Mercurial > repos > greg > validate_affy_metadata
comparison validate_affy_metadata.py @ 23:84478b80cc47 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 15 Feb 2019 08:57:22 -0500 |
| parents | 90688364136c |
| children | 8a826d1afe69 |
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| 22:e5f68d7f238e | 23:84478b80cc47 |
|---|---|
| 74 line = line.rstrip("\r\n") | 74 line = line.rstrip("\r\n") |
| 75 if i > 97: | 75 if i > 97: |
| 76 accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).") | 76 accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).") |
| 77 stop_error(accumulated_msgs) | 77 stop_error(accumulated_msgs) |
| 78 items = line.split("\t") | 78 items = line.split("\t") |
| 79 if len(items) != 30: | 79 if len(items) != 32: |
| 80 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 30)." % (i, len(items))) | 80 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 30)." % (i, len(items))) |
| 81 stop_error(accumulated_msgs) | 81 stop_error(accumulated_msgs) |
| 82 # Required and validated. | 82 # Required and validated. |
| 83 # Required. | 83 # Required. |
| 84 user_specimen_id = items[0] | 84 user_specimen_id = items[0] |
| 159 sperm_motility = items[28] | 159 sperm_motility = items[28] |
| 160 accumulated_msgs = validate_decimal(i, sperm_motility, accumulated_msgs) | 160 accumulated_msgs = validate_decimal(i, sperm_motility, accumulated_msgs) |
| 161 # Required and validated. | 161 # Required and validated. |
| 162 healing_time = items[29] | 162 healing_time = items[29] |
| 163 accumulated_msgs = validate_decimal(i, healing_time, accumulated_msgs) | 163 accumulated_msgs = validate_decimal(i, healing_time, accumulated_msgs) |
| 164 # Optional. | |
| 165 dna_extraction_method = items[9] | |
| 166 # Optional. | |
| 167 dna_concentration = items[31] | |
| 168 # If dna_concentration has a value, then it must be decimal. | |
| 169 if len(dna_concentration) > 0: | |
| 170 accumulated_msgs = validate_decimal(i, dna_concentration, accumulated_msgs) | |
| 171 | |
| 164 | 172 |
| 165 if len(accumulated_msgs) > 0: | 173 if len(accumulated_msgs) > 0: |
| 166 stop_error(accumulated_msgs) | 174 stop_error(accumulated_msgs) |
| 167 | 175 |
| 168 shutil.copyfile(args.input, args.output) | 176 shutil.copyfile(args.input, args.output) |