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I have had trouble with constructing a dictionary of phylogenetic groups after annotation using the annotate_MSA script because some annotations contain a vertical bar symbol in the description string ex:

"DNLJ_ZYMMO|DNA ligase {ECO:0000255|HAMAP-Rule:MF_01588}|Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)|Bacteria,Proteobacteria,Alphaproteobacteria,Sphingomonadales,Sphingomonadaceae,Zymomonas."

A different delimiter is probably necessary.

I found an issue related to the MSAsearch function in scaTools.py. I am new to python and just came up with a naive solution. But the output it not consist with that described in the pySCA tutorial.

Firstly I have ggsearch36 installed, which means I can use ggsearch36 in command lines :

$ ggsearch36
USAGE
 ggsearch36 [-options] query_file library_file
 ggsearch36 -help for a complete option list

DESCRIPTION
 GGSEARCH performs a global/global database searches
 version: 36.3.8 Jul, 2015

COMMON OPTIONS (options must preceed query_file library_file)
 -s:  scoring matrix;
 -f:  gap-open penalty;
 -g:  gap-extension penalty;
 -S   filter lowercase (seg) residues;
 -b:  high scores reported (limited by -E by default);
 -d:  number of alignments shown (limited by -E by default);
 -I   interactive mode;

And in python3, I tried
./scaProcessMSA.py Inputs/s1Ahalabi_1470_nosnakes.an -s 3TGI -c E -t -n
to do MSA for the S1A family.

It gives error outputs:

Trying MSASearch with ggsearch
Trying MSASearch with EMBOSS
Trying MSASearch with BioPython
Error!!! Something wrong with PDBid or path...

After debugging for days I found this issue comes from this line in scaTools.py:
i_0 = [i for i in range(len(hd)) if output.split('\t')[1] in hd[i]]

It is that the byte type is not consist with str. I just solved it by modifying it to:
i_0 = [i for i in range(len(hd)) if output.split(b'\t')[1] in bytes(hd[i],'utf-8')]

It works and could give the final MSA outputs, but with 205 positions for S1A instead of 245.

Thank you very much for your help.

test_case.zip

Hello, running the following script (attached input files), I get the following error:

Code/./scaProcessMSA.py Inputs/aln-kaic.fasta --refseq ref_seq_KaiC_elongatus.fa -c A --output Outputs/KaiC1_processed.db

Using reference sequence but no position list provided! Just numbering positions 1 to length(sequence)
Traceback (most recent call last):
  File "Code/./scaProcessMSA.py", line 85, in <module>
    options.refpos = range(len(options.refseq))+1
TypeError: can only concatenate list (not "int") to list

I presume you meant options.refpos = range(len(options.refseq)+1). After changing that line, I run the same command and get the following error:

Using reference sequence but no position list provided! Just numbering positions 1 to length(sequence)
Using the reference sequence and position list...
Loaded alignment of 1194 sequences, 1530 positions.
Checking alignment for non-standard amino acids
Aligment size after removing sequences with non-standard amino acids: 1194
Trimming alignment for highly gapped positions (80% or more).
Alignment size post-trimming: 536 positions
Finding reference sequence using provided sequence file...
Trying MSASearch with ggsearch
Trying MSASearch with EMBOSS
Trying MSASearch with BioPython
Error!!  Can't find reference sequence...

In line 174, I print out h_tmp and s_tmp[0] and get

(['Elongatus_KaiC'], 'MTSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIKDSFRNFERIISGSPTRITVDEKSELSRIVRGVQEKGPES')

Python version:
'2.7.13 |Enthought, Inc. (x86_64)| (default, Mar 2 2017, 08:20:50) \n[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]'

Biopython version:
1.71

Thanks in advance!

Main idea of SCA is to use MSA as a foundation stone. My question does it equally reliable for oligomeric protein?

The ftp url provided for downloading pfamseq.txt (ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/database_files/) is not active. It would be helpful to know which release of pfamseq was used when writing the code for annotate MSA.py, as the current release does not seem to work.

I have been having an issue with the scaSectors.py tool. When I input the command:
./scaSectorID.py ./PF00028.db
I received the error
Selected kpos=4 significant eigenmodes.
Traceback (most recent call last):
File "./scaSectorID.py", line 70, in
ics,icsize,sortedpos,cutoff,scaled_pd, pd = sca.icList(Vpica,kpos,Csca, p_cut=options.cutoff)
File "/home/dylan/pySca-master/scaTools.py", line 998, in icList
h_params = np.histogram(Vpica[:,k], nbins)
File "/home/dylan/anaconda2/lib/python2.7/site-packages/numpy/lib/function_base.py", line 719, in histogram
'bins must be an integer, a string, or an array')
TypeError: bins must be an integer, a string, or an array

I was wondering if anyone had insight into this error?