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diff --git a/Code/count_AGI_in_cDNA.py b/Code/count_AGI_in_cDNA.py
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+# Usage: python count_AGI_in_cDNA.py
+#
+# Purpose: print the number of unique AGIs in Arabidopsis_thaliana.TAIR10.cdna.all.fa.  An AGI looks like AT4G28720.
+#          Check that all thermomorphogenesis genes are in Arabidopsis_thaliana.TAIR10.cdna.all.fa.
+# 
+# Created on 5 December 2019 by Hui Lan (lanhui@zjnu.edu.cn)
+
+cdna = '/home/lanhui/brain/Salmon/Arabidopsis_thaliana.TAIR10.cdna.all.fa'
+f = open(cdna)
+d = {}  # hold all unique AGIs as keys
+for line in f:
+    line = line.strip()
+    if line.startswith('>AT'):
+        lst = line.split()
+        gene_id = lst[0][1:] # remove '>'
+        key = gene_id.split('.')[0] # discard '.1' 
+        d[key] = 1
+        
+f.close()
+print(len(d))
+
+thermomorphogenesis_genes = [
+    'AT4G28720',
+    'AT2G25930',
+    'AT2G40080',
+    'AT3G46640',
+    'AT5G11260',
+    'AT2G43010',
+    'AT3G59060',
+    'AT4G10180',
+    'AT2G32950',
+    'AT3G13550',
+    'AT4G05420',
+    'AT4G21100',
+    'AT2G46340',
+    'AT4G11110',
+    'AT3G15354',
+    'AT1G53090',
+    'AT1G02340',
+    'AT4G08920',
+    'AT4G39950',
+    'AT2G22330',
+    'AT2G42870',
+    'AT5G39860',
+    'AT1G70560',
+    'AT3G62980',
+    'AT4G03190',
+    'AT3G26810',
+    'AT1G12820',
+    'AT4G24390',
+    'AT5G49980',
+    'AT5G01830',
+    'AT5G18010',
+    'AT5G18020',
+    'AT5G18050',
+    'AT5G18060',
+    'AT5G18080',
+    'AT1G29440',
+    'AT1G29510',
+    'AT4G18710',
+    'AT1G75080',
+    'AT1G30330',
+    'AT1G19850',
+    'AT3G33520',
+    'AT4G16280',
+    'AT2G43060',
+    'AT2G18300',
+    'AT4G16780',
+    'AT1G01060',
+    'AT1G22770',
+    'AT4G25420',
+    'AT1G15550',
+    'AT1G78440',
+    'AT5G43700',
+    'AT4G32280',
+    'AT2G38120',
+    'AT1G15580',
+]
+
+# If a thermomorphogenesis is not in d, then print it.
+for g in thermomorphogenesis_genes:
+    if not g in d:
+        print(g)