[Feature] RdRp / sOTU search based on sequence

[ababaian]

To enable Open Virome to search via sequence input, an input sequence must be compared against palmDB sOTU, which is a fasta file. See schematic from palmID

Performing this alignment, plus a percentage query slider return (see Issue #27) will enable searching all palmDB/SRA based on a query

My experience is that this plot has been the most informative for interpreting this information: which could be rendered IFF a query contains a sequence-based entry (i.e. sOTU xxxx +20% divergence)

How to implement

palmID performs a search to extract a palmprint first, this is unneccesary and we can search the input sequence directly against palmDB sOTU. For now we should support protein sequence as input only.

# RUN DIAMOND =============================================
# Uses a PROTEIN SEQUENCE as input

echo ''
echo '-- running DIAMOND search of palmDB...'
echo ''

# diamond 1e-6 cutoff 
diamond blastp \
  -q $OUTDIR/$OUTNAME.trim.fa\
  -d $DB \
  --masking 0 -e 0.00001 \
  --tmpdir /tmp \
  --ultra-sensitive -k0 \
  -f 6 qseqid  qstart qend qlen \
       sseqid  sstart send slen \
       pident evalue cigar \
       full_sseq \
  > $OUTDIR/$OUTNAME.pro.tmp

# Sort by alignment identity
sort -nr -k9 $OUTDIR/$OUTNAME.pro.tmp > $OUTDIR/$OUTNAME.pro
rm $OUTDIR/$OUTNAME.pro.tmp

echo " hits in palmDB: $(wc -l $OUTDIR/$OUTNAME.pro)"

This will return all hits in palmDB. Those sequence identifiers form the basis of the Virome Query.

Limits

• Return only 200 top-matches, otherwise things like Narnaviruses will query for 10,000s of sOTU at once and grind to a halt
• Allow for returning of matches within a range from 0-100 of percent identity as reported in diamond pident field (you could probably simplify the output reporting to be minimal to the information we need)
• In this mode, all returning sOTU in the query would only return exact sOTU matches.
• The output of the lambda for diamond which is a list of sOTU and their pid can itself be used with palm_graph to query for known sOTU based on other sOTU related to them and a set threshold of identity.