<filename>metawibele/common/prepare_uniprot_annotation.py
#!/usr/bin/env python

"""
MetaWIBELE: prepare_uniprot_annotation module
Extract the annotation from UniProt data file

Copyright (c) 2019 Harvard School of Public Health

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import sys
import os
import re
import argparse

try:
	from metawibele.common import utils
	from metawibele import config
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
			" Please check your install.")


#==============================================================
# Download the latest version of uniprot dat file
#==============================================================
def download_dat (output_path):
	dat_file = os.path.join(output_path, "uniprot.dat.gz")
	if os.path.isfile(dat_file):
		config.logger.info ("WARNING! Already exist file and skip this step: " + dat_file)
		return dat_file

	os.chdir(output_path)
	download_cmd = "connect ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/"
	download_cmd = download_cmd + "\n" + "get reldate.txt"
	download_cmd = download_cmd + "\n" + "get uniprot_sprot.dat.gz"
	download_cmd = download_cmd + "\n" + "get uniprot_trembl.dat.gz"
	mydownload = os.path.join(output_path, "download_uniref.lftp")
	open_out = open(mydownload, "w")
	open_out.write(download_cmd + "\n")
	open_out.close()
	os.system("lftp -f " + mydownload)

	# combine Swiss-Prot and TrEMBLE data
	combine_cmd = "less uniprot_sprot.dat.gz > uniprot.dat"
	combine_cmd = combine_cmd + "; less uniprot_trembl.dat.gz >> uniprot.dat"
	combine_cmd = combine_cmd + "; gzip uniprot.dat"
	os.system(combine_cmd)

	return dat_file


#==============================================================
# Extract annotation info
#==============================================================
def extract_annotation_info (datfile, output_path):
	title = "Entry\tEntry name\tGene names\tProtein names\tOrganism\tNCBI_TaxID\tLength\tGene ontology (biological process)\tGene ontology (molecular function)\tGene ontology (cellular component)\tCross-reference (KEGG)\tCross-reference (KO)\tCOG\tInterpro\tTaxonomic lineage (ALL)\tSubcellular location [CC]\tTransmembrane\tSignal peptide\tCross-reference (Pfam)"
	outfile = os.path.join(output_path, "uniprot_annotation.tsv")
	outfile1 = os.path.join(output_path, "uniprot_annotation.tsv.gz")
	if not os.path.isfile(datfile):
		sys.exit("Error: please download the uniprot dat file!")
	if os.path.isfile(outfile) and not os.path.isfile(outfile1):
		os.system("gzip " + outfile)
		config.logger.info ("WARNING! Already exist file and skip this step: " + outfile1)
		return outfile1
	if os.path.isfile(outfile1):
		config.logger.info ("WARNING! Already exist file and skip this step: " + outfile1)
		return outfile1
	open_out = open(outfile, "w")
	open_out.write(title + "\n")
	entry = "NA"
	entry_name = "NA"
	prot_name = "NA"
	gene_name = "NA"
	organism = "NA"
	taxa = "NA"
	length = "NA"
	go_bp = "NA"
	go_mf = "NA"
	go_cc = "NA"
	kegg = "NA"
	ko = "NA"
	cog = "NA"
	interpro = "NA"
	tax = "NA"
	sub = "NA"
	trans = "NA"
	signal = "NA"
	pfam = "NA"
	for line in utils.gzip_bzip2_biom_open_readlines (datfile):
		line = line.strip()
		if not len(line):
			continue
		if line == "//": # end of one entry
			# output info
			if entry != "NA":
				tax = tax + ";" + organism
				open_out.write(entry + "\t" + entry_name + "\t" + gene_name + "\t" + prot_name + "\t" + organism + "\t" + taxa + "\t" + length + "\t" + go_bp + "\t" + go_mf + "\t" + go_cc + "\t" + kegg + "\t" + ko + "\t" + cog + "\t" + interpro+ "\t" + tax + "\t" + sub + "\t" + trans + "\t" + signal + "\t" + pfam + "\n")
			entry = "NA"
			entry_name = "NA"
			prot_name = "NA"
			gene_name = "NA"
			organism = "NA"
			taxa = "NA"
			length = "NA"
			go_bp = "NA"
			go_mf = "NA"
			go_cc = "NA"
			kegg = "NA"
			ko = "NA"
			cog = "NA"
			interpro = "NA"
			tax = "NA"
			sub = "NA"
			trans = "NA"
			signal = "NA"
			pfam = "NA"
			continue
		if re.search("^ID\s+", line): # entry name
			mym = re.search("^ID\s+([\S]+)\s+[\s\S]+\s+([\d]+)\s+AA", line)
			entry_name = mym.group(1)
			length = mym.group(2)
			continue
		if re.search("^AC\s+", line): # entry
			mym = re.search("AC\s+([\S]+)", line)
			entry = mym.group(1)
			entry = re.sub(";$", "", entry)
			continue
		if re.search("^GN\s+", line): # entry
			mym = re.search("GN\s+([\S]+[\s\S]+)", line)
			gene_tmp = mym.group(1)
			gene_tmp = re.sub("\s+", "", gene_tmp)
			tmps = gene_tmp.split(";")
			gene_name_tmp = ""
			for tmp in tmps:
				if re.search("\=([^\=]+)", tmp):
					mym = re.search("\=([^\=]+)", tmp)
					gene_name_tmp = gene_name_tmp + mym.group(1) + ";"
			gene_name_tmp = re.sub(";$", "", gene_name_tmp)
			if gene_name == "NA":
				gene_name = gene_name_tmp 
			else:
				gene_name = gene_name + ";" + gene_name_tmp
			continue
		if re.search("^DE\s+[\s\S]+Full\=([\S\s]+)", line): # protein name
			mym = re.search("^DE\s+[\s\S]+Full\=([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub(";$", "", mydec)
			if prot_name == "NA":
				prot_name = mydec
			else:
				prot_name = prot_name + ";" + mydec
			continue
		if re.search("^OS\s+", line): # organism
			mym = re.search("^OS\s+([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub("\.$", "", mydec)
			if organism == "NA":
				organism = mydec
			else:
				organism = organism + ";" + mydec
			continue
		if re.search("^OX\s+", line): # NCBI taxonomy ID
			mym = re.search("^OX\s+NCBI_TaxID=([\d]+)", line)
			taxa_info = mym.group(1)
			taxa_info = re.sub(";$", "", taxa_info)
			if taxa == "NA":
				taxa = taxa_info
			else:
				taxa = taxa + ";" + taxa_info
			continue
		if re.search("^OC\s+", line): # taxonomy lineage
			mym = re.search("^OC\s+([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub("\.$", "", mydec)
			mydec = re.sub(";$", "", mydec)
			if tax == "NA":
				tax = mydec
			else:
				tax = tax + ";" + mydec
			continue
		if re.search("^DR\s+KEGG;", line): # KEGG annotation
			mym = re.search("^DR\s+(KEGG;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			kegg_tmp = tmp[1]
			if kegg == "NA":
				kegg = kegg_tmp
			else:
				kegg = kegg + ";" + kegg_tmp
			continue
		if re.search("^DR\s+KO;", line): # KO annotation
			mym = re.search("^DR\s+(KO;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			ko_tmp = tmp[1]
			if ko == "NA":
				ko = ko_tmp
			else:
				ko = ko + ";" + ko_tmp
			continue
		if re.search("^DR\s+eggNOG;", line): # COG annotation
			mym = re.search("^DR\s+(eggNOG;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			cog_tmp = tmp[1]
			if cog == "NA":
				cog = cog_tmp
			else:
				cog = cog + ";" + cog_tmp
			continue
		if re.search("^DR\s+InterPro;", line): # InterPro annotation
			mym = re.search("^DR\s+(InterPro;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			inter_tmp = tmp[1]
			if interpro == "NA":
				interpro = inter_tmp
			else:
				interpro = interpro + ";" + inter_tmp
			continue
		if re.search("^DR\s+GO;", line): # GO annotation
			mym = re.search("^DR\s+(GO;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			go = tmp[1]
			go_info = tmp[2]
			if re.search("^P:", go_info):
				go_info = re.sub("^P:", "", go_info)
				if go_bp == "NA":
					go_bp = go_info + " [" + go + "]"
				else:
					go_bp = go_bp + ";" + go_info + " [" + go + "]"
			if re.search("^F:", go_info):
				go_info = re.sub("^F:", "", go_info)
				if go_mf == "NA":
					go_mf = go_info + " [" + go + "]"
				else:
					go_mf = go_mf + ";" + go_info + " [" + go + "]"
			if re.search("^C:", go_info):
				go_info = re.sub("^C:", "", go_info)
				if go_cc == "NA":
					go_cc = go_info + " [" + go + "]"
				else:
					go_cc = go_cc + ";" + go_info + " [" + go + "]"
			continue
		if re.search("^DR\s+Pfam;", line): # GO annotation
			mym = re.search("^DR\s+(Pfam;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			pfam_info = tmp[1]
			if pfam == "NA":
				pfam = pfam_info
			else:
				pfam = pfam + ";" + pfam_info
			continue
		if re.search("^CC\s+", line): # CC info
			if re.search("^CC\s+\-\!\-\s+SUBCELLULAR\s+LOCATION", line): # Subcellular
				mym = re.search("^CC\s+\-\!\-\s+SUBCELLULAR\s+LOCATION\s*([\s\S]+)", line)
				myflag = 1
				mydec = mym.group(1)
				if sub == "NA":
					sub = "SUBCELLULAR LOCATION" + mydec
				else:
					sub = sub + ";" + "SUBCELLULAR LOCATION" + mydec
			elif re.search("^CC\s+\-\!\-", line):	# not subcellular
				myflag = 0
			else:
				if myflag == 1:
					mym = re.search("^CC\s+(\S+[\s\S]+)", line)
					mydec = mym.group(1)
					mydec = re.sub("\.$", "", mydec)
					sub = sub + " " + mydec
			continue
		if re.search("^FT\s+", line): # FT info
			if re.search("^FT\s+TRANSMEM\s+", line): # transmembrane
				transflag = 1
				signalflag = 0
				if trans == "NA":
					trans = "TRANSMEM"
				else:
					trans = trans + ";" + "TRANSMEM"
			if re.search("^FT\s+SIGNAL\s+", line):	# signal
				signalflag = 1
				transflag = 0
				if signal == "NA":
					signal = "SIGNAL"
				else:
					signal = signal + ";" + "SIGNAL"
			continue
		# FT info
	# foreach line
	# last entry
	tax = tax + ";" + organism
	open_out.write(entry + "\t" + entry_name + "\t" + prot_name + "\t" + organism + "\t" + taxa + "\t" + length + "\t" + go_bp + "\t" + go_mf + "\t" + go_cc + "\t" + kegg + "\t" + ko + "\t" + interpro + "\t" + cog + "\t" + tax + "\t" + sub + "\t" + trans + "\t" + signal + "\t" + pfam + "\n")
	open_out.close()

	os.system("gzip " + outfile)
# extract_annotation_info


#==============================================================
###########  Main processing ############
#==============================================================
def main():

	### get arguments ###
	parser=argparse.ArgumentParser()
	parser.add_argument('-o', "--output", 
						help='output folder for uniprot annotation info', 
						required=True)
	values=parser.parse_args()

	config.logger.info ("### Start prepare_uniprot_annotation step ####")
	
	output = os.path.abspath(values.output)
	if not os.path.isdir(output):
		os.system("mkdir -p " + output)

	### Extraction ###
	config.logger.info ("Download uniprot info......starting")
	datfile = download_dat (output)
	config.logger.info ("Download uniprot info......done")

	config.logger.info ("Extract uniprot info......starting")
	extract_annotation_info (datfile, output)
	config.logger.info ("Extract uniprot info......done")
	
	config.logger.info ("### Finish prepare_uniprot_annotation step ####")

# end: main

if __name__ == '__main__':
	main()

<filename>metawibele/common/prepare_uniprot_annotation.py
#!/usr/bin/env python

"""
MetaWIBELE: prepare_uniprot_annotation module
Extract the annotation from UniProt data file

Copyright (c) 2019 Harvard School of Public Health

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

import sys
import os
import re
import argparse

try:
	from metawibele.common import utils
	from metawibele import config
except ImportError:
	sys.exit("CRITICAL ERROR: Unable to find the MetaWIBELE python package." +
			" Please check your install.")


#==============================================================
# Download the latest version of uniprot dat file
#==============================================================
def download_dat (output_path):
	dat_file = os.path.join(output_path, "uniprot.dat.gz")
	if os.path.isfile(dat_file):
		config.logger.info ("WARNING! Already exist file and skip this step: " + dat_file)
		return dat_file

	os.chdir(output_path)
	download_cmd = "connect ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/"
	download_cmd = download_cmd + "\n" + "get reldate.txt"
	download_cmd = download_cmd + "\n" + "get uniprot_sprot.dat.gz"
	download_cmd = download_cmd + "\n" + "get uniprot_trembl.dat.gz"
	mydownload = os.path.join(output_path, "download_uniref.lftp")
	open_out = open(mydownload, "w")
	open_out.write(download_cmd + "\n")
	open_out.close()
	os.system("lftp -f " + mydownload)

	# combine Swiss-Prot and TrEMBLE data
	combine_cmd = "less uniprot_sprot.dat.gz > uniprot.dat"
	combine_cmd = combine_cmd + "; less uniprot_trembl.dat.gz >> uniprot.dat"
	combine_cmd = combine_cmd + "; gzip uniprot.dat"
	os.system(combine_cmd)

	return dat_file


#==============================================================
# Extract annotation info
#==============================================================
def extract_annotation_info (datfile, output_path):
	title = "Entry\tEntry name\tGene names\tProtein names\tOrganism\tNCBI_TaxID\tLength\tGene ontology (biological process)\tGene ontology (molecular function)\tGene ontology (cellular component)\tCross-reference (KEGG)\tCross-reference (KO)\tCOG\tInterpro\tTaxonomic lineage (ALL)\tSubcellular location [CC]\tTransmembrane\tSignal peptide\tCross-reference (Pfam)"
	outfile = os.path.join(output_path, "uniprot_annotation.tsv")
	outfile1 = os.path.join(output_path, "uniprot_annotation.tsv.gz")
	if not os.path.isfile(datfile):
		sys.exit("Error: please download the uniprot dat file!")
	if os.path.isfile(outfile) and not os.path.isfile(outfile1):
		os.system("gzip " + outfile)
		config.logger.info ("WARNING! Already exist file and skip this step: " + outfile1)
		return outfile1
	if os.path.isfile(outfile1):
		config.logger.info ("WARNING! Already exist file and skip this step: " + outfile1)
		return outfile1
	open_out = open(outfile, "w")
	open_out.write(title + "\n")
	entry = "NA"
	entry_name = "NA"
	prot_name = "NA"
	gene_name = "NA"
	organism = "NA"
	taxa = "NA"
	length = "NA"
	go_bp = "NA"
	go_mf = "NA"
	go_cc = "NA"
	kegg = "NA"
	ko = "NA"
	cog = "NA"
	interpro = "NA"
	tax = "NA"
	sub = "NA"
	trans = "NA"
	signal = "NA"
	pfam = "NA"
	for line in utils.gzip_bzip2_biom_open_readlines (datfile):
		line = line.strip()
		if not len(line):
			continue
		if line == "//": # end of one entry
			# output info
			if entry != "NA":
				tax = tax + ";" + organism
				open_out.write(entry + "\t" + entry_name + "\t" + gene_name + "\t" + prot_name + "\t" + organism + "\t" + taxa + "\t" + length + "\t" + go_bp + "\t" + go_mf + "\t" + go_cc + "\t" + kegg + "\t" + ko + "\t" + cog + "\t" + interpro+ "\t" + tax + "\t" + sub + "\t" + trans + "\t" + signal + "\t" + pfam + "\n")
			entry = "NA"
			entry_name = "NA"
			prot_name = "NA"
			gene_name = "NA"
			organism = "NA"
			taxa = "NA"
			length = "NA"
			go_bp = "NA"
			go_mf = "NA"
			go_cc = "NA"
			kegg = "NA"
			ko = "NA"
			cog = "NA"
			interpro = "NA"
			tax = "NA"
			sub = "NA"
			trans = "NA"
			signal = "NA"
			pfam = "NA"
			continue
		if re.search("^ID\s+", line): # entry name
			mym = re.search("^ID\s+([\S]+)\s+[\s\S]+\s+([\d]+)\s+AA", line)
			entry_name = mym.group(1)
			length = mym.group(2)
			continue
		if re.search("^AC\s+", line): # entry
			mym = re.search("AC\s+([\S]+)", line)
			entry = mym.group(1)
			entry = re.sub(";$", "", entry)
			continue
		if re.search("^GN\s+", line): # entry
			mym = re.search("GN\s+([\S]+[\s\S]+)", line)
			gene_tmp = mym.group(1)
			gene_tmp = re.sub("\s+", "", gene_tmp)
			tmps = gene_tmp.split(";")
			gene_name_tmp = ""
			for tmp in tmps:
				if re.search("\=([^\=]+)", tmp):
					mym = re.search("\=([^\=]+)", tmp)
					gene_name_tmp = gene_name_tmp + mym.group(1) + ";"
			gene_name_tmp = re.sub(";$", "", gene_name_tmp)
			if gene_name == "NA":
				gene_name = gene_name_tmp 
			else:
				gene_name = gene_name + ";" + gene_name_tmp
			continue
		if re.search("^DE\s+[\s\S]+Full\=([\S\s]+)", line): # protein name
			mym = re.search("^DE\s+[\s\S]+Full\=([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub(";$", "", mydec)
			if prot_name == "NA":
				prot_name = mydec
			else:
				prot_name = prot_name + ";" + mydec
			continue
		if re.search("^OS\s+", line): # organism
			mym = re.search("^OS\s+([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub("\.$", "", mydec)
			if organism == "NA":
				organism = mydec
			else:
				organism = organism + ";" + mydec
			continue
		if re.search("^OX\s+", line): # NCBI taxonomy ID
			mym = re.search("^OX\s+NCBI_TaxID=([\d]+)", line)
			taxa_info = mym.group(1)
			taxa_info = re.sub(";$", "", taxa_info)
			if taxa == "NA":
				taxa = taxa_info
			else:
				taxa = taxa + ";" + taxa_info
			continue
		if re.search("^OC\s+", line): # taxonomy lineage
			mym = re.search("^OC\s+([\S\s]+)", line)
			mydec = mym.group(1)
			mydec = re.sub("\.$", "", mydec)
			mydec = re.sub(";$", "", mydec)
			if tax == "NA":
				tax = mydec
			else:
				tax = tax + ";" + mydec
			continue
		if re.search("^DR\s+KEGG;", line): # KEGG annotation
			mym = re.search("^DR\s+(KEGG;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			kegg_tmp = tmp[1]
			if kegg == "NA":
				kegg = kegg_tmp
			else:
				kegg = kegg + ";" + kegg_tmp
			continue
		if re.search("^DR\s+KO;", line): # KO annotation
			mym = re.search("^DR\s+(KO;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			ko_tmp = tmp[1]
			if ko == "NA":
				ko = ko_tmp
			else:
				ko = ko + ";" + ko_tmp
			continue
		if re.search("^DR\s+eggNOG;", line): # COG annotation
			mym = re.search("^DR\s+(eggNOG;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			cog_tmp = tmp[1]
			if cog == "NA":
				cog = cog_tmp
			else:
				cog = cog + ";" + cog_tmp
			continue
		if re.search("^DR\s+InterPro;", line): # InterPro annotation
			mym = re.search("^DR\s+(InterPro;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			inter_tmp = tmp[1]
			if interpro == "NA":
				interpro = inter_tmp
			else:
				interpro = interpro + ";" + inter_tmp
			continue
		if re.search("^DR\s+GO;", line): # GO annotation
			mym = re.search("^DR\s+(GO;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			go = tmp[1]
			go_info = tmp[2]
			if re.search("^P:", go_info):
				go_info = re.sub("^P:", "", go_info)
				if go_bp == "NA":
					go_bp = go_info + " [" + go + "]"
				else:
					go_bp = go_bp + ";" + go_info + " [" + go + "]"
			if re.search("^F:", go_info):
				go_info = re.sub("^F:", "", go_info)
				if go_mf == "NA":
					go_mf = go_info + " [" + go + "]"
				else:
					go_mf = go_mf + ";" + go_info + " [" + go + "]"
			if re.search("^C:", go_info):
				go_info = re.sub("^C:", "", go_info)
				if go_cc == "NA":
					go_cc = go_info + " [" + go + "]"
				else:
					go_cc = go_cc + ";" + go_info + " [" + go + "]"
			continue
		if re.search("^DR\s+Pfam;", line): # GO annotation
			mym = re.search("^DR\s+(Pfam;[\S\s]+)", line)
			mydec = mym.group(1)
			tmp = mydec.split("; ")
			pfam_info = tmp[1]
			if pfam == "NA":
				pfam = pfam_info
			else:
				pfam = pfam + ";" + pfam_info
			continue
		if re.search("^CC\s+", line): # CC info
			if re.search("^CC\s+\-\!\-\s+SUBCELLULAR\s+LOCATION", line): # Subcellular
				mym = re.search("^CC\s+\-\!\-\s+SUBCELLULAR\s+LOCATION\s*([\s\S]+)", line)
				myflag = 1
				mydec = mym.group(1)
				if sub == "NA":
					sub = "SUBCELLULAR LOCATION" + mydec
				else:
					sub = sub + ";" + "SUBCELLULAR LOCATION" + mydec
			elif re.search("^CC\s+\-\!\-", line):	# not subcellular
				myflag = 0
			else:
				if myflag == 1:
					mym = re.search("^CC\s+(\S+[\s\S]+)", line)
					mydec = mym.group(1)
					mydec = re.sub("\.$", "", mydec)
					sub = sub + " " + mydec
			continue
		if re.search("^FT\s+", line): # FT info
			if re.search("^FT\s+TRANSMEM\s+", line): # transmembrane
				transflag = 1
				signalflag = 0
				if trans == "NA":
					trans = "TRANSMEM"
				else:
					trans = trans + ";" + "TRANSMEM"
			if re.search("^FT\s+SIGNAL\s+", line):	# signal
				signalflag = 1
				transflag = 0
				if signal == "NA":
					signal = "SIGNAL"
				else:
					signal = signal + ";" + "SIGNAL"
			continue
		# FT info
	# foreach line
	# last entry
	tax = tax + ";" + organism
	open_out.write(entry + "\t" + entry_name + "\t" + prot_name + "\t" + organism + "\t" + taxa + "\t" + length + "\t" + go_bp + "\t" + go_mf + "\t" + go_cc + "\t" + kegg + "\t" + ko + "\t" + interpro + "\t" + cog + "\t" + tax + "\t" + sub + "\t" + trans + "\t" + signal + "\t" + pfam + "\n")
	open_out.close()

	os.system("gzip " + outfile)
# extract_annotation_info


#==============================================================
###########  Main processing ############
#==============================================================
def main():

	### get arguments ###
	parser=argparse.ArgumentParser()
	parser.add_argument('-o', "--output", 
						help='output folder for uniprot annotation info', 
						required=True)
	values=parser.parse_args()

	config.logger.info ("### Start prepare_uniprot_annotation step ####")
	
	output = os.path.abspath(values.output)
	if not os.path.isdir(output):
		os.system("mkdir -p " + output)

	### Extraction ###
	config.logger.info ("Download uniprot info......starting")
	datfile = download_dat (output)
	config.logger.info ("Download uniprot info......done")

	config.logger.info ("Extract uniprot info......starting")
	extract_annotation_info (datfile, output)
	config.logger.info ("Extract uniprot info......done")
	
	config.logger.info ("### Finish prepare_uniprot_annotation step ####")

# end: main

if __name__ == '__main__':
	main()

#!/usr/bin/env python MetaWIBELE: prepare_uniprot_annotation module Extract the annotation from UniProt data file  Copyright (c) 2019 Harvard School of Public Health  Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. #============================================================== # Download the latest version of uniprot dat file #============================================================== # combine Swiss-Prot and TrEMBLE data #============================================================== # Extract annotation info #============================================================== # end of one entry # output info # entry name # entry # entry # protein name # organism # NCBI taxonomy ID # taxonomy lineage # KEGG annotation # KO annotation # COG annotation # InterPro annotation # GO annotation # GO annotation # CC info # Subcellular # not subcellular # FT info # transmembrane # signal # FT info # foreach line # last entry # extract_annotation_info #============================================================== ###########  Main processing ############ #============================================================== ### get arguments ### ## Start prepare_uniprot_annotation step ####") ### Extraction ### ## Finish prepare_uniprot_annotation step ####") # end: main