-nb flag & how to view gml output file?

[kac2053]

Hi,

I followed the seekr tutorial, but it seems the -nb flag does not work for seekr_kmer_counts anymore? If -nb does still work, what does the flag do?

$ seekr_kmer_counts X_sequences_mm10.fa -o X_sequences_out_counts.csv -k 3 -nb
usage: 
Description
-----------
Generates a kmer count matrix of m rows by n columns,
where m is the number of transcripts in a fasta file and n is 4^kmer.

Examples
--------
The default settings take a .fa file and produce a labeld csv file:
    $ seekr_kmer_counts rnas.fa -o out.csv

To get a compact and efficient .npy file, set the binary flag:
    $ seekr_kmer_counts rnas.fa -o out.npy -b

You can change also change the size of the kmer you're using, and prevent normalization:
    $ seekr_kmer_counts rnas.fa -o out.csv -k 4 -uc -us -nl
    
If you ever do not want labels on a csv file:
    $ seekr_kmer_counts rnas.fa -o out.csv -rl

Notes
-----
For more sophisticated options, you cannot use the command line, but need python instead.

Issues
------
Any issues can be reported to https://github.com/CalabreseLab/seekr/issues

---
seekr_kmer_counts: error: unrecognized arguments: -nb

Is the output of seekr_kmer_counts a csv file containing the z-scores for each kmer (and not the count data)?

I was able to produce an output gml file. However, I'm not sure how to open to view it. I've googled how, but I'm hesitant to download freeware I've never heard of into the lab computer. Others require me to purchase. I've also tried opening it in a browser (as suggested in another google result), but the Mac won't let me. What do you use to open it?

Thanks.

[Jessime]

Hello!

1. The README.md is a little out of date, and will be for the next few weeks while I finish up my dissertation/defense. The -nb or --non-binary flag used to convert the output to a csv file. Now, a csv file is the default, and you can specify the -b or --binary flag, if you want a numpy array. Basically we just flipped the default to make it easier for less technical users.
2. The default output of seekr_kmer_counts is a csv file containing the log-normalized z-scores for each kmer. But you can get the raw count data instead, if you want (-uc, -us, -nl).
3. The gml files are just plain text files, and you shouldn't need anything special to view it. If you're on Mac, TextEdit is fine. Or from the command line vi, less, cat will all work. If you want to mess with the file, load it into python with networkx.