | |
| 29 # If true, it means we have finished reading at least the first contig | |
| 30 if [ -f ${temp} ] | |
| 31 then | |
| 32 if [ ${count} -eq 1 ] | |
| 33 then | |
| 34 glimmerHMM_first ${temp}; | |
| 35 count=$((count+1)) | |
| 36 else | |
| 37 glimmerHMM_without_comments ${temp}; | |
| 38 fi | |
| 39 fi | |
| 40 echo ${line} > ${temp} | |
| 41 else | |
| 42 echo ${line} >> ${temp} | |
| 43 fi | |
| 44 done < "${reference_fasta}" | |
| 45 | |
| 46 # Still last contig to process | |
| 47 glimmerHMM_without_comments ${temp}; | |
| 48 | |
| 49 # Delete the temp_contig_file | |
| 50 rm ${temp} |