--- a/peptideGenomicCoordinate.py	Sun Jun 17 04:55:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-
-# 
-# Author: Praveen Kumar
-# University of Minnesota
-# Galaxy-P Team
-# Get peptide's genomic coordinate from the protein's genomic mapping sqlite file (which is derived from the https://toolshed.g2.bx.psu.edu/view/galaxyp/translate_bed/038ecf54cbec)
-# 
-# python peptideGenomicCoordinate.py <peptide_list> <mz_to_sqlite DB> <genomic mapping file DB> <output.bed>
-# 
-#
-
-def main():
-    import sys
-    import sqlite3
-    conn = sqlite3.connect(sys.argv[2])
-    c = conn.cursor()
-    c.execute("DROP table if exists novel")
-    conn.commit()
-    c.execute("CREATE TABLE novel(peptide text)")
-    pepfile = open(sys.argv[1],"r")
-
-    for seq in pepfile.readlines():
-        seq = seq.strip()
-        c.execute('INSERT INTO novel VALUES ("'+seq+'")')
-        conn.commit()
-
-    c.execute("SELECT distinct psm.sequence, ps.id, ps.sequence from db_sequence ps, psm_entries psm, novel n, proteins_by_peptide pbp where psm.sequence = n.peptide and pbp.peptide_ref = psm.id and pbp.id = ps.id")
-    rows = c.fetchall()
-
-    conn1 = sqlite3.connect(sys.argv[3])
-    c1 = conn1.cursor()
-
-    outfh = open(sys.argv[4], "w")
-
-    master_dict = {}
-    for each in rows:
-        peptide = each[0]
-        acc = each[1]
-        acc_seq = each[2]
-    
-        c1.execute("SELECT chrom,start,end,name,strand,cds_start,cds_end FROM feature_cds_map map WHERE map.name = '"+acc+"'")
-        coordinates = c1.fetchall()
-    
-        if len(coordinates) != 0:
-            pep_start = 0
-            pep_end = 0
-            flag = 0
-            splice_flag = 0
-            spliced_peptide = []
-            for each_entry in coordinates:
-                chromosome = each_entry[0]
-                start = int(each_entry[1])
-                end = int(each_entry[2])
-                strand = each_entry[4]
-                cds_start = int(each_entry[5])
-                cds_end = int(each_entry[6])
-                pep_pos_start = (acc_seq.find(peptide)*3)
-                pep_pos_end = pep_pos_start + (len(peptide)*3)
-                if (pep_pos_start >= cds_start) and (pep_pos_end <= cds_end):
-                    if strand == "+":
-                        pep_start = start + pep_pos_start - cds_start
-                        pep_end = start + pep_pos_end - cds_start
-                        pep_thick_start = 0
-                        pep_thick_end = len(peptide)
-                        flag == 1
-                    else:
-                        pep_end = end - pep_pos_start + cds_start
-                        pep_start = end - pep_pos_end + cds_start
-                        pep_thick_start = 0
-                        pep_thick_end = len(peptide)
-                        flag == 1
-                    spliced_peptide = []
-                    splice_flag = 0
-                else:
-                    if flag == 0:
-                        if strand == "+":
-                            if (pep_pos_start >= cds_start) and (pep_pos_start <= cds_end) and (pep_pos_end > cds_end):
-                                pep_start = start + pep_pos_start - cds_start
-                                pep_end = end
-                                pep_thick_start = 0
-                                pep_thick_end = (pep_end-pep_start)
-                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
-                                splice_flag = splice_flag + 1
-                                if splice_flag == 2:
-                                    flag = 1
-                            elif (pep_pos_end >= cds_start) and (pep_pos_end <= cds_end) and (pep_pos_start < cds_start):
-                                pep_start = start
-                                pep_end = start + pep_pos_end - cds_start
-                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
-                                pep_thick_end = (len(peptide)*3)
-                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
-                                splice_flag = splice_flag + 1
-                                if splice_flag == 2:
-                                    flag = 1
-                            else:
-                                pass
-                        else:
-                            if (pep_pos_start >= cds_start) and (pep_pos_start <= cds_end) and (pep_pos_end >= cds_end):
-                                pep_start = start
-                                pep_end = end - pep_pos_start - cds_start
-                                pep_thick_start = 0
-                                pep_thick_end = (pep_end-pep_start)
-                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
-                                splice_flag = splice_flag + 1
-                                if splice_flag == 2:
-                                    flag = 1
-                            elif (pep_pos_end >= cds_start) and (pep_pos_end <= cds_end) and (pep_pos_start <= cds_start):
-                                pep_start = end - pep_pos_end + cds_start
-                                pep_end = end
-                                pep_thick_start = (len(peptide)*3)-(pep_end-pep_start)
-                                pep_thick_end = (len(peptide)*3)
-                                spliced_peptide.append([pep_start,pep_end,pep_thick_start,pep_thick_end])
-                                splice_flag = splice_flag + 1
-                                if splice_flag == 2:
-                                    flag = 1
-                            else:
-                                pass
-            if len(spliced_peptide) == 0:
-                if strand == "+":
-                    bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
-                else:
-                    bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"]
-                outfh.write("\t".join(bed_line)+"\n")
-            else:
-                if strand == "+":
-                    pep_entry = spliced_peptide
-                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
-                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
-                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
-                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
-                    bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
-                    outfh.write("\t".join(bed_line)+"\n")
-                else:
-                    pep_entry = spliced_peptide
-                    pep_start = min([pep_entry[0][0], pep_entry[1][0]])
-                    pep_end = max([pep_entry[0][1], pep_entry[1][1]])
-                    blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))]
-                    blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))]
-                    bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)]
-                    outfh.write("\t".join(bed_line)+"\n")
-    c.execute("DROP table novel")
-    conn.commit()
-    conn.close()
-    conn1.close()
-    outfh.close()
-    pepfile.close()
-    
-    return None
-if __name__ == "__main__":
-    main()