QA scripts: Difference between revisions
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(changed "fl nm" to "flnm" and "tbl nm" to "tblnm" and "db nm" to "dbnm" because I think it is eaiser to read/understand) |
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| Line 1: | Line 1: | ||
==Shorthand Key:== | ==Shorthand Key:== | ||
file name | file name flnm | ||
database name dbnm | database name dbnm | ||
table name | table name tblnm | ||
==Scripts== | ==Scripts== | ||
| Line 8: | Line 8: | ||
nice top see who is doing what & the time on the server | nice top see who is doing what & the time on the server | ||
up time load average | up time load average | ||
featureBits | featureBits dbnm tblnm compares total amount of data in table compared to the entire assembly (not including gaps) | ||
checkCoverage.csh | checkCoverage.csh dbnm tblnm [chrom] finds non-gap places in table where there is no data and gives you the largest places with browser link to top 3 | ||
findLevel.csh | findLevel.csh dbnm tblnm searches trackDb hierarchy for your table and corresponding .html file | ||
commTrio.csh sorts & compares two files | commTrio.csh sorts & compares two files | ||
encodeEmail.p codes email addresses for html pages | encodeEmail.p codes email addresses for html pages | ||
countPerChrom.csh | countPerChrom.csh dbnm tblnm number of material on each chrom | ||
countPerChrom.csh aplCal1 rmsk | awk '{ print $2 "\t" $1}' | grep '^0' | countPerChrom.csh aplCal1 rmsk | awk '{ print $2 "\t" $1}' | grep '^0' | ||
alternative: to see those chroms with data: hgsql -e "select tName from all_mrna;" aplCal1 | sort| uniq -c | sort -rn | less (per Hiram; more efficient) | alternative: to see those chroms with data: hgsql -e "select tName from all_mrna;" aplCal1 | sort| uniq -c | sort -rn | less (per Hiram; more efficient) | ||
Revision as of 15:59, 30 March 2011
Shorthand Key:
file name flnm database name dbnm table name tblnm
Scripts
catchBOT.csh check usage of highest users nice top see who is doing what & the time on the server up time load average featureBits dbnm tblnm compares total amount of data in table compared to the entire assembly (not including gaps) checkCoverage.csh dbnm tblnm [chrom] finds non-gap places in table where there is no data and gives you the largest places with browser link to top 3 findLevel.csh dbnm tblnm searches trackDb hierarchy for your table and corresponding .html file commTrio.csh sorts & compares two files encodeEmail.p codes email addresses for html pages
countPerChrom.csh dbnm tblnm number of material on each chrom
countPerChrom.csh aplCal1 rmsk | awk '{ print $2 "\t" $1}' | grep '^0'
alternative: to see those chroms with data: hgsql -e "select tName from all_mrna;" aplCal1 | sort| uniq -c | sort -rn | less (per Hiram; more efficient)
