extract sequences from pdb files with BioPandas

[stephprince]

Motivation

Currently sequence extraction using the biopython SeqIO parser creates fasta files with incorrectly shortened sequences. This seems to occur because SeqIO ignores out-of-order residues, and residues added to the beginning of the pdb file by pdb-fixer are given out-of-order sequence numbers (see 3M8J_A.pdb for an example).

The proposed changes use BioPandas instead to extract the sequence information from the pdb files.

How to test the behavior?

extract-seq -f /path/to/input.pdb -o /path/to/output.fasta

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
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• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

Attention: Patch coverage is 97.36842% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 94.38%. Comparing base (aab0700) to head (fc3e6ea).

Files	Patch %	Lines
tests/test_extract_seq.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main       #5       +/-   ##
===========================================
+ Coverage   80.95%   94.38%   +13.42%     
===========================================
  Files           2        3        +1     
  Lines          63       89       +26     
===========================================
+ Hits           51       84       +33     
+ Misses         12        5        -7     

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