# snip-bandage.txt
# MIT License
#
# Copyright (c) 2023 microgrim / Sharon Grim <sharon.grim@whoi.edu>
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
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# SOFTWARE.

###########

# Usage: ./snip-bandage.txt Sample#

# This snippet describes how I evaluated the de Brujin graph of contigs in a metagenomic assembly
# to visualize the linkages between contigs and allow the user to curate their
# metagenome-assembled-genomic (MAG) binning efforts.

# We start with a metagenomic assembly from Megahit,
# and a text file of the contigs in a MAG bin from Anvi'o.
# We're using Megahit, bandage, and a Unix environment.

# in this snippet, I worked in the directory "/geomicro/data7/sgrim/MIS2015-2017mtg/117911/"
# the code in here is from 2016. I have not verified versions or updates of any software used. YMMV.

##Names report: /geomicro/data7/sgrim/MIS2015-2017mtg/117911/117911-fixed.fa.namesreport
#Bins: /geomicro/data7/sgrim/MIS2015-2017mtg/117911/METABAT/117911_bin*.fa
#assembly file: /geomicro/data7/sgrim/MIS2015-2017mtg/117911/ASSEMBLY/k21_141_s12/intermediate_contigs

###########

# From the assembly, create the bandage-compatible fastg file.

cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/ASSEMBLY/k21_141_s12/intermediate_contigs
megahit_toolkit contig2fastg 141 k141.contigs.fa > 117911_k141.fastg

#open 117911_k141.fastg in bandage

#make the binning directory we need (a la anvio's summarize function)
mkdir /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/
mkdir /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_by_bin/
cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/METABAT/
rename "s/117911_bin\./117911_bin_/" 117911_bin*.fa
#rename "s/117911_bin_/117911_bin\./" 117911_bin*.fa

for i in `ls 117911_bin*.fa | awk 'BEGIN{FS="."}{print $1}'`; do
	mkdir /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_by_bin/$i
	cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_by_bin/$i
	ln -s /geomicro/data7/sgrim/MIS2015-2017mtg/117911/METABAT/$i.fa $i-contigs.fa
	cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/METABAT/
done

###########

# Use another script to extract the anvio-analyzed contigs and rename them to be compatible with the assembly:

cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage
# does this still exist?
# wget https://github.com/tylerbarnum/perchlorate-metagenome-2018/raw/master/anvi-renamed-contigs-to-bandage-csv.py
chmod a+x anvi-renamed-contigs-to-bandage-csv.py

ls /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_by_bin/ > /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_names.txt

python2 anvi-renamed-contigs-to-bandage-csv.py --bins /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/bin_names.txt --directory /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/ --delimiter "k141_" --report /geomicro/data7/sgrim/MIS2015-2017mtg/117911/117911-fixed.fa.namesreport --output /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage/all_bins_to_bandage.csv

cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage
ln -s /geomicro/data7/sgrim/MIS2015-2017mtg/117911/ASSEMBLY/k21_141_s12/intermediate_contigs/117911_k141.fastg .

# get into an interactive session:
# ssh -X {user}@{domain.com}
# ssh -X {server}

#bandage load 117911_k141.fastg 

# So now that works. I want to manually check a bin I identified as a Spirulina sp.
# that bin is labeled "bin_9" in my analyses.
# I pull all the contigs labeled "bin_9" from the parsed contigs file:

cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage
grep "bin_9" all_bins_to_bandage.csv | awk 'BEGIN{FS=","}{print $1","}' > 117911_bin_9.nodes.txt

# manually add some contigs I wanted to evaluate in the graph:
#grep "c_000000670588" /geomicro/data7/sgrim/MIS2015-2017mtg/117911/117911-fixed.fa.namesreport
#702880
#c_000000453097
#483248
#c_000000542840
#573756
#add to the end of  117911_bin_9.nodes.txt
printf "702880,\n483248,\n573756,\n" >> 117911_bin_9.nodes.txt

tr -d '\n' < 117911_bin_9.nodes.txt > 117911_bin_9.inline.nodes.txt

head 117911_bin_9.inline.nodes.txt

cd /geomicro/data7/sgrim/MIS2015-2017mtg/117911/bandage
bandage reduce 117911_k141.fastg 117911_bin_9.gfa --scope aroundnodes --distance 50 --nodes `cat 117911_bin_9.inline.nodes.txt`
bandage load 117911_bin_9.gfa