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Add SeqIO read/write support for NCBI 5-column tab-delimited feature tables#5032

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michaelfm1211:feature-table
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Add SeqIO read/write support for NCBI 5-column tab-delimited feature tables#5032
michaelfm1211 wants to merge 5 commits intobiopython:masterfrom
michaelfm1211:feature-table

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@michaelfm1211 michaelfm1211 commented Jul 21, 2025

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Closes #4943

This PR adds a SeqIO parser and writer for the 5-column tab-delimited feature table (.tbl) format used for preparing GenBank submissions.

@AgustinPardo's feedback on this may be helpful, as he opened the linked issue and wrote his own parser too.

@michaelfm1211 michaelfm1211 requested a review from peterjc as a code owner July 21, 2025 22:05
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codecov bot commented Jul 21, 2025 •
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Codecov Report

Attention: Patch coverage is 98.36957% with 3 lines in your changes missing coverage. Please review.

Project coverage is 86.19%. Comparing base (66ad0a0) to head (b8298a0).

Files with missing lines Patch % Lines
Bio/SeqIO/FeatureTableIO.py 98.36% 3 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #5032      +/-   ##
==========================================
+ Coverage   85.45%   86.19%   +0.74%     
==========================================
  Files         286      287       +1     
  Lines       59851    60035     +184     
==========================================
+ Hits        51144    51749     +605     
+ Misses       8707     8286     -421

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michaelfm1211 commented Jul 22, 2025

Tests are still failing, but the error messages are a little less cryptic now. The .tbl reader works fine and tests seem to pass if the writer is commented out from Bio/SeqIO/__init__.py. The writer seems to be failing thetest_SeqIO.py tests which read from one format and writes in another and checks for consistency. There seems to be a lot of stuff that other features support but .tbl doesn't (for example, .tbl doesn't even explicitly store the sequence length, however, the length of the reference feature is usually the same as the length of the sequence). I'll convert this PR to a draft for now.

@michaelfm1211 michaelfm1211 marked this pull request as draft July 22, 2025 17:28
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peterjc commented Jul 24, 2025

We should probably explicitly silence the warnings here:

test_SeqIO ... /Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/Bio/SeqIO/FeatureTableIO.py:71: BiopythonParserWarning: Reference has Medline ID, but only PubMed IDs are officially supported in .tbl files: type: REFERENCE
location: [0:880](+)
qualifiers:
    Key: Medline, Value: ['92329728']

  warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/Bio/SeqIO/FeatureTableIO.py:71: BiopythonParserWarning: Reference has Medline ID, but only PubMed IDs are officially supported in .tbl files: type: REFERENCE
location: [0:513](+)
qualifiers:
    Key: Medline, Value: ['92119220']

  warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/Bio/SeqIO/FeatureTableIO.py:71: BiopythonParserWarning: Reference has Medline ID, but only PubMed IDs are officially supported in .tbl files: type: REFERENCE
location: [0:741](+)
qualifiers:
    Key: Medline, Value: ['94311827']

  warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-packages/Bio/SeqIO/FeatureTableIO.py:71: BiopythonParserWarning: Reference has Medline ID, but only PubMed IDs are officially supported in .tbl files: type: REFERENCE
location: [0:182](+)
qualifiers:
    Key: Medline, Value: ['83265757']

  warnings.warn(
FAIL

In the new tests specific to this new parser we can test the expected warnings appear.

More generally, test_SeqIO.py has a bunch of special casing by format as differences are common.

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NCBI Sequin tbl format parser

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