first draft of MicroFinder

Dockerfile

@@ -7,4 +7,10 @@ RUN bundle install
 
 COPY . .
 
-ENTRYPOINT ["/usr/src/app/sort_fasta.rb"]
+# add miniprot
+RUN cd /opt && \
+    git clone --depth=1 https://github.com/lh3/miniprot && \
+    cd miniprot && \
+    make
+
+ENTRYPOINT ["/usr/src/app/MicroFinder.v0.2.sh"]

MicroFinder.v0.2.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# v0.2 script - in future will update locations of gene set, tools etc. so will work with a release.
+
+# Changes from v0.1: Updated to MicroFinder naming.
+
+# Currently needs to be run in curation_v2 env.
+
+if [ $# -ne 2 ]; then
+    echo $0: usage: bash MircoFinder.sh input_assembly scaffold_length_cutoff
+    exit 1
+fi 
+
+# vars
+
+input_assembly=$1
+length_cutoff=$2
+
+# map gene set
+
+/opt/miniprot/miniprot --gff ${input_assembly} /usr/src/app/data/MicroFinder_prot_set.v0.1.fa.gz > ${input_assembly}.MicroFinder.gff
+
+# Filter hits
+
+awk '$3== "mRNA"' ${input_assembly}.MicroFinder.gff | grep -w "Rank=1" | cut -f1,9 | tr ";" "\t" | cut -f1,4,5,6,7 | sed 's/Identity=//g' | sed 's/Positive=//g' | awk '$2 >= 0.7' |  cut -f1 | sort | uniq -c | sort -k1,1nr | awk '{print $2 "\t" $1}' > ${input_assembly}.MicroFinder.order.tsv
+
+# Reorder assembly
+
+/usr/src/app/sort_fasta.rb -f ${input_assembly} -o ${input_assembly}.MicroFinder.order.tsv -l ${length_cutoff} > ${input_assembly}.MicroFinder.ordered.fa