5 Manipulating the data in PyRanges
PyRanges is a thin wrapper around genomic data contained in pandas dataframes. This dataframe is accessible with the df attribute of the PyRanges object.
import pyranges as pr
gr = pr.data.chipseq()
print(gr)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 212609534 | 212609559 | U0 | 0 | + |
## | chr1 | 169887529 | 169887554 | U0 | 0 | + |
## | chr1 | 216711011 | 216711036 | U0 | 0 | + |
## | chr1 | 144227079 | 144227104 | U0 | 0 | + |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | U0 | 0 | - |
## | chrY | 13517892 | 13517917 | U0 | 0 | - |
## | chrY | 8010951 | 8010976 | U0 | 0 | - |
## | chrY | 7405376 | 7405401 | U0 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.print(gr.df.head(5))## Chromosome Start End Name Score Strand
## 0 chr1 212609534 212609559 U0 0 +
## 1 chr1 169887529 169887554 U0 0 +
## 2 chr1 216711011 216711036 U0 0 +
## 3 chr1 144227079 144227104 U0 0 +
## 4 chr1 148177825 148177850 U0 0 +To access a column of this dataframe, you can ask for the name directly from the PyRanges object.
print(gr.Start.head())## 18 212609534
## 70 169887529
## 129 216711011
## 170 144227079
## 196 148177825
## Name: Start, dtype: int32You can directly insert a column by setting the attribute on the PyRanges object:
gr.stupid_example = "Hi There!"
print(gr)## +--------------+-----------+-----------+------------+-----------+-------+
## | Chromosome | Start | End | Name | Score | +2 |
## | (category) | (int32) | (int32) | (object) | (int64) | ... |
## |--------------+-----------+-----------+------------+-----------+-------|
## | chr1 | 212609534 | 212609559 | U0 | 0 | ... |
## | chr1 | 169887529 | 169887554 | U0 | 0 | ... |
## | chr1 | 216711011 | 216711036 | U0 | 0 | ... |
## | chr1 | 144227079 | 144227104 | U0 | 0 | ... |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | U0 | 0 | ... |
## | chrY | 13517892 | 13517917 | U0 | 0 | ... |
## | chrY | 8010951 | 8010976 | U0 | 0 | ... |
## | chrY | 7405376 | 7405401 | U0 | 0 | ... |
## +--------------+-----------+-----------+------------+-----------+-------+
## Stranded PyRanges object has 10,000 rows and 7 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 2 hidden columns: Strand, stupid_examplegr = gr.drop("stupid_example")
print(gr)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 212609534 | 212609559 | U0 | 0 | + |
## | chr1 | 169887529 | 169887554 | U0 | 0 | + |
## | chr1 | 216711011 | 216711036 | U0 | 0 | + |
## | chr1 | 144227079 | 144227104 | U0 | 0 | + |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | U0 | 0 | - |
## | chrY | 13517892 | 13517917 | U0 | 0 | - |
## | chrY | 8010951 | 8010976 | U0 | 0 | - |
## | chrY | 7405376 | 7405401 | U0 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.And as you can see, you can drop columns from the PyRanges using drop. Using drop by itself removes all metadata-columns.
To insert a dataframe into a PyRanges object, you can use insert. Insert supports an optional insertion index loc:
df = pd.DataFrame({"A1": [1, 2] * 5000, "A2": [3, 4, 5, 6] * 2500})
print(df.head())## A1 A2
## 0 1 3
## 1 2 4
## 2 1 5
## 3 2 6
## 4 1 3print(gr.insert(df))## +--------------+-----------+-----------+------------+-----------+-------+
## | Chromosome | Start | End | Name | Score | +3 |
## | (category) | (int32) | (int32) | (object) | (int64) | ... |
## |--------------+-----------+-----------+------------+-----------+-------|
## | chr1 | 212609534 | 212609559 | U0 | 0 | ... |
## | chr1 | 169887529 | 169887554 | U0 | 0 | ... |
## | chr1 | 216711011 | 216711036 | U0 | 0 | ... |
## | chr1 | 144227079 | 144227104 | U0 | 0 | ... |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | U0 | 0 | ... |
## | chrY | 13517892 | 13517917 | U0 | 0 | ... |
## | chrY | 8010951 | 8010976 | U0 | 0 | ... |
## | chrY | 7405376 | 7405401 | U0 | 0 | ... |
## +--------------+-----------+-----------+------------+-----------+-------+
## Stranded PyRanges object has 10,000 rows and 8 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Strand, A1, A2print(gr.insert(df, loc=3))## +--------------+-----------+-----------+-----------+-----------+-------+
## | Chromosome | Start | End | A1 | A2 | +3 |
## | (category) | (int32) | (int32) | (int64) | (int64) | ... |
## |--------------+-----------+-----------+-----------+-----------+-------|
## | chr1 | 212609534 | 212609559 | 1 | 3 | ... |
## | chr1 | 169887529 | 169887554 | 2 | 4 | ... |
## | chr1 | 216711011 | 216711036 | 1 | 5 | ... |
## | chr1 | 144227079 | 144227104 | 2 | 6 | ... |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | 1 | 3 | ... |
## | chrY | 13517892 | 13517917 | 2 | 4 | ... |
## | chrY | 8010951 | 8010976 | 1 | 5 | ... |
## | chrY | 7405376 | 7405401 | 2 | 6 | ... |
## +--------------+-----------+-----------+-----------+-----------+-------+
## Stranded PyRanges object has 10,000 rows and 8 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 3 hidden columns: Name, Score, StrandTo rename the columns you can use the set_columns() method.
If you want to remove duplicates based on position, you can use drop_duplicate_positions:
print(gr.drop_duplicate_positions(strand=False)) # defaults to True## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 212609534 | 212609559 | U0 | 0 | + |
## | chr1 | 169887529 | 169887554 | U0 | 0 | + |
## | chr1 | 216711011 | 216711036 | U0 | 0 | + |
## | chr1 | 144227079 | 144227104 | U0 | 0 | + |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | U0 | 0 | - |
## | chrY | 13517892 | 13517917 | U0 | 0 | - |
## | chrY | 8010951 | 8010976 | U0 | 0 | - |
## | chrY | 7405376 | 7405401 | U0 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 9,924 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.All columns, including Chromosome, Start, End and Strand can be changed in any way you please and more metadata-columns can be added by setting it on the PyRanges object.
import pandas as pd
gr.Name = gr.Chromosome.astype(str) + "_" + pd.Series(range(len(gr)), index=gr.Chromosome.index).astype(str)
print(gr)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 212609534 | 212609559 | chr1_0 | 0 | + |
## | chr1 | 169887529 | 169887554 | chr1_1 | 0 | + |
## | chr1 | 216711011 | 216711036 | chr1_2 | 0 | + |
## | chr1 | 144227079 | 144227104 | chr1_3 | 0 | + |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | chrY_9996 | 0 | - |
## | chrY | 13517892 | 13517917 | chrY_9997 | 0 | - |
## | chrY | 8010951 | 8010976 | chrY_9998 | 0 | - |
## | chrY | 7405376 | 7405401 | chrY_9999 | 0 | - |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.gr.Strand = "."
print(gr)## +--------------+-----------+-----------+------------+-----------+--------------+
## | Chromosome | Start | End | Name | Score | Strand |
## | (category) | (int32) | (int32) | (object) | (int64) | (category) |
## |--------------+-----------+-----------+------------+-----------+--------------|
## | chr1 | 212609534 | 212609559 | chr1_0 | 0 | . |
## | chr1 | 169887529 | 169887554 | chr1_1 | 0 | . |
## | chr1 | 216711011 | 216711036 | chr1_2 | 0 | . |
## | chr1 | 144227079 | 144227104 | chr1_3 | 0 | . |
## | ... | ... | ... | ... | ... | ... |
## | chrY | 15224235 | 15224260 | chrY_9996 | 0 | . |
## | chrY | 13517892 | 13517917 | chrY_9997 | 0 | . |
## | chrY | 8010951 | 8010976 | chrY_9998 | 0 | . |
## | chrY | 7405376 | 7405401 | chrY_9999 | 0 | . |
## +--------------+-----------+-----------+------------+-----------+--------------+
## Unstranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome.
## Considered unstranded due to these Strand values: '.'