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load_lrs does not deduplicate LR pairs when species="mouse" #357

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load_lrs does not deduplicate LR pairs when species="mouse"#357

Description

@newmana
newmana
opened on Jul 12, 2026

The existing code would deduplicate LR pairs for humans but not mice.

For humans:

lrs_full_arr = np.unique(np.array(lrs_full))

For mice it reused lrs_full, not lrs_full_arr:

 genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.

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var __re = new RegExp('^' + "github\\.com" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
      Skip to content
      load_lrs does not deduplicate LR pairs when species="mouse" #357
      Closed
      Closed
      load_lrs does not deduplicate LR pairs when species="mouse"#357
      Description
      @newmana
      newmana
      opened on Jul 12, 2026
      The existing code would deduplicate LR pairs for humans but not mice.
      For humans:
      lrs_full_arr = np.unique(np.array(lrs_full))

      For mice it reused lrs_full, not lrs_full_arr:
       genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

      Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
          Skip to content
          load_lrs does not deduplicate LR pairs when species="mouse" #357
          Closed
          Closed
          load_lrs does not deduplicate LR pairs when species="mouse"#357
          Description
          @newmana
          newmana
          opened on Jul 12, 2026
          The existing code would deduplicate LR pairs for humans but not mice.
          For humans:
          lrs_full_arr = np.unique(np.array(lrs_full))

          For mice it reused lrs_full, not lrs_full_arr:
           genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

          Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
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, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
              Skip to content
              load_lrs does not deduplicate LR pairs when species="mouse" #357
              Closed
              Closed
              load_lrs does not deduplicate LR pairs when species="mouse"#357
              Description
              @newmana
              newmana
              opened on Jul 12, 2026
              The existing code would deduplicate LR pairs for humans but not mice.
              For humans:
              lrs_full_arr = np.unique(np.array(lrs_full))

              For mice it reused lrs_full, not lrs_full_arr:
               genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

              Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
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, 'i');
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
                  Skip to content
                  load_lrs does not deduplicate LR pairs when species="mouse" #357
                  Closed
                  Closed
                  load_lrs does not deduplicate LR pairs when species="mouse"#357
                  Description
                  @newmana
                  newmana
                  opened on Jul 12, 2026
                  The existing code would deduplicate LR pairs for humans but not mice.
                  For humans:
                  lrs_full_arr = np.unique(np.array(lrs_full))

                  For mice it reused lrs_full, not lrs_full_arr:
                   genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

                  Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
                  Metadata
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, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
                      Skip to content
                      load_lrs does not deduplicate LR pairs when species="mouse" #357
                      Closed
                      Closed
                      load_lrs does not deduplicate LR pairs when species="mouse"#357
                      Description
                      @newmana
                      newmana
                      opened on Jul 12, 2026
                      The existing code would deduplicate LR pairs for humans but not mice.
                      For humans:
                      lrs_full_arr = np.unique(np.array(lrs_full))

                      For mice it reused lrs_full, not lrs_full_arr:
                       genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

                      Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
                      Metadata
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
                          Skip to content
                          load_lrs does not deduplicate LR pairs when species="mouse" #357
                          Closed
                          Closed
                          load_lrs does not deduplicate LR pairs when species="mouse"#357
                          Description
                          @newmana
                          newmana
                          opened on Jul 12, 2026
                          The existing code would deduplicate LR pairs for humans but not mice.
                          For humans:
                          lrs_full_arr = np.unique(np.array(lrs_full))

                          For mice it reused lrs_full, not lrs_full_arr:
                           genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

                          Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
                          Metadata
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})();
load_lrs does not deduplicate LR pairs when species="mouse" · Issue #357 · BiomedicalMachineLearning/stLearn · GitHub
                              Skip to content
                              load_lrs does not deduplicate LR pairs when species="mouse" #357
                              Closed
                              Closed
                              load_lrs does not deduplicate LR pairs when species="mouse"#357
                              Description
                              @newmana
                              newmana
                              opened on Jul 12, 2026
                              The existing code would deduplicate LR pairs for humans but not mice.
                              For humans:
                              lrs_full_arr = np.unique(np.array(lrs_full))

                              For mice it reused lrs_full, not lrs_full_arr:
                               genes1 = [lr_.split("_")[0] for lr_ in lrs_full] genes2 = [lr_.split("_")[1] for lr_ in lrs_full]
lrs_full_arr = np.array(
[
genes1[i][0]
+ genes1[i][1:].lower()
+ "_"
+ genes2[i][0]
+ genes2[i][1:].lower()
for i in range(len(lrs_full))
],
)

                              Change - lrs is now a set and mouse output for the multi-database calls goes from 6364 entries (2293 duplicated) to 4071 unique, sorted. Existing mouse results won't reproduce exactly.
                              Metadata
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                              Assignees
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