Fix AttributeError: 'SeqFeature' object has no attribute 'strand' (Biopython >1.80 compatibility)

[falatfernando]

Hi, I've been using ISMapper for a large-scale analysis and encountered a crash when running it on a fresh conda installation.

Summary Recent versions of Biopython (v1.80+) have removed the .strand shortcut attribute from SeqFeature objects, causing ISMapper to crash with an AttributeError. The strand information must now be accessed via .location.strand.

I've performed a test with the documentation test genomes and the pipeline and strand column is now correct.

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Environment

ISMapper Version: Installed from the bioconda channel.

BioPython Version: >1.80 (Automatically installed with fresh environment).

The Error When create_output.py attempts to read the strand of flanking genes, it fails because the SeqFeature object no longer exposes .strand directly.

AttributeError: 'SeqFeature' object has no attribute 'strand'

Analysis
Initially, I attempted to patch this using getattr(feature, 'strand', None). While this prevented the crash, it resulted in data loss (all strand columns in the output table became None).

Further investigation confirmed that the attribute has been deprecated and moved. To maintain functionality and ensure correct output (1 for forward, -1 for reverse), the code must be updated to access the attribute from the feature's location.

Proposed Solution (Implemented)
I have updated create_output.py script to correctly access the strand information compatible with modern Biopython versions.

Original (Broken): self.left_strand = left_feature.strand

Fix: self.left_strand = left_feature.location.strand

This restores the correct 1 / -1 values in the final output table.