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Fixed cell table output cut off
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@victorskl
victorskl committed Oct 7, 2022
1 parent 3ea2e3f commit 0349d23
Showing 1 changed file with 25 additions and 25 deletions.
50 changes: 25 additions & 25 deletions 07_querying_lakehouse.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -386,30 +386,30 @@
"name": "stdout",
"output_type": "stream",
"text": [
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----------+-----+------------------+-----+----------------------------+\n",
"| SequenceRunName|SubjectID|Gender|Phenotype|StudyID| DiseaseCode| SNOMED|SampleID|GT_SampleID|CHROM| REF| ALT|array_size(alternateAlleles)|\n",
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----------+-----+------------------+-----+----------------------------+\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| AT| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| A| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| T| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| T| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| C| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| T| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| T| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| T| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| A| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9| G|[GAA]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| NA12878| chr9|AATGTGGGGCATACACAT| [A]| 1|\n",
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----------+-----+------------------+-----+----------------------------+\n",
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
"| SequenceRunName|SubjectID|Gender|Phenotype|StudyID| DiseaseCode| SNOMED|SampleID|CHROM| REF| ALT|array_size(alternateAlleles)|\n",
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| AT| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [C]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G|[GAA]| 1|\n",
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9|AATGTGGGGCATACACAT| [A]| 1|\n",
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
"only showing top 20 rows\n",
"\n"
]
Expand All @@ -418,7 +418,7 @@
"source": [
"spark.sql(\"select \\\n",
" m.SequenceRunName, m.SubjectID, m.Gender, m.Phenotype, m.StudyID, m.DiseaseCode, m.SNOMED, m.SampleID, \\\n",
" s.genotypes_sampleId as GT_SampleID, s.contigName as CHROM, s.referenceAllele as REF, s.alternateAlleles as ALT, array_size(s.alternateAlleles) \\\n",
" s.contigName as CHROM, s.referenceAllele as REF, s.alternateAlleles as ALT, array_size(s.alternateAlleles) \\\n",
"from metadata_table as m \\\n",
"join somatic_table as s on s.genotypes_sampleId = m.SampleID\").show()"
]
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