Skip to content

Commit 5825ab5

Browse files
victorsklvictorskl
committed
Fixed cell output table size
1 parent 0349d23 commit 5825ab5

File tree

1 file changed

+26
-26
lines changed

1 file changed

+26
-26
lines changed

‎07_querying_lakehouse.ipynb‎

Lines changed: 26 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@
2727
},
2828
{
2929
"cell_type": "code",
30-
"execution_count": null,
30+
"execution_count": 3,
3131
"metadata": {},
3232
"outputs": [],
3333
"source": [
@@ -386,30 +386,30 @@
386386
"name": "stdout",
387387
"output_type": "stream",
388388
"text": [
389-
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
390-
"| SequenceRunName|SubjectID|Gender|Phenotype|StudyID| DiseaseCode| SNOMED|SampleID|CHROM| REF| ALT|array_size(alternateAlleles)|\n",
391-
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
392-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| AT| [A]| 1|\n",
393-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
394-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
395-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
396-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
397-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
398-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
399-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
400-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [G]| 1|\n",
401-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
402-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
403-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
404-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [A]| 1|\n",
405-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
406-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [C]| 1|\n",
407-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
408-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
409-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
410-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G|[GAA]| 1|\n",
411-
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9|AATGTGGGGCATACACAT| [A]| 1|\n",
412-
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+----------------------------+\n",
389+
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+-------+\n",
390+
"| SequenceRunName|SubjectID|Gender|Phenotype|StudyID| DiseaseCode| SNOMED|SampleID|CHROM| REF| ALT|ALT_cnt|\n",
391+
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+-------+\n",
392+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| AT| [A]| 1|\n",
393+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
394+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
395+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
396+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
397+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
398+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
399+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
400+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [G]| 1|\n",
401+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
402+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [G]| 1|\n",
403+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [C]| 1|\n",
404+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| T| [A]| 1|\n",
405+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
406+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [C]| 1|\n",
407+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| C| [T]| 1|\n",
408+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| A| [G]| 1|\n",
409+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G| [A]| 1|\n",
410+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9| G|[GAA]| 1|\n",
411+
"|221007_A00130_000...| SBJ00001|Female| normal|NA12878|MONDO:0007254|429740004| NA12878| chr9|AATGTGGGGCATACACAT| [A]| 1|\n",
412+
"+--------------------+---------+------+---------+-------+-------------+---------+--------+-----+------------------+-----+-------+\n",
413413
"only showing top 20 rows\n",
414414
"\n"
415415
]
@@ -418,7 +418,7 @@
418418
"source": [
419419
"spark.sql(\"select \\\n",
420420
" m.SequenceRunName, m.SubjectID, m.Gender, m.Phenotype, m.StudyID, m.DiseaseCode, m.SNOMED, m.SampleID, \\\n",
421-
" s.contigName as CHROM, s.referenceAllele as REF, s.alternateAlleles as ALT, array_size(s.alternateAlleles) \\\n",
421+
" s.contigName as CHROM, s.referenceAllele as REF, s.alternateAlleles as ALT, array_size(s.alternateAlleles) as ALT_cnt \\\n",
422422
"from metadata_table as m \\\n",
423423
"join somatic_table as s on s.genotypes_sampleId = m.SampleID\").show()"
424424
]

0 commit comments

Comments
 (0)