comprna
Command is not defined
Hi ! I continue having this same message :
python /Dataset/AS_MDA/MoSEA-master/mosea.py scan --pfm --fasta test1.fa --out_dir /Dataset/AS_MDA/fmo_outdir --pfm_path /Dataset/AS_MDA/MoSEA/test_files/motifs/pfms Error in parsing: name 'commands' is not defined usage: mosea.py [-h] {getfasta,scan,enrich,overlap} ... Runs motif scan & enrichment positional arguments: {getfasta,scan,enrich,overlap} commands help getfasta Extract Fasta sequences from input bedfile and genome.fa scan Perform motif scanning on fasta sequences enrich Perform enrichment analysis between regulated and control (background) set overlap Compares motif lists. optional arguments: -h, --help show this help message and exit
Could you help me ? Thank you
Hi,
thanks for your message
The command line seems fine
But it's the error message what I don't understand. It seems to complain about using the word "commands" in the command line.
Have you been able to run it as described in the github?
E.
On Sat, 3 May 2025 at 00:11, Djoudjou2 @.***> wrote:
Djoudjou2 created an issue (comprna/MoSEA#8) https://github.com/comprna/MoSEA/issues/8
Hi ! I continue having this same message :
python /Dataset/AS_MDA/MoSEA-master/mosea.py scan --pfm --fasta test1.fa --out_dir /Dataset/AS_MDA/fmo_outdir --pfm_path /Dataset/AS_MDA/MoSEA/test_files/motifs/pfms
Error in parsing: name 'commands' is not defined usage: mosea.py [-h] {getfasta,scan,enrich,overlap} ...
Runs motif scan & enrichment
positional arguments: {getfasta,scan,enrich,overlap} commands help getfasta Extract Fasta sequences from input bedfile and genome.fa scan Perform motif scanning on fasta sequences enrich Perform enrichment analysis between regulated and control (background) set overlap Compares motif lists.
optional arguments: -h, --help show this help message and exit
Could you help me ? Thank you
— Reply to this email directly, view it on GitHub https://github.com/comprna/MoSEA/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB2UHNZNVNBRVEXRMN324N4HHAVCNFSM6AAAAAB4KEIG7OVHI2DSMVQWIX3LMV43ASLTON2WKOZTGAZTMMJSGYYTINQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
