brain: add python and R code to local repository.

1 files changed, 172 insertions, 0 deletions

diff --git a/Code/slice_binding_to_JSON.py b/Code/slice_binding_to_JSON.py
new file mode 100644
index 0000000..6421fed
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+++ b/Code/slice_binding_to_JSON.py
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+# Usage: python slice_binding_to_JSON.py parameter_for_net.txt
+import sys, os, operator, itertools
+import numpy as np
+import json
+
+JSON_DIR = '../Data/history/bind/json2' # contains json for all genes
+
+GLB_PARAM_SYMBOL    = '%%'
+DATA_SYMBOL         = '@'
+
+def read_matrix_data(fname):
+    ''' 
+    fname - a file, first line is head, first column is row name.
+    '''
+    
+    lineno = 0
+    colid = []
+    rowid = []
+    d =  {}  # {gene1:{cond1:val1, cond2:val2, ...}, gene2: {...}, ...}
+    d2 = {} # {cond1:{gene1:val1, gene2:val2, ...}, cond2: {...}, ...}
+    d3 = {} # {gene1: [], gene2: [], ...}
+    d4 = {} # {cond1:[], cond2:[], ...}
+
+    f = open(fname)
+    lines = f.readlines()
+    f.close()
+
+    head_line = lines[0].strip()
+    lst = head_line.split()
+    colid = lst[1:]
+
+    for c in colid:
+        d2[c] = {}
+        d4[c] = []
+    
+    for line in lines[1:]:
+        line = line.strip()
+        lst = line.split()
+        g = lst[0]
+        rowid.append(g)
+        d[g] = {}
+        levels = lst[1:]
+        if len(levels) != len(colid):
+            print('Incomplete columns at row %s' % (g))
+            sys.exit()
+            
+        d3[g] = []
+        for i in range(len(colid)):
+            c = colid[i]
+            d[g][c]  = float(levels[i])
+            d2[c][g] = float(levels[i])
+            d3[g].append(float(levels[i]))
+            d4[c].append(float(levels[i]))
+        lineno += 1
+
+    d_return = {}
+    d_return['xy'] = d  # first gene, then condition
+    d_return['yx'] = d2 # first condition, then gene
+    d_return['xx'] = d3 # each item is an array of gene expression levels, i.e., each item is a row
+    d_return['yy'] = d4 # each item is an array of gene expression levels, i.e., each item is a column
+    d_return['nrow'] = lineno - 1
+    d_return['ncol'] = len(colid)
+    d_return['rowid'] = rowid
+    d_return['colid'] = colid    
+
+    d4_sorted = {}
+    for k in d4:
+        d4_sorted[k] = sorted(d4[k], reverse=True)
+    d_return['yy_sorted'] = d4_sorted
+
+    return d_return
+
+# read paramters
+
+
+def get_key_value(s):
+    lst = s.split('=')
+    k, v = lst[0], lst[1]
+    return (k.strip(), v.strip())
+
+
+def get_value(s, delimit):
+    lst = s.split(delimit)
+    return lst[1].strip()
+
+def read_info_data(fname):
+    ''' Read chip-seq data information '''
+
+    if not os.path.exists(fname):
+        print('%s not exists.' % (fname) )
+        sys.exit()
+        
+    d = {'ID_LIST':[]}
+    f = open(fname)
+    lines = f.readlines()
+    f.close()
+    for line in lines:
+        line = line.strip()
+        if line == '' or line.startswith('#') or line.startswith('%'):
+            continue
+        if line.startswith(DATA_SYMBOL):
+            s = line[line.rfind(DATA_SYMBOL[-1])+1:]
+            s = s.strip()
+            if s in d:
+                print('ID %s duplicate' % (s))
+                sys.exit()
+            d[s] = {'PROTEIN_ID':'', 'PROTEN_NAME':'', 'DATA_NAME':'', 'DATA_FORMAT':'', 'DESCRIPTION':'', 'LOCATION':'', 'NOTE':''}
+            d['ID_LIST'].append(s)
+        if line.startswith('DESCRIPTION:'):
+            d[s]['DESCRIPTION'] = get_value(line, ':')
+        elif line.startswith('PROTEN_NAME:'):
+            d[s]['PROTEN_NAME'] = get_value(line, ':')
+        elif line.startswith('PROTEIN_ID:'):
+            d[s]['PROTEIN_ID'] = get_value(line, ':')
+        elif line.startswith('DATA_NAME:'):
+            d[s]['DATA_NAME'] = get_value(line, ':')                        
+        elif line.startswith('DATA_FORMAT:'):
+            d[s]['DATA_FORMAT'] = get_value(line, ':')
+        elif line.startswith('LOCATION:'):
+            d[s]['LOCATION'] = get_value(line, ':')
+        elif line.startswith('NOTE:'):
+            d[s]['NOTE'] = get_value(line, ':')
+
+    return d
+
+
+def make_global_param_dict(fname):
+    f = open(fname)
+    d = {}
+    for line in f:
+        line = line.strip()
+        if line.startswith(GLB_PARAM_SYMBOL):
+            s = line[line.rfind(GLB_PARAM_SYMBOL[-1])+1:]
+            lst = s.split('\t')  # separate items by TAB
+            for x in lst:
+                if x != '':
+                    k, v = get_key_value(x)
+                    d[k] = v
+    f.close()
+    return d
+
+
+def make_json_file(bind_dict, bind_info_dict, dir_name, glb_param_dict):
+    if not os.path.isdir(dir_name): # create the directory if not exist
+        os.makedirs(dir_name)
+
+    d = bind_dict['xy']
+    col_name_lst = bind_dict['colid']
+    row_name_lst = bind_dict['rowid']
+    for g in row_name_lst:
+        #print(g)
+        d2 = d[g]
+        d3 = {}
+        for k in sorted(d2.keys()):
+            data_type = bind_info_dict[k]['DATA_FORMAT'].upper()
+            if data_type == 'NARROWPEAK':
+                data_type = 'NP' # short name for narrowPeak
+            value = d2[k]
+            d3[k] = {'v':value, 't':data_type}
+        filename = os.path.join(dir_name, g + '.json')
+        with open(filename, 'w') as f:
+            json.dump(d3, f)
+    
+
+### main
+param_file = sys.argv[1] # a single prameter file
+glb_param_dict = make_global_param_dict(param_file)
+#print('Read binding matrix ...')
+binding_dict = read_matrix_data(glb_param_dict['BINDING_MATRIX'])
+bind_info_dict = read_info_data(glb_param_dict['BINDING_INFO'])
+#print('Make json files ...')
+make_json_file(binding_dict, bind_info_dict, JSON_DIR, glb_param_dict)