A. Murat Eren (Meren) meren

## gist:122505bee27838ef3ceda84515708802
https://www.dropbox.com/scl/fi/eg9rki2bld2u24bdjy542/PROTEIN-STRUCURES.pptx?rlkey=exrmkb6pfakunhsfqnokjawpm&dl=0

## anvi-ubuntu-setup.sh
#!/bin/bash

# save this file somewhere on your disk. open your terminal, and go there. then type these commands:
#
# chmod +x anvi-ubuntu-setup.sh
# ./anvi-ubuntu-setup.sh
#
# and then get some coffee, and come back to see whether it's your lucky day.

set -e

## anvi-script-gen-alluvial
#!/usr/bin/env python

# lousy script that works with the outputs of `anvi-export-collection`
# to reconcstruct the fate of contigs for a given algorithm and bin and
# spit out some text to be visualized on https://app.rawgraphs.io/

import sys

from collections import OrderedDict

## gist:f8debee8322f40c2ddde
#################################################################################
#
#           PREPARING RELEASE NOTES FOR A MAJOR RELEASE
#
#################################################################################

# if this is a major release,
# prepare a new logo.
# prepare comprehensive release notes. see examples for release notes here:
#     https://github.com/meren/anvio/releases

## simple_for_loop_for_mapping.sh
#!/bin/bash

# A simple loop to serially map all samples.
# referenced from within http://merenlab.org/tutorials/assembly_and_mapping/

# how many threads should each mapping task use?
NUM_THREADS=4

for sample in `awk '{print $1}' samples.txt`
do

## get_genes.py
from anvio.dbops import ContigsSuperclass

# if your args object contains a `contigs_db` entry in its
# namespace all you don't need the following two lines and
# you can directly pass it to the ContigsSuperclass.
import argparse
args = argparse.Namespace(contigs_db="INFANT-GUT-TUTORIAL/SPLITAH/E_facealis/CONTIGS.db")

# get an instance of the contigs super:
contigs_db = ContigsSuperclass(args)

## gff_parser.py
#!/usr/bin/env python

## Antti Karkman
## University of Gothenburg
## antti.karkman@gmail.com
## 2017

import gffutils
import argparse

## gen_primer_match_report.py
# run this script like this:
#
#           python gen_primer_match_report.py primers.txt sequences.txt
#
# it will generate a report file called `primer_matches_report.txt`
#
# example primers file (TAB-delimited, no spaces):
#
#           name	pair	direction	sequence
#           PolF	P1	F	TGCGAYCCSAARGCBGACTC

## demultiplex.py
import sys
import IlluminaUtils.lib.fastqlib as u
import IlluminaUtils.lib.fastalib as f
from IlluminaUtils.utils.helperfunctions import reverse_complement

# call this script like this:
#
# python demultiplex.py barcode_to_sample_name_file index_fastq_file quality_filtered_fasta_file
#
# expected file formats are shown below.

## 01-gen-nucmer-jobs.py
#!/usr/bin/env python

# you run this first:
#
#    python 01-gen-nucmer-jobs.py affiliations.txt MAGs_input_dir
#

import os
import sys
import anvio.fastalib as u
	#!/bin/bash

	# save this file somewhere on your disk. open your terminal, and go there. then type these commands:
	#
	# chmod +x anvi-ubuntu-setup.sh
	# ./anvi-ubuntu-setup.sh
	#
	# and then get some coffee, and come back to see whether it's your lucky day.

	set -e
	#!/usr/bin/env python

	# lousy script that works with the outputs of `anvi-export-collection`
	# to reconcstruct the fate of contigs for a given algorithm and bin and
	# spit out some text to be visualized on https://app.rawgraphs.io/

	import sys

	from collections import OrderedDict
	#################################################################################
	#
	# PREPARING RELEASE NOTES FOR A MAJOR RELEASE
	#
	#################################################################################

	# if this is a major release,
	# prepare a new logo.
	# prepare comprehensive release notes. see examples for release notes here:
	# https://github.com/meren/anvio/releases
	#!/bin/bash

	# A simple loop to serially map all samples.
	# referenced from within http://merenlab.org/tutorials/assembly_and_mapping/

	# how many threads should each mapping task use?
	NUM_THREADS=4

	for sample in `awk '{print $1}' samples.txt`
	do
	from anvio.dbops import ContigsSuperclass

	# if your args object contains a `contigs_db` entry in its
	# namespace all you don't need the following two lines and
	# you can directly pass it to the ContigsSuperclass.
	import argparse
	args = argparse.Namespace(contigs_db="INFANT-GUT-TUTORIAL/SPLITAH/E_facealis/CONTIGS.db")

	# get an instance of the contigs super:
	contigs_db = ContigsSuperclass(args)
	#!/usr/bin/env python

	## Antti Karkman
	## University of Gothenburg
	## antti.karkman@gmail.com
	## 2017

	import gffutils
	import argparse
	# run this script like this:
	#
	# python gen_primer_match_report.py primers.txt sequences.txt
	#
	# it will generate a report file called `primer_matches_report.txt`
	#
	# example primers file (TAB-delimited, no spaces):
	#
	# name pair direction sequence
	# PolF P1 F TGCGAYCCSAARGCBGACTC
	import sys
	import IlluminaUtils.lib.fastqlib as u
	import IlluminaUtils.lib.fastalib as f
	from IlluminaUtils.utils.helperfunctions import reverse_complement

	# call this script like this:
	#
	# python demultiplex.py barcode_to_sample_name_file index_fastq_file quality_filtered_fasta_file
	#
	# expected file formats are shown below.
	#!/usr/bin/env python

	# you run this first:
	#
	# python 01-gen-nucmer-jobs.py affiliations.txt MAGs_input_dir
	#

	import os
	import sys
	import anvio.fastalib as u