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Fun little exercise, find the :shakefist: :shakefi...
# mag
j
Fun little exercise, find the shakefist shakefist shakefist shakefist shakefist shakefist
Copy code
$ for i in *; do echo "$i: $(zcat $i | head -n 1)"; done
FLYE-COMEBin-CAPES_S11.0.fa.gz: >contig_1
FLYE-MetaBAT2-CAPES_S11.1.fa.gz: >contig_850
FLYE-MetaBinner-CAPES_S11.1.fa.gz: >contig_144
MEGAHIT-COMEBin-CAPES_S11.10076.fa.gz: >k119_313
MEGAHIT-MetaBAT2-CAPES_S11.30.fa.gz: >k119_95
MEGAHIT-MetaBinner-CAPES_S7.6.fa.gz: >k119_24 flag=1 multi=29.0000 len=44633
SPAdes-COMEBin-CAPES_S11.0.fa.gz: >NODE_1_length_183591_cov_18.473891
SPAdes-MetaBAT2-CAPES_S7.12.fa.gz: >NODE_1_length_456608_cov_52.704910
SPAdes-MetaBinner-CAPES_S11.2.fa.gz: >NODE_5_length_164182_cov_24.232771
d
Who would ever use 
i
for something other than an iterator? 😉
😆 1
j
It's not that
d
(Suspected that.)
😆 1
👀 1
j
MetaBinner leaves the FASTA comment intact...
shakefist 1
j
FFS
j
Was that your problem? Or are you seeing something else... I have stared at this for two minutes now
j
Actually it wasn't 😆 , at least not yet
But something I noticed
And why we can't have nice things
(I thought it was related, but it wasn't exactly
j
Actually almost all of the binning tools drop the FASTA comments, which TBH I think is incorrect behaviour
💯 2
j
WHY
I vaugely remember someone saying VAMB does the same thing too ro soemething...
j
Vamb wants you to rename your contigs before you supply them
j
That's the one
j
>${sample}{splitter}{contigID}
But in its defence it does use that information
And it will operate without doing it
j
Oh it does work without renaming?
j
Yeah but in a more limited way
👍 1
The idea is that you bin all the contigs from all sample-level assemblies together, and then it writes per-sample bins
So it needs to know about which sample a contig came from
If you only have one sample you don't need to do that
j
Ahhh I see
Shame you couldn't just give that as an input map or something
j
Or just separate files...
👍 1
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