Upload make_cas_database.py

Author: HwangDoHyun28

make_cas_database.py

@@ -0,0 +1,63 @@
+with open('SLmic1.0_gene_models.gff') as fp:
+    data = fp.readlines()
+    data = [item.replace('\n','') for item in data]
+    for i in range(len(data)):
+        data[i] = data[i].split()
+cds_dict = {}
+for i in range(len(data)):
+    #print(data[i][0])
+    cds_dict[f'{data[i][0]}'] = []
+# print(cds_dict)
+for i in range(len(data)):
+    if data[i][2] == 'CDS':
+        cds_dict[f'{data[i][0]}'].append([data[i][-1][3:13],int(data[i][3])-1,int(data[i][4])])# 파일의 1-based에서 0-based로 바뀐 것을 고려(단, 슬라이싱을 고려하여 end좌표는 1을 빼지 않음)
+cds_dict = {key:value for key,value in cds_dict.items() if key == 'SLmic1.0_chr1'
+            or key == 'SLmic1.0_chr2'
+            or key == 'SLmic1.0_chr3'
+            or key == 'SLmic1.0_chr4'
+            or key == 'SLmic1.0_chr5'
+            or key == 'SLmic1.0_chr6'
+            or key == 'SLmic1.0_chr7'
+            or key == 'SLmic1.0_chr8'
+            or key == 'SLmic1.0_chr9'
+            or key == 'SLmic1.0_chr10' 
+            or key == 'SLmic1.0_chr11'
+            or key == 'SLmic1.0_chr12'}
+
+from Bio import SeqIO
+# 파일 형식: (sequence), (chr), (location), (+/-), (gene)
+cleavage_dict = {}
+chromo_list = ['SLmic1.0_chr1','SLmic1.0_chr2','SLmic1.0_chr3','SLmic1.0_chr4','SLmic1.0_chr5','SLmic1.0_chr6','SLmic1.0_chr7','SLmic1.0_chr8','SLmic1.0_chr9','SLmic1.0_chr10','SLmic1.0_chr11','SLmic1.0_chr12']
+
+for i in chromo_list:
+    cleavage_dict[i] = []
+
+
+for seq_record in SeqIO.parse("GCA_012431665.1_SLYMIC_genomic.fa", "fasta"):
+    seq = seq_record.seq
+
+    seq=str(seq.upper()) 
+
+    print(seq_record.id)
+
+    # cleavage, start_point, sequence, ngg/ccn list
+    if seq_record.id in chromo_list:
+        for i in range(21,len(seq)-1):
+            if seq[i] == 'G' and seq[i+1]=='G':# ngg-3, ngg-20, sequence
+                cleavage_dict[f'{seq_record.id}'].append([i-4,i-21,seq[i-21:i+2],'+'])
+        for i in range(len(seq)-24):
+            if seq[i] == 'C' and seq[i+1]=='C' and (seq_record.id in chromo_list):# ccn+6, ccn, sequence
+                cleavage_dict[f'{seq_record.id}'].append([i+5,i,seq[i:i+23][::1],'-'])
+
+
+# 파일 형식: (sequence), (chr), (location), (+/-), (gene)
+f = open("first.txt", 'w')
+f.write('# (sequence), (chr), (location), (+/-), (gene)\n')
+for i in cleavage_dict:
+    print(i)
+    for j in cds_dict[i]:
+        for k in cleavage_dict[i]:
+            if (j[1] <= k[0]) and (k[0] < j[2]) :
+                f.write(f'({k[2]}), ({i}), ({k[1]}), ({k[-1]}), ({j[0]})\n')
+f.close()
+