| [fg_atlas@ebi-005 archive]$ mkdir /var/tmp/array-designs | |
| [fg_atlas@ebi-005 archive]$ cp ensembl_87_34/homo_sapiens*A-*.tsv /var/tmp/array-designs | |
| [fg_atlas@ebi-005 archive]$ cd /var/tmp/array-designs | |
| [fg_atlas@ebi-005 array-designs]$ for file in `ls ` ; do cat <(echo -e "ensgene\tdesign_element") <(grep -E "\w+\W\w+" $file) > $file.tmp ; mv $file.tmp $file ; done | |
| [fg_atlas@ebi-005 array-designs]$ wc -l * | |
| 8684 homo_sapiens.A-AFFY-10.tsv | |
| 6938 homo_sapiens.A-AFFY-11.tsv | |
| 5155 homo_sapiens.A-AFFY-12.tsv | |
| 6835 homo_sapiens.A-AFFY-13.tsv | |
| 25196 homo_sapiens.A-AFFY-141.tsv |
| [fg_atlas@ebi-005 E-ATMX-20]$ for exp in $(comm -13 <( ls $ATLAS_EXPS | grep 'E-.*' | sort ) <( ls $ATLAS_FTP/experiments | grep 'E-.*' | sort )) ; do find $ATLAS_FTP/experiments/$exp -name '*-analytics.tsv' ; done | xargs ls -ld | |
| -rw-r--r-- 1 fg_atlas microarray 5561657 Mar 2 2014 /ebi/ftp/pub/databases/microarray/data/atlas/experiments/E-GEOD-10041/E-GEOD-10041_A-AFFY-44-analytics.tsv | |
| -rw-r--r-- 1 fg_atlas microarray 1062342 Feb 19 2014 /ebi/ftp/pub/databases/microarray/data/atlas/experiments/E-GEOD-12332/E-GEOD-12332_A-AFFY-17-analytics.tsv | |
| -rw-r--r-- 1 fg_atlas microarray 7589235 Apr 22 2014 /ebi/ftp/pub/databases/microarray/data/atlas/experiments/E-GEOD-12667/E-GEOD-12667_A-AFFY-44-analytics.tsv | |
| -rw-r--r-- 1 fg_atlas microarray 3393121 Mar 2 2014 /ebi/ftp/pub/databases/microarray/data/atlas/experiments/E-GEOD-12767/E-GEOD-12767_A-AFFY-44-analytics.tsv | |
| -rw-r--r-- 1 fg_atlas microarray 1330410 Mar 14 2016 /ebi/ftp/pub/databases/microarray/data/atlas/experiments/E-GEOD-14895/E-GEOD-14895_A-AFFY-33-ana |
| [fg_atlas@ebi-005 ~]$ ls $ATLAS_EXPS | grep 'E-.*' | tee /var/tmp/atlas-exps-exps | wc -l | |
| 3165 | |
| [fg_atlas@ebi-005 ~]$ ls $ATLAS_PROD/analysis/*/*/experiments | grep 'E-.*' | tee /var/tmp/atlas-prod-exps | wc -l | |
| 3244 | |
| [fg_atlas@ebi-005 ~]$ sort /var/tmp/atlas-prod-exps -o /var/tmp/atlas-prod-exps | |
| [fg_atlas@ebi-005 ~]$ sort /var/tmp/atlas-exps-exps -o /var/tmp/atlas-exps-exps | |
| # experiments in atlas exps but not in atlas prod | |
| [fg_atlas@ebi-005 ~]$ comm -13 /var/tmp/atlas-prod-exps /var/tmp/atlas-exps-exps | |
| E-GEOD-53580 | |
| E-GEOD-73312 |
| #!/bin/bash | |
| # Look at the header of the file, splay it into lines, then use grep -n to find out the position it's in | |
| head -n1 $ATLAS_FTP/bioentity_properties/ensembl/mus_musculus.ensgene.tsv | tr '\t' '\n' | grep -n mgi_id | cut -f 1 -d : | |
| #16 | |
| head -n1 $ATLAS_PROD/bioentity_properties/ensembl/mus_musculus.ensgene.tsv | tr '\t' '\n' | grep -n mgi_id | cut -f 1 -d : | |
| #16 |
| echo "Clear previous Ensembl data from the public all subdirs of ${ATLAS_FTP}/bioentity_properties" | |
| for dir in ensembl mirbase reactome go interpro wbps; do | |
| rm -rf ${ATLAS_FTP}/bioentity_properties/${dir}/* | |
| done | |
| echo "Copy all array design mapping files into the public Ensembl data directory (this directory is used only for Solr index build)" | |
| cp ${ATLAS_PROD}/bioentity_properties/ensembl/*.A-*.tsv ${ATLAS_FTP}/bioentity_properties/ensembl/ | |
| pushd ${ATLAS_PROD}/bioentity_properties/ensembl | |
| echo "Copy all Ensembl matrices to the public Ensembl data directory" |
| Abbreviations | |
| ---- | |
| v value | |
| exp experiment | |
| c contrast | |
| id identifier | |
| as analytics search, which the query either matches or it doesn't | |
| cs conditions search, which the query either matches or it doesn't | |
| Sets considered |