multiple output of cli pyscenic ctx

[ccshao]

From the cli, the pyscenic ctx could only take one argument of -o, so one has to run twice to get the enriched motif and regulon, while each run is very time consuming. Could it be possible to output enriched motif and regulon simultaneously？Thanks!

[bramvds]

Dear,

Good suggestion. A workaround, for now, could be to convert the motif file into regulons via a Python code snippet:

import pickle
from pyscenic.utils import load_motifs
from pyscenic.prune import df2regulons

MOTIFS_FNAME = "" # To be completed.
REGULONS_FNAME = ""# To be completed.

df = load_motifs(MOTIFS_FNAME)
regulons = df2regulons(df)
with open(REGULONS_FNAME, 'wb') as f:
    pickle.dump(regulons, f)

Kindest regards, Bram

[ccshao]

Thanks the quick help. I just found another minor issue: the output argument with gmt/dat(pickle?) don't work. As above I used the latest version (0.9.18)

gmt output:

pyscenic ctx -o test2.gmt --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb

(base) 01_cli $ pyscenic ctx -o test2.gmt --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb /home/shao/miniconda3/lib/python3.7/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. data = yaml.load(f.read()) or {}

2019-10-09 09:18:13,909 - pyscenic.cli.pyscenic - INFO - Creating modules.

2019-10-09 09:18:13,921 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2019-10-09 09:18:19,910 - pyscenic.utils - INFO - Calculating Pearson correlations.

2019-10-09 09:18:19,910 - pyscenic.utils - WARNING ... Dropout masking is currently set to [False].

2019-10-09 09:18:21,623 - pyscenic.utils - INFO - Creating modules.

2019-10-09 09:18:43,545 - pyscenic.cli.pyscenic - INFO - Loading databases. .... 2019-10-09 09:20:28,286 - pyscenic.cli.pyscenic - INFO - Writing results to file. Traceback (most recent call last): File "/home/shao/miniconda3/bin/pyscenic", line 10, in sys.exit(main()) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 408, in main args.func(args) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 165, in prune_targets_command save_enriched_motifs(df_motifs, args.output.name) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/utils.py", line 177, in save_enriched_motifs GeneSignature.to_gmt(fname, regulons) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/genesig.py", line 94, in to_gmt signature.metadata(gene_separator), field_separator, TypeError: 'str' object is not callable

Similar errorr for dat output with command:

pyscenic ctx -o test2.dat --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb

2019-10-09 09:28:02,682 - pyscenic.cli.pyscenic - INFO - Writing results to file. Traceback (most recent call last): File "/home/shao/miniconda3/bin/pyscenic", line 10, in sys.exit(main()) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 408, in main args.func(args) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 165, in prune_targets_command save_enriched_motifs(df_motifs, args.output.name) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/utils.py", line 175, in save_enriched_motifs pickle.dump(regulons, fname) TypeError: file must have a 'write' attribute

I tried pickl:

(base) 01_cli $ pyscenic ctx -o test2.pickle --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb

provides error:

Traceback (most recent call last): File "/home/shao/miniconda3/bin/pyscenic", line 10, in sys.exit(main()) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 408, in main args.func(args) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 165, in prune_targets_command save_enriched_motifs(df_motifs, args.output.name) File "/home/shao/miniconda3/lib/python3.7/site-packages/pyscenic/cli/utils.py", line 181, in save_enriched_motifs raise ValueError("Unknown file format "{}".".format(fname)) ValueError: Unknown file format "test2.pickle".

YAML and json work fine,

pyscenic ctx -o regulons.json --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb
pyscenic ctx -o regulons2.yaml --annotations_fname $motifanno --expression_mtx_fname $inmtx -t grnresults_lite.csv $regdb

[bramvds]

These bugs should be fixed in release 0.9.19.

[ccshao]

Good to know these.