Mercurial > repos > bornea > saint_preprocessing
comparison SAINT_preprocessing_mq_pep.py @ 40:8102ffab0f85 draft
Uploaded
| author | bornea |
|---|---|
| date | Thu, 19 May 2016 10:35:15 -0400 |
| parents | e414a55b4c42 |
| children | ca0649bf68e3 |
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| 39:e414a55b4c42 | 40:8102ffab0f85 |
|---|---|
| 249 bait_index = [] | 249 bait_index = [] |
| 250 for bait_item in bait: | 250 for bait_item in bait: |
| 251 bait_index.append(header.index(bait_item[0])) | 251 bait_index.append(header.index(bait_item[0])) |
| 252 proteins = read_MaxQuant(MaxQuant_input).proteins | 252 proteins = read_MaxQuant(MaxQuant_input).proteins |
| 253 errors = [] | 253 errors = [] |
| 254 valid_prots = [] | |
| 254 for e in err: | 255 for e in err: |
| 255 errors.append(e[0]) | 256 errors.append(e[0]) |
| 256 for a in proteins: | 257 for a in proteins: |
| 257 a = a.replace("\n", "") | 258 a = a.replace("\n", "") |
| 258 # Remove \n for input into function. | 259 # Remove \n for input into function. |
| 259 a = a.replace("\r", "") | 260 a = a.replace("\r", "") |
| 260 # Ditto for \r. | 261 # Ditto for \r. |
| 261 seq = get_info(a).seqlength | 262 seq = get_info(a).seqlength |
| 262 GN = get_info(a).genename | 263 GN = get_info(a).genename |
| 263 if seq == 'NA': | 264 if seq != 'NA': |
| 264 if GN == 'NA': | 265 if GN != 'NA': |
| 265 errors.append(a) | 266 valid_prots.append(a) |
| 266 with open('inter.txt', 'w') as input_file: | 267 with open('inter.txt', 'w') as input_file: |
| 267 l = 0; a = 0 | 268 l = 0; a = 0 |
| 268 for bb in bait: | 269 for bb in bait: |
| 269 for lst in data: | 270 for lst in data: |
| 270 if proteins[a] not in errors: | 271 if valid_prots[a] not in errors: |
| 271 input_file.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' | 272 input_file.write(header[bait_index[l]] + '\t' + bb[1] + '\t' + proteins[a] + '\t' |
| 272 + lst[bait_index[l]] + '\n') | 273 + lst[bait_index[l]] + '\n') |
| 273 a += 1 | 274 a += 1 |
| 274 if a == len(proteins): | 275 if a == len(valid_prots): |
| 275 l += 1; a = 0 | 276 l += 1; a = 0 |
| 276 | 277 |
| 277 | 278 |
| 278 def bait_check(bait, MaxQuant_input): | 279 def bait_check(bait, MaxQuant_input): |
| 279 # Check that bait names share header titles. | 280 # Check that bait names share header titles. |