print mash results to a TSV file

[kapsakcj]

Hey Rachael, I tried out Centroid today and was curious to see "behind the curtain" for how the centroid genome is chosen from a set of genomes.

So here's a simple little PR that does the following:

• takes the rows of Output which is tab-delimited already
• uses .decode("utf-8") to strip off the byte encoding from each row
• adds the rows to a file called mash-output.tsv

I'm not a pythonista, so there may be some non-best practice code 😬 , but this works for me and creates a TSV as expected:

# 5 assemblies
$ ls asms/
SAMN19774594_contigs.fasta  SAMN19774612_contigs.fasta  SAMN19774623_contigs.fasta  SAMN19774642_contigs.fasta  SAMN19774644_contigs.fasta

# run centroid on dir of assemblies
$ python3 ~/github/centroid-kapsakcj-fork/centroid.py asms/
Sketching asms/SAMN19774644_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774644_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774644_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774644_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774644_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774594_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774594_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774594_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774594_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774594_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774612_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774612_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774612_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774612_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774612_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774642_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774642_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774642_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774642_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774642_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774623_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774623_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774623_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774623_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
Sketching asms/SAMN19774623_contigs.fasta (provide sketch file made with "mash sketch" to skip)...done.
b'asms/SAMN19774594_contigs.fasta'

# show centroid out file
$ cat centroid_out.txt 
SAMN19774594_contigs.fasta

# show mash-results.tsv but with nice tabular-aware spacing
$ column -t -s $'\t' -n mash-results.tsv 
asms/SAMN19774594_contigs.fasta  asms/SAMN19774594_contigs.fasta  0            0  1000/1000
asms/SAMN19774594_contigs.fasta  asms/SAMN19774612_contigs.fasta  0.000361208  0  985/1000
asms/SAMN19774594_contigs.fasta  asms/SAMN19774623_contigs.fasta  0.00390583   0  854/1000
asms/SAMN19774594_contigs.fasta  asms/SAMN19774642_contigs.fasta  0.0023533    0  908/1000
asms/SAMN19774594_contigs.fasta  asms/SAMN19774644_contigs.fasta  0.00294054   0  887/1000
asms/SAMN19774612_contigs.fasta  asms/SAMN19774594_contigs.fasta  0.000361208  0  985/1000
asms/SAMN19774612_contigs.fasta  asms/SAMN19774612_contigs.fasta  0            0  1000/1000
asms/SAMN19774612_contigs.fasta  asms/SAMN19774623_contigs.fasta  0.00408721   0  848/1000
asms/SAMN19774612_contigs.fasta  asms/SAMN19774642_contigs.fasta  0.00210772   0  917/1000
asms/SAMN19774612_contigs.fasta  asms/SAMN19774644_contigs.fasta  0.00308338   0  882/1000
asms/SAMN19774623_contigs.fasta  asms/SAMN19774594_contigs.fasta  0.00390583   0  854/1000
asms/SAMN19774623_contigs.fasta  asms/SAMN19774612_contigs.fasta  0.00408721   0  848/1000
asms/SAMN19774623_contigs.fasta  asms/SAMN19774623_contigs.fasta  0            0  1000/1000
asms/SAMN19774623_contigs.fasta  asms/SAMN19774642_contigs.fasta  0.00433199   0  840/1000
asms/SAMN19774623_contigs.fasta  asms/SAMN19774644_contigs.fasta  0.00384578   0  856/1000
asms/SAMN19774642_contigs.fasta  asms/SAMN19774594_contigs.fasta  0.0023533    0  908/1000
asms/SAMN19774642_contigs.fasta  asms/SAMN19774612_contigs.fasta  0.00210772   0  917/1000
asms/SAMN19774642_contigs.fasta  asms/SAMN19774623_contigs.fasta  0.00433199   0  840/1000
asms/SAMN19774642_contigs.fasta  asms/SAMN19774642_contigs.fasta  0            0  1000/1000
asms/SAMN19774642_contigs.fasta  asms/SAMN19774644_contigs.fasta  0.00375609   0  859/1000
asms/SAMN19774644_contigs.fasta  asms/SAMN19774594_contigs.fasta  0.00294054   0  887/1000
asms/SAMN19774644_contigs.fasta  asms/SAMN19774612_contigs.fasta  0.00308338   0  882/1000
asms/SAMN19774644_contigs.fasta  asms/SAMN19774623_contigs.fasta  0.00384578   0  856/1000
asms/SAMN19774644_contigs.fasta  asms/SAMN19774642_contigs.fasta  0.00375609   0  859/1000
asms/SAMN19774644_contigs.fasta  asms/SAMN19774644_contigs.fasta  0            0  1000/1000