docs: handle whitespace in blocks2hap example (#237)

docs/api/examples.rst

@@ -6,9 +6,9 @@ examples
 
 Converting a ``.blocks.det`` file into a ``.hap`` file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-You can use the :ref:`data API <api-data>` to easily convert `a PLINK 1.9 .blocks.det file <https://www.cog-genomics.org/plink/1.9/formats#blocks>`_ into a ``.hap`` file.
+You can use the :ref:`data API <api-data>` to convert `a PLINK 1.9 .blocks.det file <https://www.cog-genomics.org/plink/1.9/formats#blocks>`_ into a ``.hap`` file.
 
-As an example, let's say we would like to convert `the following .blocks.det file <https://github.com/cast-genomics/haptools/blob/main/tests/data/simple.blocks.det>`_.
+As an example, let's say we would like to convert `the following simple.blocks.det file <https://github.com/cast-genomics/haptools/blob/main/tests/data/simple.blocks.det>`_.
 
 .. include:: ../../tests/data/simple.blocks.det
   :literal:
@@ -31,7 +31,7 @@ As an example, let's say we would like to convert `the following .blocks.det fil
         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")
+            chrom, bp1, bp2, kb, nsnps, snps = line.strip().split()
 
             # create a haplotype line in the .hap file
             hp.data[hap_id] = data.Haplotype(
@@ -72,7 +72,7 @@ Then your ``.hap`` file might look something like this.
 .. include:: ../../tests/data/apoe.hap
   :literal:
 
-You can easily use the :ref:`data API <api-data>` and the :ref:`simphenotype API <api-haptools-sim_phenotype>` to create such a file.
+You can use the :ref:`data API <api-data>` and the :ref:`simphenotype API <api-haptools-sim_phenotype>` to create such a file.
 
 .. code-block:: python
 

docs/commands/transform.rst

@@ -6,7 +6,7 @@ transform
 
 Transform a set of genotypes via a list of haplotypes. Create a new VCF containing haplotypes instead of variants.
 
-The ``transform`` command takes as input a set of genotypes and a list of haplotypes and outputs a set of haplotype *pseudo-genotypes*, where each haplotype is encoded as a bi-allelic variant record in the output. In other words, each sample will have a genotype of ``0|0``, ``1|0``, ``0|1``, or ``1|1`` indicating whether each of their two chromosome copies contains the alleles of a haplotype.
+The ``transform`` command takes as input a set of **phased** genotypes and a list of haplotypes and outputs a set of haplotype *pseudo-genotypes*, where each haplotype is encoded as a bi-allelic variant record in the output. In other words, each sample will have a genotype of ``0|0``, ``1|0``, ``0|1``, or ``1|1`` indicating whether each of their two chromosome copies contains the alleles of a haplotype.
 
 .. figure:: https://drive.google.com/uc?id=1GyluoQ3IeGXo9FjWsCC3XwaRuflr68pn
   :figwidth: 600

tests/data/simple.blocks.det

@@ -1,4 +1,4 @@
-CHR	BP1	BP2	KB	NSNPS	SNPS
-1	10114	10117	2.001	2	1:10114:T:C|1:10116:A:G
-1	10114	10119	2.007	2	1:10114:T:C|1:10117:C:A
-1	10116	10119	2.011	2	1:10116:A:G|1:10117:C:A
+CHR  BP1	 BP2	 KB   NSNPS  SNPS
+ 1	10114	10117	2.001	2	1:10114:T:C|1:10116:A:G
+ 1	10114	10119	2.007	2	1:10114:T:C|1:10117:C:A
+ 1	10116	10119	2.011	2	1:10116:A:G|1:10117:C:A

tests/test_data.py

@@ -2129,7 +2129,7 @@ def test_blocks2hap(self):
             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")
+                chrom, bp1, bp2, kb, nsnps, snps = line.strip().split()
 
                 # create a haplotype line in the .hap file
                 hp.data[hap_id] = Haplotype(