--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pep_pointer.py	Fri Dec 29 12:37:22 2017 -0500
@@ -0,0 +1,221 @@
+
+# 
+# Author: Praveen Kumar
+# Updated: Nov 8th, 2017
+# 
+# 
+# 
+
+import re
+
+
+def main():
+    import sys
+    if len(sys.argv) == 4:
+        inputFile = sys.argv
+        infh = open(inputFile[1], "r")
+        # infh = open("Mus_musculus.GRCm38.90.chr.gtf", "r")
+        
+        gtf = {}
+        gtf_transcript = {}
+        gtf_gene = {}
+        for each in infh.readlines():
+            a = each.split("\t")
+            if re.search("^[^#]", each):
+                if re.search("gene_biotype \"protein_coding\"", a[8]) and int(a[4].strip()) != int(a[3].strip()):
+                    type = a[2].strip()
+                    if type == "gene" or type == "exon" or type == "CDS" or type == "five_prime_utr" or type == "three_prime_utr":
+                        chr = "chr" + a[0].strip()
+                        strand = a[6].strip()
+                        if strand == "+":
+                            start = a[3].strip()
+                            end = a[4].strip()
+                        elif strand == "-":
+                            if int(a[4].strip()) > int(a[3].strip()):
+                                start = a[3].strip()
+                                end = a[4].strip()
+                            elif int(a[4].strip()) < int(a[3].strip()):
+                                start = a[4].strip()
+                                end = a[3].strip()
+                            else:
+                                print "Something fishy in start end coordinates"
+                        else:
+                            print "Something fishy in reading"
+                        if not gtf.has_key(strand):
+                            gtf[strand] = {}
+                        if not gtf[strand].has_key(type):
+                            gtf[strand][type] = []
+                        b = re.search("gene_id \"(.+?)\";", a[8].strip())
+                        gene = b.group(1)
+                        if type == "gene":
+                            transcript = ""
+                        else:
+                            b = re.search("transcript_id \"(.+?)\";", a[8].strip())
+                            transcript = b.group(1)
+                        data = (chr, start, end, gene, transcript, strand, type)
+                        gtf[strand][type].append(data)
+                
+                        if type == "exon":
+                            if gtf_transcript.has_key(chr+"#"+strand):
+                                if gtf_transcript[chr+"#"+strand].has_key(transcript+"#"+gene):
+                                    gtf_transcript[chr+"#"+strand][transcript+"#"+gene][0].append(int(start))
+                                    gtf_transcript[chr+"#"+strand][transcript+"#"+gene][1].append(int(end))
+                                else:
+                                    gtf_transcript[chr+"#"+strand][transcript+"#"+gene] = [[],[]]
+                                    gtf_transcript[chr+"#"+strand][transcript+"#"+gene][0].append(int(start))
+                                    gtf_transcript[chr+"#"+strand][transcript+"#"+gene][1].append(int(end))
+                            else:
+                                gtf_transcript[chr+"#"+strand] = {}
+                                gtf_transcript[chr+"#"+strand][transcript+"#"+gene] = [[],[]]
+                                gtf_transcript[chr+"#"+strand][transcript+"#"+gene][0].append(int(start))
+                                gtf_transcript[chr+"#"+strand][transcript+"#"+gene][1].append(int(end))
+                
+                        if type == "gene":
+                            if gtf_gene.has_key(chr+"#"+strand):
+                                gtf_gene[chr+"#"+strand][0].append(int(start))
+                                gtf_gene[chr+"#"+strand][1].append(int(end))
+                                gtf_gene[chr+"#"+strand][2].append(gene)
+                            else:
+                                gtf_gene[chr+"#"+strand] = [[0],[0],["no_gene"]]
+                                gtf_gene[chr+"#"+strand][0].append(int(start))
+                                gtf_gene[chr+"#"+strand][1].append(int(end))
+                                gtf_gene[chr+"#"+strand][2].append(gene)
+                        
+                        
+    
+        # "Starting Reading Intron . . ."
+    
+        gtf["+"]["intron"] = []
+        gtf["-"]["intron"] = []
+        for chr_strand  in gtf_transcript.keys():
+            chr = chr_strand.split("#")[0]
+            strand = chr_strand.split("#")[1]
+        
+            for transcript_gene in gtf_transcript[chr_strand].keys():
+                start_list = gtf_transcript[chr_strand][transcript_gene][0]
+                end_list = gtf_transcript[chr_strand][transcript_gene][1]
+                sorted_start_index = [i[0] for i in sorted(enumerate(start_list), key=lambda x:x[1])]
+                sorted_end_index = [i[0] for i in sorted(enumerate(end_list), key=lambda x:x[1])]
+                if sorted_start_index == sorted_end_index:
+                    sorted_start = sorted(start_list)
+                    sorted_end = [end_list[i] for i in sorted_start_index]
+                    for x in range(len(sorted_start))[1:]:
+                        intron_start = sorted_end[x-1]+1
+                        intron_end = sorted_start[x]-1
+                        transcript = transcript_gene.split("#")[0]
+                        gene = transcript_gene.split("#")[1]
+                        data = (chr, str(intron_start), str(intron_end), gene, transcript, strand, "intron")
+                        gtf[strand]["intron"].append(data)
+                    
+    
+        # "Starting Reading Intergenic . . ."
+    
+        gtf["+"]["intergenic"] = []
+        gtf["-"]["intergenic"] = []
+        for chr_strand  in gtf_gene.keys():
+            chr = chr_strand.split("#")[0]
+            strand = chr_strand.split("#")[1]
+            start_list = gtf_gene[chr_strand][0]
+            end_list = gtf_gene[chr_strand][1]
+            gene_list = gtf_gene[chr_strand][2]
+            sorted_start_index = [i[0] for i in sorted(enumerate(start_list), key=lambda x:x[1])]
+            sorted_end_index = [i[0] for i in sorted(enumerate(end_list), key=lambda x:x[1])]
+        
+            sorted_start = sorted(start_list)
+            sorted_end = [end_list[i] for i in sorted_start_index]
+            sorted_gene = [gene_list[i] for i in sorted_start_index]
+            for x in range(len(sorted_start))[1:]:
+                intergene_start = sorted_end[x-1]+1
+                intergene_end = sorted_start[x]-1
+                if intergene_start < intergene_end:
+                    intergene_1 = sorted_gene[x-1]
+                    intergene_2 = sorted_gene[x]
+                    gene = intergene_1 + "-#-" + intergene_2
+                    data = (chr, str(intergene_start), str(intergene_end), gene, "", strand, "intergenic")
+                    gtf[strand]["intergenic"].append(data)
+    
+        import sqlite3
+        # conn = sqlite3.connect('gtf_database.db')
+        conn = sqlite3.connect(":memory:")
+        c = conn.cursor()
+        # c.execute("DROP TABLE IF EXISTS gtf_data;")
+        # c.execute("CREATE TABLE IF NOT EXISTS gtf_data(chr text, start int, end int, gene text, transcript text, strand text, type text)")
+        c.execute("CREATE TABLE gtf_data(chr text, start int, end int, gene text, transcript text, strand text, type text)")
+    
+        for strand in gtf.keys():
+            if strand == "+":
+                st = "positive"
+            elif strand == "-":
+                st = "negative"
+            else:
+                print "Something fishy in writing . . ."
+        
+            for type in gtf[strand].keys():
+                data = gtf[strand][type]
+                c.executemany('INSERT INTO gtf_data VALUES (?,?,?,?,?,?,?)', data)
+            
+        conn.commit()
+    
+        infh = open(inputFile[2], "r")
+        # infh = open("Mouse_Data_All_peptides_withNewDBs.txt", "r")
+        data = infh.readlines()
+        # output file
+        outfh = open(inputFile[3], 'w')
+        # outfh = open("classified_1_Mouse_Data_All_peptides_withNewDBs.txt", "w")
+    
+        for each in data:
+            a = each.split("\t")
+            chr = a[0].strip()
+            pep_start = a[1].strip()
+            pep_end = a[2].strip()
+            strand = a[5].strip()
+            c.execute("select * from gtf_data where type = 'CDS' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+            rows = c.fetchall()
+            if len(rows) > 0:
+                outfh.write(each.strip() + "\tCDS\n")
+            else:
+                c.execute("select * from gtf_data where type = 'five_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                rows = c.fetchall()
+                if len(rows) > 0:
+                    outfh.write(each.strip() + "\tfive_prime_utr\n")
+                else:
+                    c.execute("select * from gtf_data where type = 'three_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                    rows = c.fetchall()
+                    if len(rows) > 0:
+                        outfh.write(each.strip() + "\tthree_prime_utr\n")
+                    else:
+                        c.execute("select * from gtf_data where type = 'exon' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                        rows = c.fetchall()
+                        if len(rows) > 0:
+                            outfh.write(each.strip() + "\texon\n")
+                        else:
+                            c.execute("select * from gtf_data where type = 'intron' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                            rows = c.fetchall()
+                            if len(rows) > 0:
+                                outfh.write(each.strip() + "\tintron\n")
+                            else:
+                                c.execute("select * from gtf_data where type = 'gene' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                                rows = c.fetchall()
+                                if len(rows) > 0:
+                                    outfh.write(each.strip() + "\tgene\n")
+                                else:
+                                    c.execute("select * from gtf_data where type = 'intergenic' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ")
+                                    rows = c.fetchall()
+                                    if len(rows) > 0:
+                                        outfh.write(each.strip() + "\tintergene\n")
+                                    else:
+                                        outfh.write(each.strip() + "\tOVERLAPPING_ON_TWO_REGIONS: PLEASE_LOOK_MANUALLY (Will be updated in next version)\n")
+    
+        conn.close()
+        outfh.close()
+    else:
+        print "USAGE: python pep_pointer.py <input GTF file> <input tblastn file> <name of output file>"
+    return None
+
+if __name__ == "__main__":
+    main()
+
+
+
+
+