From 97fdefab064f63642fa3ece05b807d29b459df31 Mon Sep 17 00:00:00 2001
From: Hui Lan <lanhui@zjnu.edu.cn>
Date: Wed, 4 Dec 2019 19:03:19 +0800
Subject: brain: add python and R code to local repository.
---
Code/make_parameter_dapseq3.py | 75 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 75 insertions(+)
create mode 100644 Code/make_parameter_dapseq3.py
(limited to 'Code/make_parameter_dapseq3.py')
diff --git a/Code/make_parameter_dapseq3.py b/Code/make_parameter_dapseq3.py
new file mode 100644
index 0000000..405b3dc
--- /dev/null
+++ b/Code/make_parameter_dapseq3.py
@@ -0,0 +1,75 @@
+# Usage: python make_parameter_dapseq3.py
+# Because dap-seq dose not include all TFs, so include other TFs. The idea is that TFs within a same family are very conservative in binding.
+#
+
+import sys, glob, os, operator
+from geneid2name import make_gene_name_AGI_map_dict
+
+DAPSEQ_DIR = '/home/hui/network/dapseq_merged'
+MAP_FILE = '/home/hui/network/dapseq_merged/tffamily.simple.txt'
+
+def get_name(s):
+ lst = s.split('_')
+ result = []
+ for x in lst:
+ if x != 'tnt':
+ result.append(x)
+ return '_'.join(result)
+
+def make_dapseq_dictionary(dirname):
+
+ d = {}
+
+ files = glob.glob(os.path.join(dirname, '*.narrowPeak'))
+
+ for f in files:
+ lst = f.split('/')
+ tf_name = lst[-1].split('.')[0]
+ tf_name = get_name(tf_name)
+ if not tf_name in d:
+ d[tf_name] = f
+ else:
+ print('ERROR: transcription factor name not unique.')
+ sys.exit()
+
+ return d
+
+
+d = make_dapseq_dictionary(DAPSEQ_DIR)
+
+f = open(MAP_FILE)
+lines = f.readlines()
+f.close()
+
+# since MAP_FILE contain duplicate lines
+d_family = {}
+for line in lines:
+ line = line.strip()
+ lst = line.split()
+ tf = lst[0].upper()
+ tf_name = lst[1]
+ family = lst[2]
+ if not tf in d_family:
+ d_family[tf] = (tf_name, family)
+ else:
+ if family != d_family[tf][1]:
+ print('WARNING: %s conflict [%s %s]!' % (tf, family, d_family[tf][1]))
+
+count = 1
+for k in sorted(d_family.keys()):
+ g = k
+ gname = d_family[k][0]
+ key = d_family[k][1]
+ if key in d:
+ cid = 'C0003%09d' % (count)
+ count += 1
+ print('@%s' % (cid))
+ print('PROTEIN_ID:%s' % (g))
+ print('PROTEIN_NAME:%s' % (gname))
+ print('DATA_NAME:%s' % (gname))
+ print('DATA_FORMAT:%s' % ('narrowPeak'))
+ print('DESCRIPTION:inferred from dapseq')
+ #print('LOCATION:%s' % (os.path.join(DAPSEQ_DIR, d[key])))
+ print('LOCATION:%s' % (d[key]))
+ print('NOTE:')
+ print('')
--
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