Feature: rename samples #6
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| class NameMap(dict): |
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This class handles parsing sample names from argument lists or files.
| yield FastqFile(source_path, sample_name, read, self.prefix) | ||
| new_name = self.sample_name_map[sample_name] | ||
| yield FastqFile(source_path, new_name, read, self.prefix) |
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This is really the only place where the new sample name is used. All the other changes in this file are variable name changes that don't really affect how the code works.
ezfastq/cli.py
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| epilog_text = """ | ||
| Examples: | ||
| ezfastq /path/to/fastqs/ sample1 sample2 sample3 | ||
| ezfastq /path/to/fastqs/ s1:Sample1 s2:Sample2 s3:Sample3 | ||
| ezfastq /path/to/fastqs/ samplenames.txt | ||
| ezfastq /path/to/fastqs/ samplenames.txt --workdir /path/to/projectdir/ --subdir seq/Run01/ | ||
| ezfastq /path/to/fastqs/ samplenames.txt --pair-mode 2 | ||
| """ | ||
| epilog = Text(epilog_text, no_wrap=True) |
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Added an epilog to the argument parser since showing examples is the best way to describe how the sample renaming is done.
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This file has unit tests for the new NameMap class.
| def test_copier_with_renaming(tmp_path): | ||
| sample_names = NameMap.from_arglist( | ||
| ["test1:TestSampleA", "test2:TestSampleB", "test3:TestSampleC"] | ||
| ) |
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Also added a test for the FastqCopier test to make sure it renames files correctly on copy.
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This looks great! I've grown to really appreciate instantiating classes with classmethods. It seems to provide a lot more flexibility, i.e. from file or arglist than with one function containing a lot of logic statements. |
This PR adds support for renaming samples in the process of copying. Sample names are current specified one of two ways: as a list of string arguments...
...or as a file containing one sample name for each line.
This update allows sample renaming in both cases. For lists of string arguments, this is done by specifying the old name and new name separated by a colon.
For sample name files, this is done by adding a new column with a tab-separated value.