Short read mapping pipeline pig: Difference between revisions
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== Basic execution == | == 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 == | == 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 "ABGSA03%" group by ABG_individual_id' >list300.txt | |||
cat list100.txt list200.txt list300.txt | sort | uniq >list100-200-300.txt | |||
FILES=`cat list100-200-300.txt` | |||
for ID in $FILES; do python ABGC_mapping_v2.py -i $ID -a /lustre/nobackup/WUR/ABGC/shared/Pig/ABGSA/ -r /lustre/nobackup/WUR/ABGC/shared/Pig/Sscrofa_build10_2/Ensembl72/Sus_scrofa.Sscrofa10.2.72.dna.toplevel.fa -t 4; done | |||
</source> | |||
== Output files == | == Output files == | ||
Revision as of 19:51, 27 December 2013
The latest short-read mapping pipeline for the pig project is based on a Python3 script that creates a shell script that can subsequently be executed
Prerequisites
Basic execution
<source lang='bash'> (testenv)[megen002@nfs01 rundir]$ 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 "ABGSA03%" group by ABG_individual_id' >list300.txt cat list100.txt list200.txt list300.txt | sort | uniq >list100-200-300.txt FILES=`cat list100-200-300.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>