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License: GNU General Public License v3.0

R 98.44% Shell 1.56%

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heath1210 jbdoto

intsiteuploader's Issues

Enforce foreign key relationships in database schema

samples.sampleID = sites.sampleID
sites.siteID = pcrbreakpoints.siteID
sites.multihitClusterID = multihitlengths.multihitClusterID

Need to do table lock before write, need to fail for any database error.

Consider extracting functions in intSiteUploader.R

Lines 88-132 and lines 140-177 seem like they could be extracted into new functions

remove selects from uploading because we are using transaction

Should use file.path to construct file paths

The paste0 function is used instead of file.path in intSiteUploader.R lines 84-86

miseqid.txt dependancy

Rscript requires miseqid.txt in primary analysis directory. This should be included in the readme or requested in a message. Without it, the script fails on the unique(readLines()) portion calling the file.

octal code requirement

I don't know how important this is, but I couldn't access as the requirement in script is "0600" but the my.cnl file I received from Yinghua was "0664". I commented out the stop and everything ran fine. Maybe we should changed the stop?

increased maxid to accommodate 454 data

ref genome should not be empty

enforce naming scheme for alias names and check GTSP DB

add on the fly check the identity of input and output.

Anatoly?

multihit database conflict

Filtering on multihitID=1014 I got

multihitID sampleID position chr strand
1014 68 319757 chr5_h2_hap1 -
1014 67 507396 chr17_random -
1014 67 515377 chr17_random -
1014 67 520266 chr17_random -
1014 67 526414 chr17_random -
1014 67 555352 chr17_random +
1014 69 1874165 chr6_random -
1014 67 2608573 chr17_random -
1014 64 3657207 chr6_qbl_hap2 +
1014 64 3849289 chr6_cox_hap1 +
1014 63 29956509 chr16 +
1014 63 32207527 chr1 +
1014 64 32550328 chr6 +
1014 62 37413562 chr7 -
1014 63 37870891 chr19 -
1014 67 38821755 chr17 -
1014 63 48892932 chr12 -
1014 63 54600289 chrX +
1014 63 56798235 chr17 +
1014 66 57741533 chrY +
1014 68 68861004 chr5 -
1014 63 73204332 chr9 -
1014 63 88408320 chr12 -
1014 63 91456639 chr12 +
1014 62 106338254 chr10 -
1014 70 109826340 chr2 -
1014 70 110852608 chr2 +
1014 66 154882333 chrX +
1014 69 157988060 chr6 -
1014 65 159810682 chr1 -
1014 65 159892522 chr1 -
1014 63 226276698 chr1 +

Use branch upload_to_microb237 for testing

For testing purpose, please use upload_to_microb237. It is debugged and tested OK for Frances' run. You will for sure run into file not found error. The file you need is ~/.my.cnf and it should not be in the repo. Also, connections to the test database can only be established from microbxxx and pmacs.

e.g.

gener is char(1) trying to insert "male" should fail.