CGATOxford/cgat — pull request #7 by IanSudbery (2014-03-06 14:24:08+00:00)
Title: Fixing expression.py load cuff diff

Hi Guys,

1. This branch has two main purposes. Both in the loadCuffDiff function of Expression.py The first is that I fixed a couple of indenting issues that were introduced by makeing the code pep8 compliant. Beware! The process left a couple of code blocks at the wrong indent level. This is not the first time these blocks have ended up at the wrong level. Please be careful with them.

2. I have change the loading of cuffdiff quantitated FPKMs so that they are loaded using the sample sample ids that we use in the pipeline. This is clearly better than using CuffDiffs internal identifiers, but could cause a problem if anyone is using them.

**If you are using the CuffDiff sample ids, please let me know before the branch is merged or your code may break**
CuffDiff sample ids look like: Condition1_0, Condition2_0 etc in the `{design}_{geneset}_cuffdiff_{isoform|gene|tss|cds}sample_fpkm` tables.

Ian
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