From 2fc2957dbfb4ae28be75b84ed2a082f3df36abda Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Tue, 19 Nov 2024 22:21:26 +0100
Subject: [PATCH] added hox alignment script

---
 07-analysis/genes.sh | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 07-analysis/genes.sh

diff --git a/07-analysis/genes.sh b/07-analysis/genes.sh
new file mode 100644
index 0000000..d79b6eb
--- /dev/null
+++ b/07-analysis/genes.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+
+# a script to keep track of what I have aligned against what
+# so we can find it again when it is time to write the paper.
+
+# references
+FLYE=/Users/npapadop/Documents/data/sequences/plit/flye.fasta
+SHASTA=/Users/npapadop/Documents/data/sequences/plit/shasta.fasta
+HIFIASM=/Users/npapadop/Documents/data/sequences/plit/hifiasm.fa
+FLYE_OMNI=/Users/npapadop/Documents/data/sequences/plit/draft_filtered.fasta
+
+# output format
+M8FORMAT="query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,qlen"
+
+# queries
+SMART_ARACHNIDA_HOX=/Users/npapadop/Documents/data/sequences/plit/2023-10-16_SMART_arachnida.fasta
+NCBI_CHELICERATA_HOX=/Users/npapadop/Documents/data/sequences/plit/2023-10-16_chelicerata-hox.fasta
+PYCLIT_HOX=/Users/npapadop/Documents/data/sequences/plit/Plit_HoxGenes.fasta
+
+WORKDIR=/Users/npapadop/Documents/projects/pycnogonum/2024-05-28_wnt_finder
+mkdir -p $WORKDIR
+cd $WORKDIR || exit 1
+
+### Finding hox genes
+cd /Users/npapadop/Documents/projects/pycnogonum/2023-10-16_hox_finder || exit 1
+mmseqs easy-search $SMART_ARACHNIDA_HOX $SHASTA smart_shasta.m8 tmp
+mmseqs easy-search $SMART_ARACHNIDA_HOX $HIFIASM smart_hifiasm.m8 tmp
+mmseqs easy-search $SMART_ARACHNIDA_HOX $FLYE_OMNI smart_draft.m8 tmp
+mmseqs easy-search $NCBI_CHELICERATA_HOX $FLYE ncbi_flye.m8 tmp
+mmseqs easy-search $NCBI_CHELICERATA_HOX $SHASTA ncbi_shasta.m8 tmp
+mmseqs easy-search $NCBI_CHELICERATA_HOX $HIFIASM ncbi_hifiasm.m8 tmp
+mmseqs easy-search $NCBI_CHELICERATA_HOX $FLYE_OMNI ncbi_draft.m8 tmp
+
+### Using hand-picked hox gene sequences
+cd /Users/npapadop/Documents/projects/pycnogonum/2023-10-16_hox_finder || exit 1
+mmseqs easy-search $PYCLIT_HOX $FLYE pyclit.m8 tmp --format-output $M8FORMAT
+mmseqs easy-search $PYCLIT_HOX $FLYE_OMNI pyclit.m8 tmp --format-output $M8FORMAT
+mmseqs easy-search $BRANCHO_ABDA $FLYE abda.m8 tmp --format-output $M8FORMAT
+mmseqs easy-search $BRANCHO_ABDA contig_2855.fa abda.m8 tmp --format-output $M8FORMAT
\ No newline at end of file
-- 
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