Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 57:cb779a45537b draft

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Uploaded
author davidvanzessen
date Tue, 18 Jul 2017 04:28:11 -0400
parents ee807645b224
children 7b9481fa4a70
comparison
equal deleted inserted replaced
56:ee807645b224 57:cb779a45537b
46 echo "Unrecognized format $type" > $log 46 echo "Unrecognized format $type" > $log
47 exit 1 47 exit 1
48 fi 48 fi
49 49
50 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt 50 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
51 cat "`find $PWD/files/ -name "2_*"`" > $PWD/gapped_nt.txt
51 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt 52 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
52 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt 53 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
53 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt 54 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
54 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt 55 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
55 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt 56 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
56 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt 57 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
58 cat "`find $PWD/files/ -name "9_*"`" > $PWD/aa_change_stats.txt
57 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt 59 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
58 60
59 echo "---------------- unique id check ----------------" 61 echo "---------------- unique id check ----------------"
60 62
61 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt 63 Rscript $dir/check_unique_id.r $PWD/summary.txt $PWD/gapped_nt.txt $PWD/sequences.txt $PWD/gapped_aa.txt $PWD/aa.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/aa_change_stats.txt $PWD/hotspots.txt
62 64
63 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then 65 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
64 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}" 66 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
65 else 67 else
66 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin" 68 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
75 echo "---------------- merge_and_filter.r ----------------" 77 echo "---------------- merge_and_filter.r ----------------"
76 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 78 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
77 79
78 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1 80 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
79 81
80 if [[ "${naive_output}" == "yes" ]] ; then 82 if [[ "${naive_output}" == "yes" ]] || [[ "$fast" == "no" ]] ; then
81 83
82 echo "---------------- creating new IMGT zips ----------------" 84 echo "---------------- creating new IMGT zips ----------------"
83 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 85 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
84 86
85 mkdir $outdir/new_IMGT 87 mkdir $outdir/new_IMGT
86 88
87 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt" 89 cp $PWD/summary.txt "$outdir/new_IMGT/1_Summary.txt"
88 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt" 90 cp $PWD/gapped_nt.txt "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
89 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt" 91 cp $PWD/sequences.txt "$outdir/new_IMGT/3_Nt-sequences.txt"
90 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt" 92 cp $PWD/gapped_aa.txt "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
91 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt" 93 cp $PWD/aa.txt "$outdir/new_IMGT/5_AA-sequences.txt"
92 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt" 94 cp $PWD/junction.txt "$outdir/new_IMGT/6_Junction.txt"
93 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt" 95 cp $PWD/mutationanalysis.txt "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
94 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt" 96 cp $PWD/mutationstats.txt "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
95 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt" 97 cp $PWD/aa_change_stats.txt "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
96 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt" 98 cp $PWD/hotspots.txt "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
97 99
98 mkdir $outdir/new_IMGT_IGA 100 mkdir $outdir/new_IMGT_IGA
99 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA 101 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
100 102
101 mkdir $outdir/new_IMGT_IGA1 103 mkdir $outdir/new_IMGT_IGA1