# %load_ext autoreload
# %autoreload 2

# # path2human = "/home/matteo/Projects/furious_fastas/4peaks/human.fasta"
# # path2human = "/Users/matteo/Projects/furious_fastas/test/human.fasta"

# from furious_fastas.download import download
# from furious_fastas.uniprot import uniprot_url

# human_raw = download(uniprot_url['human'])
# with open('/home/matteo/Projects/furious_fastas/data/tests/human_raw.fasta', 'w') as f:
# 	f.write(human_raw)


# from furious_fastas.parse import parse_uniprot_fastas
# from furious_fastas import UniprotFastas, NCBIgeneralFastas

# from pathlib import Path

# pp = Path("/Users/matteo/Projects/furious_fastas/")

# human = UniprotFastas()
# human.read(pp/"data/human_raw.fasta")
# rep_seq_prots = human.find_repeating_sequences()
# print(rep_seq_prots,
#       file = open(pp/"tests/multiple_proteins_same_sequence.txt", "a"))

# contaminants = UniprotFastas()
# contaminants.read(pp/"data/contaminants.fasta")

# human.append(contaminants)
# human = human.to_ncbi_general()
# human.add_reversed_fastas_for_plgs()
# human.write(pp/'data/human_gnl_reversed.fas')

# from furious_fastas.parse_conf_file import parse_conf

# # species to url
# s2u = list(parse_conf(pp/"tests/test_conf.txt"))

# from furious_fastas.update.peaks import update_peaks_fasta_db
# from furious_fastas.update.plgs import update_plgs_fasta_db
# # conts = [('contaminants', 'https://raw.githubusercontent.com/MatteoLacki/protein_contaminants/master/contaminants.fasta')]
# # db_path = pp/"tests/peaks/db"
# # update_peaks_fasta_db(db_path, conts)

# from pathlib import Path
# from furious_fastas.update.plgs import update_plgs_fasta_db

# pp = Path("/Users/matteo/Projects/furious_fastas/")
# conts = [('test1', 'https://raw.githubusercontent.com/MatteoLacki/protein_contaminants/master/contaminants.fasta'),
# 		 ('test2', 'https://raw.githubusercontent.com/MatteoLacki/protein_contaminants/master/contaminants.fasta')]
# db_path = pp/"tests/plgs/db"
# update_plgs_fasta_db(db_path, conts)




# from furious_fastas.contaminants import uniprot_contaminants
# from furious_fastas.fastas import UniprotFastas, NCBIgeneralFastas
# from furious_fastas.download import download
# from furious_fastas.parse.fastas import parse_uniprot_fastas

# uf == uf
# uf == uniprot_contaminants


# uf = UniprotFastas()
# uf.append(uniprot_contaminants)
# uf.append(uf)
# uf + uf

# uniprot_contaminants + uniprot_contaminants
# uniprot_contaminants.append(uniprot_contaminants)

# human = UniprotFastas()
# human_raw = download("http://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606&format=fasta")
# human.parse_raw(human_raw)


# human_uni = UniprotFastas()
# human_uni.read('/home/matteo/Projects/furious_fastas/data/human_raw.fasta')
# human_uni.append(uniprot_contaminants)
# human_gnl = human_uni.to_ncbi_general()

# human_gnl.write('/home/matteo/Projects/furious_fastas/data/human_raw_gnl.fasta')
# human_gnl = NCBIgeneralFastas()
# human_gnl.read('/home/matteo/Projects/furious_fastas/data/human_raw_gnl.fasta')
# human_gnl.add_reversed_fastas_for_plgs()
# human_gnl.write('/home/matteo/Projects/furious_fastas/data/human_gnl_reversed.fasta')