8000 `to_bed` reorders bed columns · Issue #274 · pyranges/pyranges · GitHub
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to_bed reorders bed columns #274

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fairliereese opened this issue Jul 20, 2022 · 1 comment
Open

to_bed reorders bed columns #274

fairliereese opened this issue Jul 20, 2022 · 1 comment

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@fairliereese
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I'm having trouble with PyRanges reordering columns in my bed file when I try to write it. Here's a minimal example:

import pandas as pd
import pyranges as pr

chrs = [1,1,1]
starts = [1,1,1]
ends = [2,3,4]
st = ['+', '+', '+']
other1 = [1,1,1]
other2 = [2,2,2]

df = pd.DataFrame()
df['Chromosome'] = chrs
df['Start'] = starts
df['End'] = ends
df['Strand'] = st
df['other1'] = other1
df['other2'] = other2

df = pr.PyRanges(df)
df.head()
df.to_bed('test_example.bed')

Output from df.head():

Screen Shot 2022-07-20 at 4 34 49 PM

Heading test_example.bed:
Screen Shot 2022-07-20 at 4 35 23 PM

As you can see, the columns have been swapped. Any idea if this behavior can be rectified?
@fairliereese fairliereese changed the title to_bed reorders non-canonical columns to_bed reorders non-canonical bed columns Jul 20, 2022
@fairliereese
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Update: This also fails when you add canonical bed columns:

import pandas as pd
import pyranges as pr

chrs = [1,1,1]
starts = [1,1,1]
ends = [2,3,4]
st = ['+', '+', '+']
other1 = [1,1,1]
other2 = [2,2,2]

df = pd.DataFrame()
df['Chromosome'] = chrs
df['Start'] = starts
df['End'] = ends
df['Strand'] = st
df['ThickStart'] = other1
df['ThickEnd'] = other2

df = pr.PyRanges(df)
df.to_bed('test_example.bed')

Screen Shot 2022-07-21 at 8 59 57 AM

vs.

Screen Shot 2022-07-21 at 9 00 15 AM

@fairliereese fairliereese changed the title to_bed reorders non-canonical bed columns to_bed reorders bed columns Jul 21, 2022
@fairliereese fairliereese mentioned this issue Jul 21, 2022
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