fix buggy example in api docs

CAST-genomics · Jan 12, 2024 · d06d50a · d06d50a
1 parent 7963267
commit d06d50a
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/docs/api/examples.rst b/docs/api/examples.rst
@@ -28,13 +28,15 @@ As an example, let's say we would like to convert `the following .blocks.det fil
 
     # iterate through lines of the .blocks.det file
     with open("tests/data/simple.blocks.det") as blocks_file:
-        for idx, line in enumerate(blocks_file.readlines()):
+        for idx, line in enumerate(blocks_file.read().splitlines()[1:]):
             # initialize variables and parse line from the blocks file
             hap_id = f"H{idx}"
             chrom, bp1, bp2, kb, nsnps, snps = line.split("\t")
 
             # create a haplotype line in the .hap file
-            hp.data[hap_id] = data.Haplotype(chrom=chrom, start=bp1, end=bp2, id=hap_id)
+            hp.data[hap_id] = data.Haplotype(
+                chrom=chrom, start=int(bp1), end=int(bp2), id=hap_id
+            )
 
             # fetch alleles from the genotypes file
             snp_gts = gt.subset(variants=tuple(snps.split("|")))

diff --git a/tests/test_data.py b/tests/test_data.py
@@ -2073,13 +2073,15 @@ def test_blocks2hap(self):
 
         # iterate through lines of the .blocks.det file
         with open(DATADIR / "simple.blocks.det") as blocks_file:
-            for idx, line in enumerate(blocks_file.readlines()):
+            for idx, line in enumerate(blocks_file.read().splitlines()[1:]):
                 # initialize variables and parse line from the blocks file
                 hap_id = f"H{idx}"
                 chrom, bp1, bp2, kb, nsnps, snps = line.split("\t")
 
                 # create a haplotype line in the .hap file
-                hp.data[hap_id] = Haplotype(chrom=chrom, start=bp1, end=bp2, id=hap_id)
+                hp.data[hap_id] = Haplotype(
+                    chrom=chrom, start=int(bp1), end=int(bp2), id=hap_id
+                )
 
                 # fetch alleles from the genotypes file
                 snp_gts = gt.subset(variants=tuple(snps.split("|")))