From b54eee5365a0fad35d2f6168eaac82ff5a359222 Mon Sep 17 00:00:00 2001 From: Sean Upchurch Date: Wed, 18 May 2011 10:59:28 -0700 Subject: [PATCH] minor bug fixes --- checkrmask.py | 4 ++-- distalPairs.py | 6 ++++-- makewiggle.py | 1 + 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/checkrmask.py b/checkrmask.py index 99d74a5..457e4c1 100755 --- a/checkrmask.py +++ b/checkrmask.py @@ -192,7 +192,7 @@ def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cacheP outfile.write(outline + "\n") if len(finalresults) == 0: - outline = "%s\tNR\tNR\t%0.00" % line + outline = "%s\tNR\tNR\t0.00" % line print outline outfile.write(outline + "\n") @@ -201,4 +201,4 @@ def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cacheP if __name__ == "__main__": - main(sys.argv) \ No newline at end of file + main(sys.argv) diff --git a/distalPairs.py b/distalPairs.py index be40310..dc83650 100755 --- a/distalPairs.py +++ b/distalPairs.py @@ -147,13 +147,15 @@ def addSplicesToUniqReads(RDS, uniqDict): for readID in splicesDict: theRead = splicesDict[readID] read0 = theRead[0] - del read0[1] + read0["start"] = read0["startL"] + del read0["stopL"] try: uniqDict[readID].append(read0) except: if len(theRead) == 4: read2 = theRead[2] - del read2[1] + read2["start"] = read2["startL"] + del read2["stopL"] uniqDict[readID] = [read0,read2] diff --git a/makewiggle.py b/makewiggle.py index 7440a79..139924e 100755 --- a/makewiggle.py +++ b/makewiggle.py @@ -115,6 +115,7 @@ def makewiggle(name, hitfilename, outfilename, doNormalize=True, color=None, alt if limitChrom is not None: chromLimit = True + groupName = "" if group: groupName = "group=%s" % group -- 2.30.2