Short read mapping pipeline pig: Difference between revisions
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<source lang='bash'> | <source lang='bash'> | ||
mysql -u ABGSAuser -h scomp1095.wurnet.nl -p ABGSAschema -e 'select ABG_individual_id from ABGSAschema_main where archive_name like " | mysql -u ABGSAuser -h scomp1095.wurnet.nl -p ABGSAschema -e 'select ABG_individual_id from ABGSAschema_main where archive_name like "ABGSA0%" group by ABG_individual_id' >list.txt | ||
FILES=`cat list.txt` | |||
FILES=`cat | |||
for ID in $FILES; do python ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4; done | for ID in $FILES; do python ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4; done | ||
</source> | </source> | ||
Revision as of 19:52, 27 December 2013
The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed
Prerequisites
Basic execution
<source lang='bash'> (testenv)[megen002@nfs01 rundir]$ python ABGC_mapping_v2.py -i LW22F04 -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4 </source>
Automated runfile creation
<source lang='bash'> mysql -u ABGSAuser -h scomp1095.wurnet.nl -p ABGSAschema -e 'select ABG_individual_id from ABGSAschema_main where archive_name like "ABGSA0%" group by ABG_individual_id' >list.txt FILES=`cat list.txt` for ID in $FILES; do python ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4; done </source>