<filename>bin/fasta_sort_by_abundance.py<gh_stars>1-10
#! /usr/bin/env python
# Copyright 2014 <NAME>
#
# 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 sys
import argparse
from collections import defaultdict

from seqtools import FastaIterator

argparser = argparse.ArgumentParser(description=None)
argparser.add_argument('input',nargs='?',type=argparse.FileType('r'),default=sys.stdin)
argparser.add_argument('output',nargs='?',type=argparse.FileType('w'),default=sys.stdout)
args = argparser.parse_args()

counts = defaultdict(list)
for (name,seq) in FastaIterator(args.input):
    counts[seq].append(name)

for seq in sorted(counts.keys(), key=lambda k: len(counts[k]), reverse=True):
    for name in counts[seq]:
        args.output.write(">%s\n%s\n" % (name,seq))

<filename>bin/fasta_sort_by_abundance.py<gh_stars>1-10
#! /usr/bin/env python
# Copyright 2014 <NAME>
#
# 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 sys
import argparse
from collections import defaultdict

from seqtools import FastaIterator

argparser = argparse.ArgumentParser(description=None)
argparser.add_argument('input',nargs='?',type=argparse.FileType('r'),default=sys.stdin)
argparser.add_argument('output',nargs='?',type=argparse.FileType('w'),default=sys.stdout)
args = argparser.parse_args()

counts = defaultdict(list)
for (name,seq) in FastaIterator(args.input):
    counts[seq].append(name)

for seq in sorted(counts.keys(), key=lambda k: len(counts[k]), reverse=True):
    for name in counts[seq]:
        args.output.write(">%s\n%s\n" % (name,seq))

#! /usr/bin/env python # Copyright 2014 <NAME> # # 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.