Add --both flag to output left and right terminal repeats

[Copilot]

Adds --both option to tsplit TIR and tsplit LTR to extract both terminal repeats instead of only the leftmost.

Changes

• CLI: Added --both flag to TIR and LTR parsers
• Output naming:
  • With --both: element_L_TIR/element_R_TIR or element_L_LTR/element_R_LTR
  • Without: element_TIR or element_LTR (unchanged)
• Orientation: Right TIR is reverse complemented (inverted repeats on opposite strands); right LTR is not (direct repeats on same strand)
• Gap removal: Terminal repeat sequences have gaps stripped via str().replace('-', '')
• Mode interaction: Only affects --splitmode in {all, split, external}

Implementation

Modified getTIRs() and getLTRs() in parseAlign.py:

if both:
    # Left TIR
    leftSeg = rec[ref_start : ref_end + 1]
    leftSeg.seq = Seq(str(leftSeg.seq).replace('-', ''))
    leftSeg.id = f'{leftSeg.id}_L_TIR'
    yield leftSeg
    
    # Right TIR - reverse complemented for alignment
    rightSeg = rec[qry_start : qry_end + 1]
    rightSeg.seq = Seq(str(rightSeg.seq).replace('-', ''))
    rightSeg = rightSeg.reverse_complement(id=f'{rec.id}_R_TIR', ...)
    yield rightSeg

Testing

Added 21 tests covering:

• Both flag behavior with different split modes
• Correct reverse complementation for TIRs
• No reverse complementation for LTRs
• Gap removal
• Suffix naming conventions

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Feature: Add option to output both terminal repeats</issue_title>
<issue_description>## Current behaviour

The modules tsplit TIR and tsplit LTR currently have the --splitmode options {all,split,internal,external,None}

When using the --splitmode options {all,split,external} the leftmost terminal repeat is reported in the output fasta. This will have the suffix '_TIR' or '_LTR' depending on which tsplit tool is being used.

New feature

Add a new feature that will output both left and right terminal repeats if set.

Detailed tasks

• Add new arg to tsplit TIR and tsplit LTR called --both. When "both" option is set and --splitmodeoption is one of{all,split,external}` then the output should include both the left an right instance of the detected terminal repeat.
• Extract the righthand terminal repeat sequence from the alignment record of the lefthand terminal repeat.
• If reporting both termini then suffix should indicate which end the repeat was extracted from i.e '_L_TIR', '_R_TIR' for TIRs, or '_L_LTR', '_R_LTR' for LTRs depending on which tool is called.
• When reporting both TIRs the right end copy of the TIR (Terminal Inverted Repeat) should be reported as the reverse complement sequence so that it is align-able to the left TIR. The right LTR however should not be reverse complemented as it will already be in the same orientation as the left LTR.
• For TIRs, check if the righthand terminal repeat is already in the same orientation as the lefthand repeat when it is extracted from the biopython alignment object.
• Reported terminal repeats should not contain gaps
• Write thorough best practice pytests for all new features.
  </issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Feature: Add option to output both terminal repeats #3

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