...
You may use standard text processing tools like SED, AWK and TR to process the report file, eg to collect statistics: please note that these are only examples
For example: Count warnings and errors per locus :
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
# Count warnings and errors per locus : # Replace all # by newline, get the lines with locus errors, then pick the first part before: , sort it, and count unique values ~$ tr '#' '\n' < testreport.txt |grep 'at locu' | cut -d':' -f1 | sort | uniq -c 32 Error at locus A* 24 Error at locus B* 112 Error at locus C* 16 Error at locus DQB1* 57 Error at locus DRB1* 76 Warning at locus A* 80 Warning at locus B* # Give all ID's that have HLA warnings tr ':' '|' <testreport.txt | cut -d'|' -f1,3,5 | grep -i 'HLA' # Give ID from records that have a warning or rejection grep -i 'sex.*rejected' testreport.txt | cut -d'|' -f3 737849095 |