83eb31f4ea1896449dce8576697627091c6ff313
angie
  Thu Jan 21 10:54:13 2021 -0800
Prevent excess warnings about varPaths problems.

diff --git src/hg/utils/otto/nextstrainNcov/nextstrain.py src/hg/utils/otto/nextstrainNcov/nextstrain.py
index a452e00..b25d3d6 100755
--- src/hg/utils/otto/nextstrainNcov/nextstrain.py
+++ src/hg/utils/otto/nextstrainNcov/nextstrain.py
@@ -641,39 +641,42 @@
 
 # File with samples and their clades, labs and variant paths
 
 apostropheSRe = re.compile("'s");
 firstLetterRe = re.compile('(\w)\w+');
 spacePunctRe = re.compile('\W');
 
 def abbreviateLab(lab):
     """Lab names are very long and sometimes differ by punctuation or typos.  Abbreviate for easier comparison."""
     labAbbrev = apostropheSRe.sub('', lab)
     labAbbrev = firstLetterRe.sub(r'\1', labAbbrev, count=0)
     labAbbrev = spacePunctRe.sub('', labAbbrev, count=0)
     return labAbbrev
 
 with open('nextstrainSamples.varPaths', 'w') as outF:
+    errCount = 0
     for sample in samples:
         lab = sample['lab']
         labAbbrev = abbreviateLab(lab)
         try:
             outF.write('\t'.join([sampleName(sample), sample['clade'], labAbbrev, lab,
                                   sample['varStr']]) + '\n');
         except:
+            if (errCount == 0):
                 print("Problem writing varPaths for sample '", sampleName(sample), "', varStr '",
-                  sample['varStr'])
+                      sample['varStr'], "'")
+            errCount += 1
 
 # Narrow down variants to "informative" set (bi-allelic, each allele supported by
 # sufficient number of samples):
 minSamples = 2
 discardedAlleles = []
 blacklist = []
 informativeVariants = []
 
 for mv in mergedVars:
     pv, alts, altCounts, sampleAlleles, backMutSamples = mv
     pos, varNameMerged, ref, altStr = pv
     recurrentAlts = []
     recurrentAltCounts = []
     for alt, altCount in zip(alts, altCounts):
         if (altCount < minSamples):