Short read mapping pipeline pig
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 from the command line or submitted to the cluster using SLURM. The latest version of the Python3 script can be found at [1].
Prerequisites
Basic execution
<source lang='bash'> (virtenv)[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> The code should produce the following shell script, ready for execution with SLURM.
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>