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This project forked from iqbal-lab-org/make_prg

2.0 2.0 2.0 9.45 MB

Code to create a PRG from a Multiple Sequence Alignment file

License: Other

Python 97.42% Shell 1.98% Dockerfile 0.60%

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kdm9 jorgeavilacartes

make_prg's Issues

Make the outputs usable by `gramtools`

Build a concatenated prg

I've been building 'genome-wide' prgs for gramtools by building one prg per msa/locus, and then adding in the linear reference genome seq in between.

I'd like an option for make_prg to do that. I can attempt implementing it myself.

The minimal info to do this is:
--ref: a ref genome
--fofn: a file of file names (or a bed file?), with the information: file name, chrom, start, end

@leoisl is the --input option a directory name currently? can a fofn be passed to make_prg?

Remove the requirement of having `MAFFT` in `PATH`

Add thorough unit tests

Required to leave from prototype state

Provide prebuilt PRGs for common databases/species

Like PanX and other DBs. pandora should auto download these PRGs

Send logging to stderr

It's kind of annoying having logging go to a mixture of stderr and stdout...

Maybe look at using https://github.com/Delgan/loguru if you want "thread-safe" logging?

Minimum python supported is 3.7

The docs state that to install locally, you need python>=3. However, as you rely on numpy==1.20.0

make_prg/setup.py

Line 14 in 8641454

"numpy==1.20.0",

the minimum supported version by that numpy version is 3.7

multiprocessing

Dear development team,

I got this error from make_prg update after the updated alignments were available:

2021-11-24 12:49:25.877 | INFO     | make_prg.subcommands.update:update:131 - Write PRG file to /net/metagenomics/data/from_moni/old.tzuhao/test_pandora/results/subset_test/by_pipeline/pangenome_updated/pangenome_updated_tmp/GC00000862_2_na_aln/GC00000862_2_na_aln.prg.fa
2021-11-24 12:49:28.138 | INFO     | make_prg.subcommands.update:update:131 - Write PRG file to /net/metagenomics/data/from_moni/old.tzuhao/test_pandora/results/subset_test/by_pipeline/pangenome_updated/pangenome_updated_tmp/GC00002479_na_aln/GC00002479_na_aln.prg.fa
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "multiprocessing/pool.py", line 119, in worker
  File "multiprocessing/pool.py", line 47, in starmapstar
  File "make_prg/subcommands/update.py", line 119, in update
  File "make_prg/prg_builder.py", line 385, in batch_update
  File "make_prg/prg_builder.py", line 418, in _update_leaf
  File "make_prg/io_utils.py", line 21, in load_alignment_file
  File "Bio/AlignIO/__init__.py", line 392, in read
ValueError: No records found in handle
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "make_prg/__main__.py", line 49, in <module>
  File "make_prg/__main__.py", line 43, in main
  File "make_prg/subcommands/update.py", line 186, in run
  File "multiprocessing/pool.py", line 274, in starmap
  File "multiprocessing/pool.py", line 644, in get
ValueError: No records found in handle
[41767] Failed to execute script __main__

My command was

/net/metagenomics/data/from_moni/old.tzuhao/test_pandora/test_make_prg/bin/make_prg update --threads 3 \
  --update_DS /net/metagenomics/data/from_moni/old.tzuhao/test_pandora/test_make_prg/results/pangenome.update_DS   \
  --denovo_paths /net/metagenomics/data/from_moni/old.tzuhao/test_pandora/results/subset_test/by_pipeline/all_denovo_paths.txt  \ 
  --output_prefix /net/metagenomics/data/from_moni/old.tzuhao/test_pandora/results/subset_test/by_pipeline/pangenome_updated/pangenome_updated

, executed using Snakemake.

Could it be some issue with the multithreading script? Otherwise, what may I need to check first? Is it likely to rerun with those updated alignments? Thank you for considering my question.

Try to build precompiled binary with musl libc

To remove GLIBC requirement

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