Mercurial > repos > bornea > saint_preproc
comparison SAINT_preprocessing_v6.py @ 17:40c88c39f8d7 draft
Uploaded
| author | bornea |
|---|---|
| date | Tue, 17 Nov 2015 12:14:10 -0500 |
| parents | 13383ba55336 |
| children | b230824e1a0e |
comparison
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| 16:413ffa0e80e7 | 17:40c88c39f8d7 |
|---|---|
| 24 fasta_db = str(tool_path) + "/SwissProt_HUMAN_2014_08.fasta" | 24 fasta_db = str(tool_path) + "/SwissProt_HUMAN_2014_08.fasta" |
| 25 make_bait= sys.argv[6] | 25 make_bait= sys.argv[6] |
| 26 | 26 |
| 27 | 27 |
| 28 baits = make_bait.split() | 28 baits = make_bait.split() |
| 29 print baits | |
| 30 i = 0 | 29 i = 0 |
| 31 bait_file_tmp = open("bait.txt", "wr") | 30 bait_file_tmp = open("bait.txt", "wr") |
| 32 order = [] | 31 order = [] |
| 33 bait_cache = [] | 32 bait_cache = [] |
| 34 | 33 |
| 133 db_len = len(lines) | 132 db_len = len(lines) |
| 134 seqlength = 0 | 133 seqlength = 0 |
| 135 count = 0 | 134 count = 0 |
| 136 for i in lines: | 135 for i in lines: |
| 137 if ">sp" in i: | 136 if ">sp" in i: |
| 137 namer = i.split("|")[2] | |
| 138 if uniprot_accession_in == i.split("|")[1]: | 138 if uniprot_accession_in == i.split("|")[1]: |
| 139 match = count+1 | |
| 140 if 'GN=' in i: | |
| 141 lst = i.split('GN=') | |
| 142 lst2 = lst[1].split(' ') | |
| 143 genename = lst2[0] | |
| 144 if 'GN=' not in i: | |
| 145 genename = 'NA' | |
| 146 while ">sp" not in lines[match]: | |
| 147 if match <= db_len: | |
| 148 seqlength = seqlength + len(lines[match].strip()) | |
| 149 match = match + 1 | |
| 150 else: | |
| 151 break | |
| 152 return ReturnValue1(seqlength, genename) | |
| 153 elif uniprot_accession_in == namer.split(" "): | |
| 139 match = count+1 | 154 match = count+1 |
| 140 if 'GN=' in i: | 155 if 'GN=' in i: |
| 141 lst = i.split('GN=') | 156 lst = i.split('GN=') |
| 142 lst2 = lst[1].split(' ') | 157 lst2 = lst[1].split(' ') |
| 143 genename = lst2[0] | 158 genename = lst2[0] |
| 240 sys.exit("Bait must share header titles with Scaffold output") | 255 sys.exit("Bait must share header titles with Scaffold output") |
| 241 | 256 |
| 242 if __name__ == '__main__': | 257 if __name__ == '__main__': |
| 243 main(infile, baitfile) | 258 main(infile, baitfile) |
| 244 | 259 |
| 245 os.rename('inter.txt', sys.argv[4]) | 260 os.rename("inter.txt", sys.argv[4]) |
| 246 os.rename("bait.txt", sys.argv[7]) | 261 os.rename("bait.txt", sys.argv[7]) |