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gencorefacility / reform

Modify existing reference fasta and gff3/gtf files to include a new sequence
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Sequential processing #16

Closed YuWei-CH closed 3 months ago

YuWei-CH commented 4 months ago

For Test:

  1. Auto-remove in test_reform.py: Implement a feature to automatically remove reformed files in the test_data folder before and after the execution of test_reform.py. This feature ensures that the test_data folder remains clean and unaffected by previous tests.
  2. New test cases: Add test case 14 and 15 to test sequential input.

For Sequential Processing:

  1. Multiple input support in argparse: Modify the argument parser to support multiple input files. Store the positions and names of input files in lists and pass them to the main function.
  2. Iteration of Positions: Use a for-loop to iterate over the list of positions or sequences (up seq and down seq) to find the position of insertion or modification. Since positions are based on the original sequence, recalculate the current position based on previous modifications after obtaining the initial position. Note that the position correction in this PR does not support positions obtained from up seq and down seq.
  3. Sequential Processing: After obtaining the position, retrieve a pair of in.fa and in.gtf files from the list and pass them to index_fasta() and create_new_gff().
  4. Temporary Files: Create two temporary files (xxx.fa and xxx.gtf (GFF3)) to store reformed files. These temporary files will be used as reference sequences in the subsequent iterations of the for-loop.

Resolve Conflict:

  1. Merge the read compressed feature from use-gz into for-loop of sequential processing.