Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 63:a7381fd96dad draft

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Uploaded
author davidvanzessen
date Fri, 25 Mar 2016 07:50:12 -0400
parents 4262e880472d
children 0fdd90f7c654
comparison
equal deleted inserted replaced
62:4262e880472d 63:a7381fd96dad
12 naive_output=$9 12 naive_output=$9
13 filter_unique=${10} 13 filter_unique=${10}
14 mkdir $outdir 14 mkdir $outdir
15 15
16 echo "---------------- read parameters ----------------" 16 echo "---------------- read parameters ----------------"
17 echo "---------------- read parameters ----------------" > $output 17 echo "---------------- read parameters ----------------<br />" > $output
18 18
19 echo "unpacking IMGT file" 19 echo "unpacking IMGT file"
20 20
21 type="`file $input`" 21 type="`file $input`"
22 if [[ "$type" == *"Zip archive"* ]] ; then 22 if [[ "$type" == *"Zip archive"* ]] ; then
41 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin" 41 #BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
42 42
43 echo "${BLASTN_DIR}" 43 echo "${BLASTN_DIR}"
44 44
45 echo "identification ($method)" 45 echo "identification ($method)"
46 echo "identification ($method)" >> $output 46 echo "identification ($method)<br />" >> $output
47 47
48 echo "blast or custom" 48 echo "blast or custom"
49 49
50 if [[ "${method}" == "custom" ]] ; then 50 if [[ "${method}" == "custom" ]] ; then
51 echo "custom" 51 echo "custom"
64 echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt 64 echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt
65 ${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt 65 ${BLASTN_DIR}/blastn -task blastn -db $dir/subclass_definition.db -query $PWD/sequences.fasta -outfmt 6 >> $outdir/identified_genes.txt
66 fi 66 fi
67 67
68 echo "---------------- merge_and_filter.r ----------------" 68 echo "---------------- merge_and_filter.r ----------------"
69 echo "---------------- merge_and_filter.r ----------------" >> $output 69 echo "---------------- merge_and_filter.r ----------------<br />" >> $output
70 70
71 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} 71 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique}
72 72
73 echo "---------------- mutation_analysis.r ----------------" 73 echo "---------------- mutation_analysis.r ----------------"
74 echo "---------------- mutation_analysis.r ----------------" >> $output 74 echo "---------------- mutation_analysis.r ----------------<br />" >> $output
75 75
76 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm" 76 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
77 echo "R mutation analysis" 77 echo "R mutation analysis"
78 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 78 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
79 79
81 #exit 0 81 #exit 0
82 82
83 83
84 84
85 echo "---------------- mutation_analysis.py ----------------" 85 echo "---------------- mutation_analysis.py ----------------"
86 echo "---------------- mutation_analysis.py ----------------" >> $output 86 echo "---------------- mutation_analysis.py ----------------<br />" >> $output
87 87
88 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt 88 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
89 echo "R AA histogram" 89 echo "R AA histogram"
90 90
91 echo "---------------- aa_histogram.r ----------------" 91 echo "---------------- aa_histogram.r ----------------"
92 echo "---------------- aa_histogram.r ----------------" >> $output 92 echo "---------------- aa_histogram.r ----------------<br />" >> $output
93 93
94 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1 94 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
95 95
96 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm) 96 genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)
97 97