billzt / primerserver2 Goto Github PK

For example, currently it shows: 281311808-281311827.

It should be 1:281311808-281311827

The default startup port for flask run is 5000. I would like to use a different port to run PrimerServer. Where should I modify it

The module progress bar seems usually conflicting with other existing modules

This is the advise from one reviewee

**hi,thanks for your great software!

When I plan to use full mode to design primers and check primer specificity, or check primer specificity, the progress bar of the task will run all the time. I checked the error and found that it displayed keyerror: 'GB | cm223420.1 |: 1023-1042'.
I have 10 genomes and found this problem in two of them. What caused this mistake?

The following is the complete error code:
Traceback (most recent call last):
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/site-packages/primerserver2-2.0.0b21-py3.8.egg/prim erserver2/core/run_blast.py", line 48, in run_ blast
report_ amplicons = filter_ Tm(amplicons['amplicons'], query_primer_seq=query_primer_seq_dict,
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/site-packages/primerserver2-2.0.0b21-py3.8.egg/prim erserver2/core/analysis_blast.py", line 123, in filter_ Tm
hit_ seq_ minus = rev_ complement(hits_seqs[region_minus]) # samtools faidx hasn't do rev_ complement yet
KeyError: 'gb|Cm223420.1|:1023-1042'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/ljm/.conda/envs/PrimerServer/bin/primertool", line 33, in
sys.exit(load_entry_point('primerserver2==2.0.0b21', 'console_scripts', 'primertool')())
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/site-packages/primerserver2-2.0.0b21-py3.8.egg/prim erserver2/cmd/primertool.py", line 204, in main
run(args)
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/site-packages/primerserver2-2.0.0b21-py3.8.egg/prim erserver2/cmd/primertool.py", line 167, in run
primers = run_ blast. run_ blast_ parallel(primers=primers, dbs=dbs, cpu=args.cpu,
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/site-packages/primerserver2-2.0.0b21-py3.8.egg/prim erserver2/core/run_blast.py", line 108, in run_ blast_ parallel
result_ data = result. get() # db and amplicons
File "/home/ljm/.conda/envs/PrimerServer/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._ value
KeyError: 'gb|Cm223420.1|:1023-1042'

FASTA is a good idea as it supports multiple sequences (site) together with sequence names.

currently only up to 10

reproduce steps:

install miniconda3
install primerserver2 using setup.py
run primertool full query_design_multiple example.fa

query_design_multiple.json is normal while query_design_multiple.tsv is blank

When I try run PrimerServer2 under python 3.8 or 3.9, it gives a error code:

attributeerror: module 'primerserver2.core.global_var' has no attribute 'stop_run'

I downgrade my python to 3.7 and reinstall again. It works properly.

Hope this will help to improve this awesome app.

cheers

primertool full 1.txt /data2/Fshare/FastaAndIndex/iwgsc_v2.0/CS_genome_v2.0 -o cSSR_full.json -t cSSR_full.tsv
/root/software/anaconda3/lib/python3.7/site-packages/ipykernel/displayhook.py:12: VisibleDeprecationWarning: zmq.eventloop.minitornado is deprecated in pyzmq 14.0 and will be removed.
    Install tornado itself to use zmq with the tornado IOLoop.
    
  from jupyter_client.session import extract_header, Session
Designning Primers: 10 Finished (100%)|#########################################################################################|Time:  0:00:00
Checking specificity: 305 Finished (100%)|######################################################################################|Time:  0:00:01
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/root/software/anaconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/root/software/anaconda3/lib/python3.7/site-packages/primerserver2/core/run_blast.py", line 36, in run_blast
    raise Exception(f'The database file is not complete: file {db}.nhr is not found')
Exception: The database file is not complete: file /data2/Fshare/FastaAndIndex/iwgsc_v2.0/CS_genome_v2.0.nhr is not found
"""

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

Traceback (most recent call last):
  File "/root/software/anaconda3/bin/primertool", line 10, in <module>
    sys.exit(main())
  File "/root/software/anaconda3/lib/python3.7/site-packages/primerserver2/cmd/primertool.py", line 156, in main
    run(args)
  File "/root/software/anaconda3/lib/python3.7/site-packages/primerserver2/cmd/primertool.py", line 140, in run
    report_amplicon_seq=args.report_amplicon_seqs, Tm_diff=args.Tm_diff, use_3_end=args.use_3_end)
  File "/root/software/anaconda3/lib/python3.7/site-packages/primerserver2/core/run_blast.py", line 99, in run_blast_parallel
    result_data = result.get()  # db and amplicons
  File "/root/software/anaconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
Exception: The database file is not complete: file /data2/Fshare/FastaAndIndex/iwgsc_v2.0/CS_genome_v2.0.nhr is not found

NCBI database

CS_genome_v2.0.00.nhr
CS_genome_v2.0.00.nin
CS_genome_v2.0.00.nog
CS_genome_v2.0.00.nsd
CS_genome_v2.0.00.nsi
CS_genome_v2.0.00.nsq
CS_genome_v2.0.01.nhr
CS_genome_v2.0.01.nin
CS_genome_v2.0.01.nog
CS_genome_v2.0.01.nsd
CS_genome_v2.0.01.nsi
CS_genome_v2.0.01.nsq
CS_genome_v2.0.02.nhr
CS_genome_v2.0.02.nin
CS_genome_v2.0.02.nog
CS_genome_v2.0.02.nsd
CS_genome_v2.0.02.nsi
CS_genome_v2.0.02.nsq
CS_genome_v2.0.03.nhr
CS_genome_v2.0.03.nin
CS_genome_v2.0.03.nog
CS_genome_v2.0.03.nsd
CS_genome_v2.0.03.nsi
CS_genome_v2.0.03.nsq
CS_genome_v2.0.nal
CS_genome_v2.0

CS_genome_v2.0 is genome fasta file.

‘’[root@iZ8vbhjgwhc1nm2b1b1kwwZ PrimerServer2]# samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.9 (using htslib )”

I have updated the software version
Thank you for your great program, but it seems that there is an error,Is it something wrong?

Now it simply replaces degenerate bases with a random normal base. However it is not suitable for primers with multiple degenerate bases since it would result in too many mismatches and lose the true amplicon