Visualization of output and maf_to_gfa1.py TabError: inconsistent use of tabs and spaces in indentation

[medvedevgroup]

Visualization of output and maf_to_gfa1.py TabError: inconsistent use of tabs and spaces in indentation

[iminkin]

Hi, thank you for reporting! I pushed a fix to the master, could you please pull and check if maf_to_gfa1 works? With regards to XMFA conversion, it relies on an external library, so there is no easy way to speed it up right away. Did it finish by now?

[devenderarora]

Dear iminkin,
Thanks for the early response.
Yesterday, I terminated XMFA conversion as it show nothing in top command.
I tried executing again maf_to_gfa1.py but ended up with an error:

(r_env) arora@info4:/680_info4/project/arora/circo/sibeliaz_out$ python maf_to_gfa1.py alignment.maf 1.fasta 2.fasta
File "maf_to_gfa1.py", line 174
print "S\t" + str(b + 1) + "\t" + blocks[b][0].body
^
SyntaxError: invalid syntax

#######
With my limited understanding to python I tried to fix:

print ("S\t" + str(b + 1) + "\t" + blocks[b][0].bod) and followed the same for all print command and ended up with

Traceback (most recent call last):
File "maf_to_gfa1.py", line 7, in
from Bio.Alphabet import IUPAC
File "/home/arora/anaconda2/envs/r_env/lib/python3.7/site-packages/Bio/Alphabet/init.py", line 21, in
"Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

#######
Following, I just silenced the library Bio.Alphabet at line 7 by # and rerun the program and ended up with

(r_env) arora@info4:/680_info4/project/arora/circo/sibeliaz_out$ python maf_to_gfa1.py alignment.maf 1.fasta 2.fasta and ended up with the error:

Traceback (most recent call last):
File "maf_to_gfa1.py", line 202, in
blocks, sequence = split_maf_blocks(args.maf)
File "maf_to_gfa1.py", line 110, in split_maf_blocks
prev_profile = profile(maf, 0)
File "maf_to_gfa1.py", line 53, in profile
return [group[i].body[column] == '-' for i in xrange(len(group))]
NameError: name 'xrange' is not defined
#######
Post update
I just changed xrange with range function and it seems working.

Please share if the library Bio.Alphabet need to be there or is this the right fix.
PS: The maf_to_gfa script still running.

Thanks
Regards
Devender Arora

[devenderarora]

Dear iminkin,
I am able to make .gfa file after successfully running mfa_to_gfa1.py fasta1 fasta2 > output.gfa
I found no support in vg to open .gfa file and tried open the respective gfa file in Bandage viewer for gfa file but it ended up with segmentation fault.
Please share how can we visualize the .gfa file I will be grateful to you.

[iminkin]

@devenderarora , what is the size of your dataset? Honestly, visualizing a maf alignment as a GFA graph is unlikely to work for any relatively large dataset; even for smaller ones, the resulting graph is quite large and clumsy.

[devenderarora]

~2.7gb. Graphical representation is what I am looking for to better understand and explain result output.
Thankyou again

[iminkin]

Sorry, but I suspect that it could be quite challenging to visualize a dataset of such size. Maybe there are solutions out there, but I don't think I can help.

[devenderarora]

No problem friend. I will look for some way out.
Thankyou.