Hi,

We download PFAM alignment and directly run in annotateMSA, but I believe there might be a problem when new annotated file was created.
All goes swimmingly, yet when we make analysis at the step pf phylogenic tree or taxonomic group -- it is giving error -- seems like the " '|' " that is in the annotated database are not being read correctly.

An example error is like

IndexError Traceback (most recent call last)
in
8 s1 = h.split('__')
9 s2 = s1[0].split('|')
---> 10 hs = s1[1].split('|')
11 tax = []
12 annot[s2[1]] = sca.Annot(s1[0], hs[2], ','.join(hs[3:-2]))

IndexError: list index out of range

We tried this for a couple of different PFAM alignments and gave us same problem? Any suggestions?

Cheers,

Mehmet

Hi,

I am running scaCore.py with command ./scaCore.py XXXX.db and it reports an error as in the following:
Computing the sequence projections.
Computing the SCA conservation and correlation values.
Computing matrix randomizations...
Traceback (most recent call last):
File "./scaCore.py", line 91, in <module> Vrand, Lrand, Crand = sca.randomize(msa_num, options.Ntrials, seqw, options.lbda)
File "/path/scaTools.py", line 1231, in randomize msa_rand = randAlg(fr01, Mseq)
File "/path/scaTools.py", line 1190, in randAlg Maa = np.random.multinomial(Mseq, frq[i,:])
File "mtrand.pyx", line 4249, in numpy.random.mtrand.RandomState.multinomial
File "_common.pyx", line 376, in numpy.random._common.check_array_constraint
File "_common.pyx", line 362, in numpy.random._common._check_array_cons_bounded_0_1 ValueError: pvals < 0, pvals > 1 or pvals contains NaNs
The XXXX.db used here is a scaProcessMSA.py treated MSA XXXX.fa with all default setting. I have 4 MSA and 1 of them could be processed successfully with scaCore.py but three of them reports the same error like I showed above. Could you please help me with this? Thank you for any inputs in advance.

In https://ranganathanlab.gitlab.io/pySCA/get_started/
it is indicated in section 3 that some eq. could be found in the Supplemental section. I searched for "Supplemental" but did not get any...

We are unable to annotate our custom psi-blast alignment. When running the annotateMSA utility, it will return an error for about 20% of accession numbers even though they are valid and exist. Some examples include MXQ93025.1, GCC37908.1, NXC41758.1, XP_023187272.1, and GCB83467.1. We tried breaking the file into smaller pieces in case it was a handler overload. We added our NCBI API key, in case it was exceeding the request limit. We tried adding the Entrez parameter idtype="acc" to line 359 of scaTools.py in case determining the type of identifier was the problem. handle = Entrez.esummary(db="protein", id=",".join(id_block), idtype="acc"). We re-installed all the latest versions of pySCA and Biopython. We tried multiple emails in case it was a user issue. We tried running pySCA on both the most recent versions of Mac OS and Windows. We got the same error each time. Each time the exact same sequences will error. I did a thorough search of possible Entrez errors and it doesn't seem that Entrez has problems handling certain accession, which makes me think it is a pySCA issue. Thank you for the help!

To initiate the annotation we used the command:
annotateMSA -i decipher.an -o align_annotate.an -a 'ncbi' -l Acc_Num

The output error:

❯ annotateMSA -i decipher.an -o align_annotate.an -a 'ncbi' -l Acc_Num
Beginning annotation
Traceback (most recent call last):
  File "/opt/anaconda3/bin/annotateMSA", line 186, in <module>
    sca.AnnotNCBI(options.Input_MSA, options.output, options.idList)
  File "/opt/anaconda3/lib/python3.8/site-packages/pysca/scaTools.py", line 361, in AnnotNCBI
    taxonList = Entrez.read(handle)
  File "/opt/anaconda3/lib/python3.8/site-packages/Bio/Entrez/__init__.py", line 508, in read
    record = handler.read(handle)
  File "/opt/anaconda3/lib/python3.8/site-packages/Bio/Entrez/Parser.py", line 304, in read
    self.parser.ParseFile(handle)
  File "/opt/concourse/worker/volumes/live/71f8613d-c53a-40aa-4c7b-351131b1952c/volume/python_1599203882312/work/Modules/pyexpat.c", line 461, in EndElement
  File "/opt/anaconda3/lib/python3.8/site-packages/Bio/Entrez/Parser.py", line 666, in endErrorElementHandler
    raise RuntimeError(value)
RuntimeError: Invalid uid MXQ93025.1 at position=29

I included the accession list file as Acc_Num.txt and the alignment file as decipher.txt.
decipher.txt
Acc_Num.txt

When attempting to run the annotation step:

python ..\bin\annotateMSA -i PF00034_full_length_sequences.fasta -o PF00034_full_length_sequences.an

I get the following output/error:

Beginning annotation Traceback (most recent call last): File "C:\Users\dlamm\pySCA\bin\annotateMSA", line 178, in <module> sca.AnnotPfam( File "C:\Users\dlamm\AppData\Local\Programs\Python\Python39\lib\site-packages\pysca\scaTools.py", line 180, in AnnotPfam with open(pfam_seq) as fp: OSError: [Errno 22] Invalid argument: '|'

In settings I have :

path2pfamseq = r"C:\Users\dlamm\pfamseq.txt"

Running on:
Windows 10
Python 3.9
pySCA 6.1