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AleksandrSl
reviewed
Oct 11, 2018
pybedtools_parser.py
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| # Ignore annotation lines. | ||
| if any(i in line_elements for i in ("#", "browser", "track")): | ||
| continue | ||
| # Check if a non-annotation line if valid. |
pybedtools_parser.py
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| continue | ||
| # Check if a non-annotation line if valid. | ||
| elif len(line_elements) < 3: | ||
| sys.exit("Program expects a valid BED file with at least 3 columns (chromosome, start and end).\n" |
Owner
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IMHO sys.exit is not the best way. Some kind of error is more suitable.
Python has multiline strings, sot there's no need in \n
pybedtools_parser.py
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| "Problem in line: %s" % line) | ||
| # End of check | ||
| else: | ||
| # Give "None" name if file is BED3 or doesn't contain name option for other BED types. |
Owner
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I think that following lines will have the same effect without else
AleksandrSl
reviewed
Nov 6, 2018
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| def check_len(line): | ||
| try: | ||
| line[2] |
Owner
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Why line, not smth like elements?) And why not if len(line) < 3:
| parsed_data.append(tuple(line_elements[0:5])) | ||
| check_len(line_elements) | ||
| check_int(line_elements) | ||
| parsed_data.append(tuple(line_elements[0:5])) |
Collaborator
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Realised we shoud either take 4 or 6 elements, not 5...
There can be score and strand information. Should we ignore it?
Owner
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Yes, we can ignore it for the moment
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