From 6fd7ac08ad65ecbd902d9cfb96d2623b6be5a115 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 2 Oct 2024 13:06:49 -0400
Subject: [PATCH] refact(call): more partial/itemgetter usage

---
 strkit/call/call_locus.py |  5 +++--
 strkit/call/output/vcf.py | 17 +++++++++++------
 strkit/call/utils.py      |  3 +++
 3 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/strkit/call/call_locus.py b/strkit/call/call_locus.py
index 8e53a50..49ce9f1 100644
--- a/strkit/call/call_locus.py
+++ b/strkit/call/call_locus.py
@@ -44,7 +44,9 @@
 from .types import (
     VCFContigFormat, AssignMethod, AssignMethodWithHP, ConsensusMethod, ReadDict, ReadDictExtra, CalledSNV, LocusResult
 )
-from .utils import idx_0_getter, find_pair_by_ref_pos, normalize_contig, get_new_seed, calculate_seq_with_wildcards
+from .utils import (
+    idx_0_getter, cn_getter, find_pair_by_ref_pos, normalize_contig, get_new_seed, calculate_seq_with_wildcards
+)
 
 
 __all__ = [
@@ -85,7 +87,6 @@
 
 
 # property getters & other partials
-cn_getter = operator.itemgetter("cn")
 weight_getter = operator.itemgetter("w")
 not_snv_out_of_range_char = functools.partial(operator.ne, SNV_OUT_OF_RANGE_CHAR)
 eq_0 = functools.partial(operator.eq, 0)
diff --git a/strkit/call/output/vcf.py b/strkit/call/output/vcf.py
index abaad71..47f6ad4 100644
--- a/strkit/call/output/vcf.py
+++ b/strkit/call/output/vcf.py
@@ -5,12 +5,12 @@
 # from os.path import commonprefix
 from pathlib import Path
 from pysam import FastaFile, VariantFile, VariantHeader, VariantRecord
-from typing import Optional
+from typing import Iterable, Optional
 
 from strkit.utils import cat_strs, is_none
 from ..allele import get_n_alleles
 from ..params import CallParams
-from ..utils import idx_0_getter
+from ..utils import idx_0_getter, cn_getter
 
 __all__ = [
     "build_vcf_header",
@@ -39,6 +39,11 @@
 VT_SNV = "snv"
 
 
+def iter_to_upper(x: Iterable[str]) -> Iterable[str]:
+    # noinspection PyTypeChecker
+    return map(str.upper, x)
+
+
 def build_vcf_header(sample_id: str, reference_file: str) -> VariantHeader:
     vh = VariantHeader()  # automatically sets VCF version to 4.2
 
@@ -134,8 +139,8 @@ def output_contig_vcf_lines(
             logger.error(f"Encountered None in results[{result_idx}].peaks.start_anchor_seqs: {peak_start_anchor_seqs}")
             continue
 
-        seqs: tuple[str, ...] = tuple(map(str.upper, peak_seqs))
-        seqs_with_anchors = tuple(zip(seqs, tuple(map(str.upper, peak_start_anchor_seqs))))
+        seqs: tuple[str, ...] = tuple(iter_to_upper(peak_seqs))
+        seqs_with_anchors = tuple(zip(seqs, tuple(iter_to_upper(peak_start_anchor_seqs))))
 
         if 0 < len(seqs) < n_alleles:
             seqs = tuple([seqs[0]] * n_alleles)
@@ -143,7 +148,7 @@ def output_contig_vcf_lines(
 
         seq_alts = sorted(
             set(filter(lambda c: not (c[0] == ref_seq and c[1] == ref_start_anchor), seqs_with_anchors)),
-            key=lambda x: x[0]
+            key=idx_0_getter
         )
 
         # common_suffix_idx = -1 * len(commonprefix(tuple(map(_reversed_str, (ref_seq, *seqs)))))
@@ -204,7 +209,7 @@ def output_contig_vcf_lines(
                         lambda pair: ":".join(map(str, pair)),
                         sorted(
                             Counter(
-                                map(lambda r: r["cn"], filter(lambda r: r.get("p") == pi, res_reads.values()))
+                                map(cn_getter, filter(lambda r: r.get("p") == pi, res_reads.values()))
                             ).items()
                         )
                     )
diff --git a/strkit/call/utils.py b/strkit/call/utils.py
index 300cc93..c21ccf5 100644
--- a/strkit/call/utils.py
+++ b/strkit/call/utils.py
@@ -10,6 +10,7 @@
 __all__ = [
     "idx_0_getter",
     "idx_1_getter",
+    "cn_getter",
     "neq_blank",
     "find_pair_by_ref_pos",
     "normalize_contig",
@@ -19,8 +20,10 @@
 ]
 
 
+# index/property getters and other partials
 idx_0_getter = operator.itemgetter(0)
 idx_1_getter = operator.itemgetter(1)
+cn_getter = operator.itemgetter("cn")
 neq_blank = partial(operator.ne, "")