Biopython update #157

pipaj97 · 2023-06-25T12:10:13Z

Description

In the latest version of biopython, some functionalities do not work anymore in OpenCADD.
This PR fixes this problem.

Todos

Notable points that this PR has either accomplished or will accomplish.

Update sequence functionalities to work with the latest biopython version
add a test for the newly implemented gap function
Check and solve CI failures

Status

Ready to go

AAriam

There were some apparent mistakes that I commented on the opencadd/structure/superposition/sequences.py file.

However, more importantly, the fasta2select function (i.e. the only part of the code being changed in this PR) does not have any explicit unit tests. Therefore, even after resolving these comments, we can't be sure of the correctness of the function until we write some explicit test-cases.

AAriam · 2024-01-30T12:12:04Z

opencadd/structure/superposition/sequences.py

@@ -190,8 +211,8 @@ def resid(nseq, ipos, t=t, s=s):
    res_list = []  # collect individual selection string

    # should be the same for both seqs
-    GAP = alignment[0].seq.alphabet.gap_char
-    if GAP != alignment[1].seq.alphabet.gap_char:
+    GAP = find_gap_character(a.seq)


Shouldn't this (Line 214) be GAP = find_gap_character(alignment[0].seq) instead?
a is a loop variable from above, and is simply equal to the last value of the loop iteration, which seems quite random. Also, the original lines were:

GAP = alignment[0].seq.alphabet.gap_char if GAP != alignment[1].seq.alphabet.gap_char:

and the second line has changed to

if GAP != find_gap_character(alignment[1].seq):

so it looks like the first line must also be:

GAP = find_gap_character(alignment[0].seq)

instead of:

GAP = find_gap_character(a.seq)

AAriam · 2024-01-30T12:17:30Z

opencadd/structure/superposition/sequences.py

@@ -175,7 +195,8 @@ def resid_factory(alignment, seq2resids):
        t = np.zeros((nseq, alignment.get_alignment_length()), dtype=int)
        s = np.zeros((nseq, alignment.get_alignment_length()), dtype=object)
        for iseq, a in enumerate(alignment):
-            GAP = a.seq.alphabet.gap_char
+            print(a.seq)


Leftover from debugging?

AAriam · 2024-01-30T12:45:08Z

opencadd/structure/superposition/sequences.py

@@ -204,4 +225,4 @@ def resid(nseq, ipos, t=t, s=s):

    ref_selection = " or ".join(sel[0])
    target_selection = " or ".join(sel[1])
-    return {"reference": ref_selection, "mobile": target_selection}
+    return {"reference": ref_selection, "mobile": target_selection}


add end-of-file newline

AAriam · 2024-01-30T12:51:52Z

opencadd/structure/superposition/sequences.py

+        return ''
+    #raise ValueError("No standard gap character found!")
+
+
 def fasta2select(


Shouldn't the gap characters be removed explicitly now that BioPython doesn't recognize them?

From BioPython Documentation:

Another case where the alphabet was used was in declaring the gap character, by default - in the various Biopython sequence and alignment parsers. If you are using a different character, you will need to pass this to the Seq object .replace() method explicitly now:

# Old style from Bio.Alphabet import generic_dna, Gapped from Bio.Seq import Seq my_dna = Seq("ACGT=TT", Gapped(generic_dna, "=")) print(my_dna.ungap())

# New style from Bio.Seq import Seq my_dna = Seq("ACGT=TT") print(my_dna.replace("=", ""))

AndreaVolkamer · 2024-01-30T13:04:12Z

@pipaj97 can you have a look at these comments please?

AndreaVolkamer · 2024-01-30T13:23:08Z

@dominiquesydow can you please have a look in the CI failures realted to the kliffs package:

 =========================== short test summary info ============================
  FAILED opencadd/tests/databases/test_klifs_local_remote.py::TestsAllQueries::test_all_interactions - bravado.exception.HTTPURITooLong: 414 Request-URI Too Long: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
  <html><head>
  <title>414 Request-URI Too Long</title>
  </head><body>
  <h1>Request-URI Too Long</h1>
  <p>The requested URL's length exceeds the capacity
  limit for this server.<br />
  </p>
  <hr>
  <address>Apache/2.4.38 (Debian) Server at klifs.net Port 443</address>
  </body></html>
  FAILED opencadd/tests/databases/test_klifs_local_remote.py::TestsAllQueries::test_all_conformations - bravado.exception.HTTPURITooLong: 414 Request-URI Too Long: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
  <html><head>
  <title>414 Request-URI Too Long</title>
  </head><body>
  <h1>Request-URI Too Long</h1>
  <p>The requested URL's length exceeds the capacity
  limit for this server.<br />
  </p>
  <hr>
  <address>Apache/2.4.38 (Debian) Server at klifs.net Port 443</address>
  </body></html>

dominiquesydow · 2024-02-25T17:34:21Z

Hi @AndreaVolkamer,

I fixed the following two items:

1. A future deprecation warning for pandas, e.g. here:

/Users/dominique/Documents/GitHub/opencadd/opencadd/databases/klifs/core.py:147: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
  The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.
  
  For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.
  
  
    dataframe["ligand_allosteric.expo_id"].replace(0, "-", inplace=True)

We are doing now instead:

dataframe["ligand_allosteric.expo_id"] = dataframe["ligand_allosteric.expo_id"].replace(0, "-")

2. Two instances of HTTPURITooLong errors when querying KLIFS.

In these two cases we are pulling all interactions and all conformations - part of that query is that we pull all structure IDs from KLIFS, to then build a URL with all of them to retrieve interactions and conformations. This URL is naturally too long (I guess they rightfully added a limit). I am now chunking over the list of structure IDs instead.

codecov-commenter · 2024-02-25T17:35:50Z

Codecov Report

Merging #157 (cb3a39f) into master (c76e87c) will increase coverage by 0.10%.
The diff coverage is 91.42%.

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

dominiquesydow · 2024-02-25T17:36:17Z

@AndreaVolkamer I did not touch any KLIFS-unrelated issues.

dominiquesydow · 2024-02-25T17:40:09Z

@AndreaVolkamer ok could not resist & applied black to the full package --- can someone look into Python 3.12, which seems to fail with conda.

pipaj97 added 3 commits June 25, 2023 13:32

use own function to find gap chars

9493f88

remove version for biopython

3472a94

rename test env to

7ca2b37

pipaj97 added the enhancement New feature or request label Jun 25, 2023

pipaj97 requested a review from AAriam June 25, 2023 12:10

pipaj97 added the module-structure-superposition Concerns opencadd.structure.superposition module label Jun 25, 2023

AAriam changed the base branch from dev to master January 30, 2024 09:17

AAriam closed this Jan 30, 2024

AAriam reopened this Jan 30, 2024

AAriam added 2 commits January 30, 2024 12:32

Update ci.yaml

ad552f4

Update ci.yaml

fb35568

AAriam reviewed Jan 30, 2024

View reviewed changes

AndreaVolkamer requested a review from dominiquesydow January 30, 2024 13:20

dominiquesydow added 2 commits February 25, 2024 17:27

future deprectation pandas: do not use inplace on copy

00260a1

fix: chunk list of IDs in request to avoid HTTPURITooLong

00a497a

chore: fix formatting with black

cb3a39f

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Biopython update #157

Biopython update #157

pipaj97 commented Jun 25, 2023 •

edited by AndreaVolkamer

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Biopython update #157

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Biopython update #157

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pipaj97 commented Jun 25, 2023 • edited by AndreaVolkamer Loading

Description

Todos

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pipaj97 commented Jun 25, 2023 •

edited by AndreaVolkamer

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