Indentation error + Error-Unable to parse alignment (after fixing indentation errors) + example.aln file missing

[vaishaliwaman]

Hi Ian,
Vaishaii here, I have a query about code:
The code had indentation errors and I fixed them. However, it still shows an error 'Unable to parse alignment' (when I tried correcting indentation corresponding block at 195-204 lines).

Please kindly help with fixing issue in code and provide me updated code.

Also, I couldn't download example.aln file, as its link is not working.

[sillitoe]

Hey Vaisahali,

Great - thanks for the input. Could you let me know where these errors were?

Would be ideal if you could make a pull request with your suggested changes, but you could also browse to the location of the issue here in GitHub, then copy and paste a link to the file and line.

I would need a bit more information on example.aln too - which link are you referring to?

Thanks,

Ian

[vaishaliwaman]

Hi Ian,
Thanks.
Regarding example.aln:
This file is given under following subheading at cathpycore/tools/GroupSim/README.md:
Other variants of the script: group_sim_sdp_no_gap_cutoff.py
Example alignment
Alignment: example.aln (This file I am unable to download)-Please find screenshot attached.

Regarding code:
I used group_sim_sdp.py cathpy.
It was showing me indentation errors at various lines ( I just added one space, wherever prompted). This code, gives : Unable to parse alignment. Hence, I am not exactly sure if I have done some wrong changes while fixing identation in the file.
I tried running following commands:
python2 group_sim_sdp.py -c 0.3 -g 0.5 example.aln group1 group2 example_id_with_gap_cutoff.groupsim.txt
python2 group_sim_sdp.py -c 0.3 -g 0.5 -m mclachlan1972.aa.dat example.aln group1 group2 > example_mc_with_gap_cutoff.groupsim.txt

For these commands, I used an example.aln file provided at original source code link (https://compbio.cs.princeton.edu/specificity/).

I haven't added the modified code to pull requests, as I am not sure if I am made right changes,

Please kindly help with the working code or advise.

Vaishali

[sillitoe]

Sorry for the delay responding - I didn't get a notification from your reply (I'm blaming gmail spam filter).

Thanks for the extra information - this makes much more sense now.

I didn't write groupsim and I didn't want to make any changes so I included it in this library with a wrapper that just ran it with the expected arguments: cathpy.core.util.GroupsimRunner.

https://github.com/UCL/cathpy/blob/master/cathpy/core/util.py#L79

An example of how this is used in the code:

from cathpy.core.align import Align
from cathpy.core.util import GroupsimRunner

# create the alignment from file 
aln = Align.from_fasta('tests/data/sc.cora.fa')

# create a groupsim runner (allows you to change default parameters)
gs_runner = GroupsimRunner()

# set the sequence cluster id for each sequence (4 seqs in aln)
seq_cluster_ids = [1, 1, 2, 2]
for seq_idx, seq in enumerate(aln.seqs):
    seq.set_cluster_id(seq_cluster_ids[seq_idx])

# run scorecons on this alignment, return a GroupsimResult
gs_result = gs_runner.run_alignment(aln)

# count the number of positions
gs_result.count_positions
# returns: 75

# get access to the groupsim scores for each position
gs_result.scores
# returns: [None, None, None, None, None, None, None, None, None, None, None, None, None, None, 0.125072, 0.102397, -0.059296, 0.126442, 0.469658, 0.165983, -0.018854, 0.173856, 0.097241, 0.501396, -0.00848, 0.199687, 0.486175, 0.128976, 0.166623, 0.527108, 0.131452, 0.066098, 0.400145, 0.175255, None, -0.243271, 0.17553, 0.562814, 0.217134, 0.518979, 0.187731, 0.176286, 0.022461, 0.170689, 0.02993, 0.048587, 0.271128, 0.238287, 0.093309, 0.240545, 0.125, 0.236748, 0.26708, 0.168755, 0.02505, -0.022767, 0.208507, -0.03425, 0.46916, -0.10896, 0.101535, 0.106619, 0.1056, None, None, None, 0.023845, -0.13125, -0.122723, 0.023894, None, None, None, None, None]

It might be really useful to include this as an example of how to use cathpy.

[vaishaliwaman]

Hi Ian, Thank you so much. This is very helpful. I will go through it today and let you know if any questions. Many thanks, Vaishali

…

On Wed, 27 May 2020, 12:04 Ian Sillitoe, ***@***.***> wrote: Sorry for the delay responding - I didn't get a notification from your reply (I'm blaming gmail spam filter). Thanks for the extra information - this makes much more sense now. I didn't write groupsim and I didn't want to make any changes so I included it in this library with a wrapper that just ran it with the expected arguments: cathpy.core.util.GroupsimRunner. https://github.com/UCL/cathpy/blob/master/cathpy/core/util.py#L79 An example of how this is used in the code: from cathpy.core.align import Align from cathpy.core.util import GroupsimRunner # create the alignment from file aln = Align.from_fasta('tests/data/sc.cora.fa') # create a groupsim runner (allows you to change default parameters) gs_runner = GroupsimRunner() # set the sequence cluster id for each sequence (4 seqs in aln) seq_cluster_ids = [1, 1, 2, 2] for seq_idx, seq in enumerate(aln.seqs): seq.set_cluster_id(seq_cluster_ids[seq_idx]) # run scorecons on this alignment, return a GroupsimResult gs_result = gs_runner.run_alignment(aln) # count the number of positions gs_result.count_positions # returns: 75 # get access to the groupsim scores for each position gs_result.scores # returns: [None, None, None, None, None, None, None, None, None, None, None, None, None, None, 0.125072, 0.102397, -0.059296, 0.126442, 0.469658, 0.165983, -0.018854, 0.173856, 0.097241, 0.501396, -0.00848, 0.199687, 0.486175, 0.128976, 0.166623, 0.527108, 0.131452, 0.066098, 0.400145, 0.175255, None, -0.243271, 0.17553, 0.562814, 0.217134, 0.518979, 0.187731, 0.176286, 0.022461, 0.170689, 0.02993, 0.048587, 0.271128, 0.238287, 0.093309, 0.240545, 0.125, 0.236748, 0.26708, 0.168755, 0.02505, -0.022767, 0.208507, -0.03425, 0.46916, -0.10896, 0.101535, 0.106619, 0.1056, None, None, None, 0.023845, -0.13125, -0.122723, 0.023894, None, None, None, None, None] It might be really useful to include this as an example of how to use cathpy. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIBVYQGA4F3TWSGPHHM4VVLRTTXULANCNFSM4NEDWKQA> .

[vaishaliwaman]

HI Ian, Thanks again. Just to update- I could use GroupSIm code successfully. At cathpy, I came across groupsim2jalview.pl <https://github.com/UCL/cathpy/blob/master/cathpy/core/tools/GroupSim/groupsim2jalview.pl> . I couldnt find its readme. Just wanted to know, whether this script can be readily used to locate and visualize, groupSIm based SDPs. Might be useful for my work (to generate figures). A quick update of neighboring Funfam - I could successfully use HHSuite to identify neighoring Funfams for gyrase. Many thanks. Vaishali On Wed, May 27, 2020 at 1:51 PM Vaishali Waman <vaishali.p.waman@gmail.com> wrote:

…

Hi Ian, Thank you so much. This is very helpful. I will go through it today and let you know if any questions. Many thanks, Vaishali On Wed, 27 May 2020, 12:04 Ian Sillitoe, ***@***.***> wrote: > Sorry for the delay responding - I didn't get a notification from your > reply (I'm blaming gmail spam filter). > > Thanks for the extra information - this makes much more sense now. > > I didn't write groupsim and I didn't want to make any changes so I > included it in this library with a wrapper that just ran it with the > expected arguments: cathpy.core.util.GroupsimRunner. > > https://github.com/UCL/cathpy/blob/master/cathpy/core/util.py#L79 > > An example of how this is used in the code: > > from cathpy.core.align import Align > from cathpy.core.util import GroupsimRunner > > # create the alignment from file > aln = Align.from_fasta('tests/data/sc.cora.fa') > > # create a groupsim runner (allows you to change default parameters) > gs_runner = GroupsimRunner() > > # set the sequence cluster id for each sequence (4 seqs in aln) > seq_cluster_ids = [1, 1, 2, 2] > for seq_idx, seq in enumerate(aln.seqs): > seq.set_cluster_id(seq_cluster_ids[seq_idx]) > > # run scorecons on this alignment, return a GroupsimResult > gs_result = gs_runner.run_alignment(aln) > > # count the number of positions > gs_result.count_positions > # returns: 75 > > # get access to the groupsim scores for each position > gs_result.scores > # returns: [None, None, None, None, None, None, None, None, None, None, None, None, None, None, 0.125072, 0.102397, -0.059296, 0.126442, 0.469658, 0.165983, -0.018854, 0.173856, 0.097241, 0.501396, -0.00848, 0.199687, 0.486175, 0.128976, 0.166623, 0.527108, 0.131452, 0.066098, 0.400145, 0.175255, None, -0.243271, 0.17553, 0.562814, 0.217134, 0.518979, 0.187731, 0.176286, 0.022461, 0.170689, 0.02993, 0.048587, 0.271128, 0.238287, 0.093309, 0.240545, 0.125, 0.236748, 0.26708, 0.168755, 0.02505, -0.022767, 0.208507, -0.03425, 0.46916, -0.10896, 0.101535, 0.106619, 0.1056, None, None, None, 0.023845, -0.13125, -0.122723, 0.023894, None, None, None, None, None] > > It might be really useful to include this as an example of how to use > cathpy. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#7 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AIBVYQGA4F3TWSGPHHM4VVLRTTXULANCNFSM4NEDWKQA> > . >

[sillitoe]

Thanks for the info.

Glad you could use GroupSim. I'm afraid I don't know much about groupsim2jalview.pl - Sayoni directed me to a the GroupSim directory and I just copied the lot into this library.

It seems reasonable to assume that script was written by Sayoni to look at groupsim assignments in Jalview - probably best to look at the code to see what it's doing.

Good news re. HH-suite

[vaishaliwaman]

Hi Ian, Thanks, will do. Vaishali

…

On Thu, 28 May 2020, 16:28 Ian Sillitoe, ***@***.***> wrote: Thanks for the info. Glad you could use GroupSim. I'm afraid I don't know much about groupsim2jalview.pl - Sayoni directed me to a the GroupSim directory and I just copied the lot into this library. It seems reasonable to assume that script was written by Sayoni to look at groupsim assignments in Jalview - probably best to look at the code to see what it's doing. Good news re. HH-suite — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIBVYQB2GYW6OPU6KWIVQVTRTZ7KNANCNFSM4NEDWKQA> .