Mercurial > repos > iuc > homer_annotatepeaks

comparison test-data/generate_tests.sh @ 2:35dc2f57d755 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
author iuc
date Mon, 13 Dec 2021 15:16:02 +0000
parents adab852c8216
children
comparison
equal deleted inserted replaced
1:38d10a69748a 2:35dc2f57d755
9 fi 9 fi
10 if [ ! -e test-data/CTCF_peaks.bed ]; then 10 if [ ! -e test-data/CTCF_peaks.bed ]; then
11 wget https://raw.githubusercontent.com/lldelisle/scriptsForWilleminEtAl2021/main/CTCF/E12_Limbs_Wt_CTCF_colored.bed -O test-data/CTCF_peaks.bed 11 wget https://raw.githubusercontent.com/lldelisle/scriptsForWilleminEtAl2021/main/CTCF/E12_Limbs_Wt_CTCF_colored.bed -O test-data/CTCF_peaks.bed
12 fi 12 fi
13 if [ ! -e test-data/CTCF_peaks_shifted.bed ]; then 13 if [ ! -e test-data/CTCF_peaks_shifted.bed ]; then
14 cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed 14 cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '$3<75000000 && $2>73740000{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed
15 fi 15 fi
16 # chr2_subset.fa was downloaded from UCSC 16 # chr2_subset.fa was downloaded from UCSC
17 # https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1136019667_XgAJOvV4a3CY4ibCu6RrUcvGxLNo&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75787000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA 17 # https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1234982067_JnS4z30UVCNarTg26Ztd1Oh6nfu6&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75000000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA
18 18
19 . <(planemo conda_env homer_gtf_to_annotation.xml) 19 . <(planemo conda_env homer_gtf_to_annotation.xml)
20 echo "$(which homer)" 20 echo "$(which homer)"
21 ## homer_gtf_to_annotation 21 ## homer_gtf_to_annotation
22 ## First test 22 ## First test
48 ## findMotifsGenome 48 ## findMotifsGenome
49 # ! Genome preparsing is giving different results... 49 # ! Genome preparsing is giving different results...
50 findMotifsGenome.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif 50 findMotifsGenome.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif
51 mv fake_phix_peaks_bed_motif test-data/motif_test1 51 mv fake_phix_peaks_bed_motif test-data/motif_test1
52 # Thus I needed to use has_text for the other outputs 52 # Thus I needed to use has_text for the other outputs
53 # gunzip -c test-data/chr2_subset.fa.gz > test-data/chr2_subset.fa
53 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif 54 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif
54 # mv CTCF_peaks_shifted_bed_motif test-data/motif_test2 55 # mv CTCF_peaks_shifted_bed_motif test-data/motif_test2
55 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mask 56 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mask
56 # mv CTCF_peaks_shifted_bed_motif test-data/motif_test3 57 # mv CTCF_peaks_shifted_bed_motif test-data/motif_test3
57 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mset plants -nomotif 58 # findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mset plants -nomotif