#! /usr/bin/env python import os import sys import argparse from Bio import SeqIO from pyutils import cleanup_id argparser = argparse.ArgumentParser(description=None) argparser.add_argument('input_file', nargs='?', type=argparse.FileType('r'), default=sys.stdin) argparser.add_argument('output_dir', nargs='?', default=os.getcwd()) args = argparser.parse_args() for record in SeqIO.parse(args.input_file, 'fasta'): output_file = os.path.join(args.output_dir, '%s.fasta' % cleanup_id(record.id)) with open(output_file, 'w') as op: print >> op, record.format('fasta')
#! /usr/bin/env python import os import sys import argparse from Bio import SeqIO from pyutils import cleanup_id argparser = argparse.ArgumentParser(description=None) argparser.add_argument('input_file',nargs='?',type=argparse.FileType('r'),default=sys.stdin) argparser.add_argument('output_dir',nargs='?',default=os.getcwd()) args = argparser.parse_args() for record in SeqIO.parse(args.input_file,'fasta'): output_file = os.path.join(args.output_dir,'%s.fasta' % cleanup_id(record.id)) with open(output_file,'w') as op: print >>op, record.format('fasta')
# Copyright 2014 Uri Laserson # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import os import argparse import vdj from pyutils import cleanup_id argparser = argparse.ArgumentParser(description=None) argparser.add_argument('input_file') argparser.add_argument('output_dir', default=os.getcwd()) args = argparser.parse_args() for chain in vdj.parse_imgt(args.input_file): output_file = os.path.join(args.output_dir, '%s.imgt' % cleanup_id(chain.id)) with open(output_file, 'w') as op: print >> op, chain
#! /usr/bin/env python # Copyright 2014 Uri Laserson # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import os import argparse import vdj from pyutils import cleanup_id argparser = argparse.ArgumentParser(description=None) argparser.add_argument('input_file') argparser.add_argument('output_dir',default=os.getcwd()) args = argparser.parse_args() for chain in vdj.parse_imgt(args.input_file): output_file = os.path.join(args.output_dir,'%s.imgt' % cleanup_id(chain.id)) with open(output_file,'w') as op: print >>op, chain
# # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import os import sys import argparse from Bio import SeqIO from pyutils import cleanup_id argparser = argparse.ArgumentParser(description=None) argparser.add_argument('input_file',nargs='?',type=argparse.FileType('r'),default=sys.stdin) argparser.add_argument('output_dir',nargs='?',default=os.getcwd()) args = argparser.parse_args() for record in SeqIO.parse(args.input_file,'fasta'): output_file = os.path.join(args.output_dir,'%s.fasta' % cleanup_id(record.id)) with open(output_file,'w') as op: print >>op, record.format('fasta')