Mercurial > repos > yating-l > multi_fasta_glimmer_hmm

annotate multi_glimmer.sh @ 9:81383b1c05d9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
author yating-l
date Thu, 04 May 2017 17:30:27 -0400
parents 36f4ba558f9f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
1 #!/bin/sh
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
2 set -e
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
3
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
4 reference_fasta=$1
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
5 trained_dir=$2
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
6 output=$3
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
7 temp="temp_contig_file"
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
8
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
9 # Write the glimmerhmm, with the comments
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
10 glimmerHMM_first () {
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
11 glimmerhmm $1 ${trained_dir} -o ${output} -g
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
12 }
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
13
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
14 # Write the glimmerhmm output without the comments
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
15 glimmerHMM_without_comments () {
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
16 glimmerhmm $1 ${trained_dir} -g | tail -n +2 >> ${output}
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
17 }
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
18
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
19 count=1
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
20 # Loop through the contigs to run glimmer on each
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
21 while read line
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
22 do
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
23 # Get the content of actual contig
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
24 #samtools_faidx_show_contig ${reference_fasta} ${contig} > contig_content
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
25 first_char=$(echo ${line} | cut -c1-1)
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
26
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
27 if [ ${first_char} = '>' ]
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
28 then
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
29 # If true, it means we have finished reading at least the first contig
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
30 if [ -f ${temp} ]
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
31 then
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
32 if [ ${count} -eq 1 ]
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
33 then
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
34 glimmerHMM_first ${temp};
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
35 count=$((count+1))
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
36 else
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
37 glimmerHMM_without_comments ${temp};
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
38 fi
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
39 fi
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
40 echo ${line} > ${temp}
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
41 else
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
42 echo ${line} >> ${temp}
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
43 fi
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
44 done < "${reference_fasta}"
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
45
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
46 # Still last contig to process
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
47 glimmerHMM_without_comments ${temp};
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
48
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
49 # Delete the temp_contig_file
36f4ba558f9f planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 1245031a7d52c922c86f33ebfd0f20eb9ddf84ac-dirty
yating-l
parents:
diff changeset
50 rm ${temp}