Refactor utils.py: add GvfFileReader class - #52
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khetherin wants to merge 13 commits into
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tcezard
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Aug 1, 2026
| if not line.startswith("#"): | ||
| f_list = line.rstrip().split("\t") | ||
| yield GvfFeatureline(f_list[0], f_list[1], f_list[2], f_list[3], f_list[4], f_list[5], f_list[6], f_list[7], f_list[8]) | ||
| class GvfFileReader: |
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If you are going to create a reader class, you might as well make it pythoninc and implement __iter__ to make it iterable. That would allow you to user is like.
for gvf_line in gvf_file_reader:
...
…base, check_ref, get_alt)
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Merge conflicts have been resolved, ready for review. |
apriltuesday
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Aug 6, 2026
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| for _ in header_reader: | ||
| break # stops at first data line |
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Suggested change
| for _ in header_reader: | |
| break # stops at first data line | |
| next(header_reader) |
| # fresh instance | ||
| gvf_reader = GvfFileReader(self.input_file) | ||
| reader_iter = iter(gvf_reader) | ||
| reader_iter = iter(gvf_reader) |
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Suggested change
| reader_iter = iter(gvf_reader) |
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Another minor PR to refactor utils.py, this time to pull read_in_gvf_header and read_in_gvf_data into a GvfFileReader class.
Files changed: