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examples/ | H | 03-May-2022 | - | 64,777 | 55,368 | |
regress/ | H | 18-Nov-2019 | - | 4,621 | 4,605 | |
00README | H A D | 18-Nov-2019 | 5.4 KiB | 100 | 79 | |
blast2profmark | H A D | 18-Nov-2019 | 126 | 11 | 5 | |
blast2tbl | H A D | 18-Nov-2019 | 121 | 11 | 5 | |
demotic_blast.pm | H A D | 18-Nov-2019 | 8.8 KiB | 286 | 216 | |
demotic_fasta.pm | H A D | 18-Nov-2019 | 11.5 KiB | 384 | 274 | |
demotic_h2.pm | H A D | 18-Nov-2019 | 5.3 KiB | 190 | 139 | |
demotic_hmmer.pm | H A D | 18-Nov-2019 | 6.1 KiB | 218 | 159 | |
demotic_infernal_tab.pm | H A D | 18-Nov-2019 | 8.8 KiB | 178 | 97 | |
fasta2profmark | H A D | 18-Nov-2019 | 127 | 12 | 5 | |
fasta2tbl | H A D | 18-Nov-2019 | 121 | 11 | 5 | |
h22profmark | H A D | 18-Nov-2019 | 117 | 11 | 5 | |
h22tbl | H A D | 18-Nov-2019 | 112 | 11 | 5 | |
hmmer2profmark | H A D | 18-Nov-2019 | 126 | 11 | 5 | |
hmmer2tbl | H A D | 18-Nov-2019 | 121 | 11 | 5 | |
infernal_tab2gff.pl | H A D | 03-May-2022 | 14.1 KiB | 270 | 175 | |
test.pl | H A D | 03-May-2022 | 451 | 16 | 10 |
00README
1demotic is a set of Perl modules for interfacing the hieroglyphic 2output of one program with the greek input of another program. 3 4original: SRE, Wed Oct 25 16:32:09 2000 5into Easel: SRE, Fri Apr 16 16:10:25 2010 6 7 demotic_blast.pm NCBI blastp; NCBI blastpgp; WU blastp 8 demotic_fasta.pm fasta; ssearch 9 demotic_hmmer.pm hmmsearch, phmmer 10 demotic_h2.pm HMMER 2.0 hmmsearch 11 12 blast2profmark 13 fasta2profmark 14 hmmer2profmark 15 h22profmark 16 17 blast2tbl 18 fasta2tbl 19 hmmer2tbl 20 h22tbl 21 22 test.pl : example of using demotic_blast "in line" in a perl script. 23 24################################################################ 25# Generating the example outputs 26 27# Config that's already in my .bashrc: 28 export SWISS=/misc/data0/databases/Uniprot/uniprot_sprot.fasta 29 export SWISS-WU=/misc/data0/databases/Uniprot/uniprot_sprot_wu.fasta 30 export PFAM_HMM=/misc/data0/databases/Pfam/Pfam-A.hmm 31 export PFAM_SEED=/misc/data0/databases/Pfam/Pfam-A.seed 32 export PFAM_FULL=/misc/data0/databases/Pfam/Pfam-A.full 33 export PERLLIB=.:${HOME}/sw/scripts 34 35# Most examples 36 esl-seqstat -a $SWISS | awk '{print $2}' | esl-selectn 2 - | esl-sfetch -f $SWISS - > examples/example.fa 37 grep -v "^#" /misc/data0/databases/pfam/pfam-24.0/Pfam-A.hmm.stat | awk '{print $2}' | esl-selectn 2 - | hmmfetch -f /misc/data0/databases/pfam/pfam-24.0/Pfam-A.hmm - > examples/example.hmm 38 39# PSIBLAST example takes some massaging, because of the way we convert Stockholm to a checkpoint .asnt file. 40 grep -v "^#" /misc/data0/databases/pfam/pfam-24.0/Pfam-A.seed.stat | awk '{print $2}' | esl-selectn 1 - | esl-afetch -f /misc/data0/databases/pfam/pfam-24.0/Pfam-A.seed - > examples/example-single.sto 41 esl-reformat -o examples/example-single.pbl psiblast examples/example-single.sto 42 esl-seqstat -a examples/example-single.sto | grep "^=" | awk '{print $2}' | esl-selectn 1 - | esl-sfetch -f examples/example-single.sto - 43 esl-seqstat -a examples/example-single.sto | grep "^=" | awk '{print $2}' | esl-selectn 1 - | esl-sfetch -f examples/example-single.sto - > examples/example-single-psiquery.fa 44 esl-reformat -o examples/example-single.fa fasta examples/example-single.sto 45 formatdb -i examples/example-single.fa 46 blastpgp -v 9999 -F T -u 1 -j 5 -J TRUE -d examples/example-single.fasta -i examples/example-single-psiquery.fa -C examples/example-single.asnt 47 48# H2 example also is a little special; build new from Stockholm, plus H2 hmmsearch can only do a single query. 49 grep -v "^#" /misc/data0/databases/pfam/pfam-24.0/Pfam-A.seed.stat | awk '{print $2}' | esl-selectn 1 - | esl-afetch -f /misc/data0/databases/pfam/pfam-24.0/Pfam-A.seed - > examples/example.sto 50 ~/releases/hmmer-2.3.2/src/hmmbuild examples/example.hmm2 examples/example.sto 51 ~/releases/hmmer-2.3.2/src/hmmcalibrate examples/example.hmm2 52 53 blastp $SWISS_WU examples/example.fa > examples/example.wu-blastp.out 54 blastall -p blastp -i examples/example.fa -d $SWISS > examples/example.ncbi-blastp.out 55 /usr/local/fasta-36x2/bin/ssearch36_t -q examples/example.fa $SWISS > examples/example.ssearch.out 56 /usr/local/fasta-36x2/bin/fasta36_t -q examples/example.fa $SWISS > examples/example.fasta.out 57 phmmer examples/example.fa $SWISS > examples/example.phmmer.out 58 hmmsearch examples/example.hmm $SWISS > examples/example.hmmsearch.out 59 ~/releases/hmmer-2.3.2/src/hmmsearch examples/example.hmm2 $SWISS > examples/example.h2.out 60 blastpgp -v 9999 -F F -q 1 -t 1 -d $SWISS -R examples/example-single.asnt > examples/example.psiblast.out 61 62################################################################ 63# Save outputs for regression 64 65 pfx=regress 66 mkdir $pfx 67 cat examples/example.wu-blastp.out | ./blast2profmark > $pfx/wu-blastp-profmark.out 68 cat examples/example.ncbi-blastp.out | ./blast2profmark > $pfx/ncbi-blastp-profmark.out 69 cat examples/example.psiblast.out | ./blast2profmark > $pfx/psiblast-profmark.out 70 cat examples/example.ssearch.out | ./fasta2profmark > $pfx/ssearch-profmark.out 71 cat examples/example.fasta.out | ./fasta2profmark > $pfx/fasta-profmark.out 72 cat examples/example.phmmer.out | ./hmmer2profmark > $pfx/phmmer-profmark.out 73 cat examples/example.hmmsearch.out | ./hmmer2profmark > $pfx/hmmsearch-profmark.out 74 cat examples/example.h2.out | ./h22profmark > $pfx/h2-profmark.out 75 76 cat examples/example.wu-blastp.out | ./blast2tbl > $pfx/wu-blastp-tbl.out 77 cat examples/example.ncbi-blastp.out | ./blast2tbl > $pfx/ncbi-blastp-tbl.out 78 cat examples/example.psiblast.out | ./blast2tbl > $pfx/psiblast-tbl.out 79 cat examples/example.ssearch.out | ./fasta2tbl > $pfx/ssearch-tbl.out 80 cat examples/example.fasta.out | ./fasta2tbl > $pfx/fasta-tbl.out 81 cat examples/example.phmmer.out | ./hmmer2tbl > $pfx/phmmer-tbl.out 82 cat examples/example.hmmsearch.out | ./hmmer2tbl > $pfx/hmmsearch-tbl.out 83 cat examples/example.h2.out | ./h22tbl > $pfx/h2-tbl.out 84 85################################################################ 86# Regression test of outputs 87 88 pfx=tmp 89 mkdir $pfx 90# Run the same stuff as above 91 92 for prg in wu-blastp ncbi-blastp psiblast ssearch fasta phmmer hmmsearch h2 ; do 93 diff --brief regress/$prg-profmark.out tmp/$prg-profmark.out 94 diff --brief regress/$prg-tbl.out tmp/$prg-tbl.out 95 done 96 97 rm -rf tmp 98 99 100