Adds script biom_phyla_summary.py

Takes in a BIOM abundance table and prints out a summary of the percent
abundance of the top 20 Families, Genera, and Species.

Also currently lists the percent abundance of important species in the oral
cavity (color complexes). This will be made an option in a later release.
Along with a more generic ability to pass in a list of any phylogenetic level
or specific OTU.

bin/biom_phyla_summary.py

@@ -0,0 +1,79 @@
+import sys
+import json
+from collections import defaultdict
+
+def biom_summary(biom):
+    tamtcounts = defaultdict(int)
+    tot_seqs = 0.0
+
+    for row, col, amt in biom['data']:
+        tot_seqs += amt
+        rtax = biom['rows'][row]['metadata']['taxonomy']
+        for i,t in enumerate(rtax):
+            t = t.strip()
+            if i == len(rtax)-1 and len(t) > 3 and len(rtax[-1]) > 3:
+                t = 's__'+rtax[i-1].strip().split('_')[-1]+'_'+t.split('_')[-1]
+            tamtcounts[t] += amt        
+
+    print 'Total sequence count: %i\n' % tot_seqs
+
+    def levelData(counts, seqCount, level='g'):
+        lvlData = sorted([(k, counts[k]) for k in counts if level+'_' in k], key=lambda x: x[1], reverse=True)
+        return ['{}: {:4.2f}%'.format(p[0], p[1]/seqCount*100) for p in lvlData]
+
+    def lookup(s, d):
+        for idx, item in enumerate(d):
+            if s in item:
+                return d[idx]
+        return s+': None'
+
+    print 'Top families:\n'
+    lvlDataF = levelData(tamtcounts, tot_seqs, 'f')
+    print lvlDataF[:20]
+
+    print '\nTop genera:\n'
+    lvlDataG = levelData(tamtcounts, tot_seqs)
+    print lvlDataG[:20]
+
+    print '\nTop species:\n'
+    lvlData = levelData(tamtcounts, tot_seqs, 's')
+    print lvlData[:20]
+
+
+    print '\nRed Complex:'
+    print lookup('s__Porphyromonas_gingivalis', lvlData)
+    print lookup('s__Treponema_denticola', lvlData)
+    print lookup('s__Tannerella_forsythia', lvlData)
+
+    print '\nOrange Complex: '
+    print lookup('s__Fusobacterium_nucleatum', lvlData)
+    print lookup('s__Prevotella_intermedia', lvlData)
+    print lookup('s__Prevotella_nigrescens', lvlData)
+    print lookup('s__Peptostreptococcus_micros', lvlData)
+
+    print '\nYellow Complex: '
+    print lookup('s__Streptococcus_sanguis', lvlData)
+    print lookup('s__Streptococcus_oralis', lvlData)
+    print lookup('s__Streptococcus_mitis', lvlData)
+    print lookup('s__Streptococcus_gordonii', lvlData)
+    print lookup('s__Streptococcus_intermedius', lvlData)
+
+    print '\nGreen Complex: '
+    print lookup('s__Aggregatibacter_actinomycetemcomitans', lvlData)
+    print lookup('s__Campylobacter_concisus', lvlData)
+    print lookup('s__Eikenella_corrodens', lvlData)
+    print lookup('g__Capnocytophaga', lvlDataG)
+
+    print '\nPurple Complex: '
+    print lookup('s__Veillonella_parvula', lvlData)
+    print lookup('s__Actinomyces_odontolyticus', lvlData)
+    print lookup('s__Selenomonas_noxia', lvlData)
+    print lookup('s__Actinomyces_naeslundii', lvlData)
+
+def main():
+    with open(sys.argv[1], 'rU') as bF:
+        biom = json.loads(bF.readline())
+        biom_summary(biom)
+
+if __name__ == '__main__':
+    main()