piedpiper
Context manager to debug method chains in Python.
It is in an alpha state, but will get much attention from me in the immediate future as I desperately need it. Watch this space :)
cat examples/pp.py
# from piedpiper import Debug
# with Debug():
# "abc".replace("a", "A").upper().lower().i_will_error().find("hi")
python examples/pp.py
# Start data:
# abc
#
# .replace("a", "A")
# Abc
#
# .upper()
# ABC
#
# .lower()
# abc
#
# .i_will_error()
# Traceback (most recent call last):
# File "examples/pp.py", line 2, in <module>
# with Debug():
# File "/home/endrebak/code/piedpiper/piedpiper/main.py", line 112, in __init__
# _run_commands(commands, frame.lineno, frame.filename, _locals)
# File "/home/endrebak/code/piedpiper/piedpiper/main.py", line 86, in _run_commands
# __dbg = eval(dirty)
# File "<string>", line 1, in <module>
# AttributeError: 'str' object has no attribute 'i_will_error'
I wrote it to make it easier to debug complex chains of commands in my PyRanges package, but it should work on all kinds of data.
Install
pip install piedpiper
TODO
- use the standard library to parse the code to be debugged
- support decomposing subcommands/subchains also
- colorization based on level of nesting
- add line numbers to each command
- IPython magic
Thanks
- Alassane Ndiaye (removing locals arg in constructor)
More complex example
Notice that .join(exons.unstrand()) is considered one call as piedpiper only looks at the top level chains.
cat examples/exons.py
# import pyranges as pr
# exons = pr.data.exons()
# cpg = pr.data.cpg()
#
# from piedpiper import Debug as D
# with D():
# cpg.join(exons.unstrand())[["CpG"]](lambda df: df.head(3))["chrX"].slack(500)
python examples/exons.py
# Start data:
# +--------------|-----------|-----------|-----------+
# | Chromosome | Start | End | CpG |
# | (category) | (int64) | (int64) | (int64) |
# |--------------|-----------|-----------|-----------|
# | chrX | 64181 | 64793 | 62 |
# | chrX | 69133 | 70029 | 100 |
# | chrX | 148685 | 149461 | 85 |
# | ... | ... | ... | ... |
# | chrY | 28773315 | 28773544 | 25 |
# | chrY | 59213794 | 59214183 | 36 |
# | chrY | 59349266 | 59349574 | 29 |
# +--------------|-----------|-----------|-----------+
# PyRanges object has 1077 sequences from 2 chromosomes.
#
# .join(exons)
#
# +--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------|--------------+
# | Chromosome | Start | End | CpG | Start_b | End_b | Name | Score | Strand |
# | (category) | (int64) | (int64) | (int64) | (int64) | (int64) | (object) | (int64) | (category) |
# |--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------|--------------|
# | chrX | 584563 | 585326 | 66 | 585078 | 585337 | NM_000451_exon_0_0_chrX_585079_f | 0 | + |
# | chrX | 10094050 | 10094406 | 26 | 10094153 | 10094346 | NM_015691_exon_14_0_chrX_10094154_f | 0 | + |
# | chrX | 13587648 | 13588221 | 49 | 13587693 | 13588054 | NM_001167890_exon_0_0_chrX_13587694_f | 0 | + |
# | ... | ... | ... | ... | ... | ... | ... | ... | ... |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NR_047607_exon_29_0_chrY_15591394_r | 0 | - |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NM_001258269_exon_29_0_chrY_15591394_r | 0 | - |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NR_047599_exon_28_0_chrY_15591394_r | 0 | - |
# +--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------|--------------+
# PyRanges object has 79 sequences from 2 chromosomes.
#
# .unstrand()
#
# +--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------+
# | Chromosome | Start | End | CpG | Start_b | End_b | Name | Score |
# | (category) | (int64) | (int64) | (int64) | (int64) | (int64) | (object) | (int64) |
# |--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------|
# | chrX | 584563 | 585326 | 66 | 585078 | 585337 | NM_000451_exon_0_0_chrX_585079_f | 0 |
# | chrX | 10094050 | 10094406 | 26 | 10094153 | 10094346 | NM_015691_exon_14_0_chrX_10094154_f | 0 |
# | chrX | 13587648 | 13588221 | 49 | 13587693 | 13588054 | NM_001167890_exon_0_0_chrX_13587694_f | 0 |
# | ... | ... | ... | ... | ... | ... | ... | ... |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NR_047607_exon_29_0_chrY_15591394_r | 0 |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NM_001258269_exon_29_0_chrY_15591394_r | 0 |
# | chrY | 15591259 | 15591720 | 33 | 15591393 | 15592550 | NR_047599_exon_28_0_chrY_15591394_r | 0 |
# +--------------|-----------|-----------|-----------|-----------|-----------|----------------------------------------|-----------+
# PyRanges object has 79 sequences from 2 chromosomes.
#
# [["CpG"]]
#
# +--------------|-----------|-----------|-----------+
# | Chromosome | Start | End | CpG |
# | (category) | (int64) | (int64) | (int64) |
# |--------------|-----------|-----------|-----------|
# | chrX | 584563 | 585326 | 66 |
# | chrX | 10094050 | 10094406 | 26 |
# | chrX | 13587648 | 13588221 | 49 |
# | ... | ... | ... | ... |
# | chrY | 15591259 | 15591720 | 33 |
# | chrY | 15591259 | 15591720 | 33 |
# | chrY | 15591259 | 15591720 | 33 |
# +--------------|-----------|-----------|-----------+
# PyRanges object has 79 sequences from 2 chromosomes.
#
# (lambda df: df.head(3))
#
# +--------------|-----------|-----------|-----------+
# | Chromosome | Start | End | CpG |
# | (category) | (int64) | (int64) | (int64) |
# |--------------|-----------|-----------|-----------|
# | chrX | 584563 | 585326 | 66 |
# | chrX | 10094050 | 10094406 | 26 |
# | chrX | 13587648 | 13588221 | 49 |
# | ... | ... | ... | ... |
# | chrY | 155322 | 155553 | 19 |
# | chrY | 1363206 | 1363503 | 23 |
# | chrY | 16941822 | 16942188 | 32 |
# +--------------|-----------|-----------|-----------+
# PyRanges object has 6 sequences from 2 chromosomes.
#
# ["chrX"]
#
# +--------------|-----------|-----------|-----------+
# | Chromosome | Start | End | CpG |
# | (category) | (int64) | (int64) | (int64) |
# |--------------|-----------|-----------|-----------|
# | chrX | 584563 | 585326 | 66 |
# | chrX | 10094050 | 10094406 | 26 |
# | chrX | 13587648 | 13588221 | 49 |
# +--------------|-----------|-----------|-----------+
# PyRanges object has 3 sequences from 1 chromosomes.
#
# .slack(500)
#
# +--------------|-----------|-----------|-----------+
# | Chromosome | Start | End | CpG |
# | (category) | (int64) | (int64) | (int64) |
# |--------------|-----------|-----------|-----------|
# | chrX | 584063 | 585826 | 66 |
# | chrX | 10093550 | 10094906 | 26 |
# | chrX | 13587148 | 13588721 | 49 |
# +--------------|-----------|-----------|-----------+
# PyRanges object has 3 sequences from 1 chromosomes.
#
# [examples/exons.py:6]
