/
deblur_rename_seqs.py
executable file
·195 lines (149 loc) · 6.96 KB
/
deblur_rename_seqs.py
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#!/usr/bin/env python
"""
Reformats a deblurred OTU table with anonymous OTU identifiers (otu1-otuX),
storing the sequence information as OTU metadata.
Also optionally outputs a FASTA file of the sequences.
"""
from __future__ import print_function
import sys
import os
import argparse
import unittest
from biom import Table, load_table
from biom.parse import biom_open
import numpy as np
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-i', '--input_biom_fp',
type=str,
help='path to deblur biom to be modified')
parser.add_argument('-o', '--output_biom_fp',
type=str,
help='path stub for output fastqs; will add ".renamed.biom" (default: biom file basename)')
parser.add_argument('-f', '--output_fasta_fp',
type=str,
help='path stub for output fastqs (default: none)')
parser.add_argument('-m', '--metadata_name',
type=str, default='deblurred_seq',
help='name to use for sequence metadata category (default: %(default)s)')
parser.add_argument('-n', '--name_stub',
type=str, default='deblur',
help='name to use for sequence headers (default: %(default)s)')
parser.add_argument('-t', '--test',
action='store_true',
help='run unittest')
class TestRename(unittest.TestCase):
def test_rename_deblur_biom(self):
input_biom = Table(np.array([[0,0,2],[0,1,3],[3,2,0]]),
['AAATC','CTTGG','ATCCG'],
['sample1','sample2','sample3'],
table_id = 'test')
exp = Table(np.array([[0,0,2],[0,1,3],[3,2,0]]),
['deblur0','deblur1','deblur2'],
['sample1','sample2','sample3'],
[{'deblurred_seq': 'AAATC'},
{'deblurred_seq': 'CTTGG'},
{'deblurred_seq': 'ATCCG'}],
table_id = 'test renamed')
obs = rename_deblur_biom(input_biom,
name_stub='deblur',
metadata_name='deblurred_seq')
self.assertEqual(exp, obs)
def test_format_seqs_from_deblur_biom(self):
input_biom_1 = Table(np.array([[0,0,2],[0,1,3],[3,2,0]]),
['AAATC','CTTGG','ATCCG'],
['sample1','sample2','sample3'],
table_id = 'test')
input_biom_2 = Table(np.array([[0,0,2],[0,1,3],[3,2,0]]),
['deblur0','deblur1','deblur2'],
['sample1','sample2','sample3'],
[{'deblurred_seq': 'AAATC'},
{'deblurred_seq': 'CTTGG'},
{'deblurred_seq': 'ATCCG'}],
table_id = 'test renamed')
input_biom_3 = Table(np.array([[0,0,2],[0,1,3],[3,2,0]]),
['deblur0','deblur1','deblur2'],
['sample1','sample2','sample3'],
[{'seq': 'AAATC'},
{'seq': 'CTTGG'},
{'seq': 'ATCCG'}],
table_id = 'test renamed')
obs1 = format_seqs_from_deblur_biom(input_biom_1, name_stub='deblur')
obs2 = format_seqs_from_deblur_biom(input_biom_2, metadata_name='deblurred_seq')
obs3 = format_seqs_from_deblur_biom(input_biom_1)
exp1 = '>deblur0\nAAATC\n>deblur1\nCTTGG\n>deblur2\nATCCG'
exp2 = '>AAATC\nAAATC\n>CTTGG\nCTTGG\n>ATCCG\nATCCG'
self.assertEqual(exp1,obs1)
self.assertEqual(exp1,obs2)
self.assertEqual(exp2,obs3)
self.assertRaises(TypeError, format_seqs_from_deblur_biom,
input_biom_1, metadata_name='deblurred_seq')
self.assertRaises(KeyError, format_seqs_from_deblur_biom,
input_biom_3, metadata_name='deblurred_seq')
def run_unittests():
TestRename('test_rename_deblur_biom').test_rename_deblur_biom()
TestRename('test_format_seqs_from_deblur_biom').test_format_seqs_from_deblur_biom()
# def write_anonymous_fasta(seqs, output_fp, name_stub='seq'):
# with open(output_fp, 'w') as f:
# i = 0
# seqnames = [] * len(seqs)
# for seq in seqs:
# seqname = name_stub + str(i)
# seqnames[i] = seqnames
# f.write('>{0}\n{1}\n'.format(seqname, seq))
# return(seqnames)
def rename_deblur_biom(biom, name_stub='deblur', metadata_name='deblurred_seq'):
seqs = biom.ids(axis='observation')
seqnames = ['{0}{1}'.format(name_stub, x) for x in range(len(seqs))]
seq_metadata = {seqname: {metadata_name: seq} for seq, seqname in zip(seqs, seqnames)}
renamed_biom = Table(biom.matrix_data,
seqnames,
biom.ids(axis='sample'),
biom.metadata(axis='observation'),
biom.metadata(axis='sample'),
table_id = biom.table_id + ' renamed')
renamed_biom.add_metadata(seq_metadata, axis='observation')
return(renamed_biom)
def format_seqs_from_deblur_biom(biom, name_stub=None, metadata_name=None):
if name_stub is None and metadata_name is None:
seqs = biom.ids(axis='observation')
seqnames = seqs
elif metadata_name is not None:
try:
observ_metadata = biom.metadata(axis='observation')
seqs = [dict(x)[metadata_name] for x in observ_metadata]
seqnames = biom.ids(axis='observation')
except KeyError as e:
#print('Supplied metadata category not present')
raise e
except TypeError as e:
#print('No supplied observation metadata')
raise e
else:
seqs = biom.ids(axis='observation')
seqnames = ['{0}{1}'.format(name_stub, x) for x in range(len(seqs))]
fasta = '\n'.join(['>{0}\n{1}'.format(seqname, seq) for seqname, seq in zip(seqnames, seqs)])
return(fasta)
def main():
args = parser.parse_args()
input_biom_fp = args.input_biom_fp
output_biom_fp = args.output_biom_fp
output_fasta_fp = args.output_fasta_fp
metadata_name = args.metadata_name
name_stub = args.name_stub
test = args.test
if test:
run_unittests()
return(0)
deblur_biom = load_table(input_biom_fp)
if output_biom_fp is None:
output_biom_fp = os.path.splitext(input_biom_fp)[0] + '.renamed.biom'
output_biom = rename_deblur_biom(deblur_biom, name_stub=name_stub, metadata_name=metadata_name)
if output_fasta_fp is not None:
fasta = format_seqs_from_deblur_biom(output_biom, metadata_name=metadata_name)
with open(output_fasta_fp, 'w') as f:
f.write(fasta)
with biom_open(output_biom_fp, 'w') as f:
output_biom.to_hdf5(f, 'deblur_relabel_merged.py')
if __name__ == "__main__":
main()