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trying in fixing unused imports
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@fasnicar
fasnicar committed May 29, 2018
1 parent 7fff2eb commit ccdff94
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Showing 11 changed files with 187 additions and 187 deletions.
6 changes: 3 additions & 3 deletions strainphlan.py
View file
Expand Up @@ -35,9 +35,9 @@
import pandas
import logging
import logging.config
import sample2markers
import copy
import threading
# import sample2markers
# import copy
# import threading
import numpy
import random
import gc
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26 changes: 13 additions & 13 deletions strainphlan_src/add_metadata_tree.py
View file
Expand Up @@ -3,28 +3,28 @@
# at CIBIO, University of Trento, Italy


import sys
import os
# import sys
# import os
import argparse as ap
import pandas
import copy
import ConfigParser
# import copy
# import ConfigParser
import dendropy
import numpy
# import numpy
# import ipdb


def read_params():
p = ap.ArgumentParser()
p.add_argument('--ifn_trees', nargs='+', required=True, default=None, type=str)
p.add_argument('--ifn_metadatas', nargs='+', required=True, default=None, type=str)
p.add_argument('--string_to_remove',
p.add_argument('--string_to_remove',
required=False, default='', type=str,
help='string to be removed in the tree node names')
p.add_argument(
'--metadatas',
nargs='+',
required=False,
'--metadatas',
nargs='+',
required=False,
default=['all'],
type=str,
help='The metadata fields that you want to add. '\
Expand Down Expand Up @@ -52,9 +52,9 @@ def main(args):
index_col = get_index_col(ifn)
df = pandas.read_csv(
ifn,
sep='\t',
sep='\t',
dtype=unicode,
header=0,
header=0,
index_col=index_col)
df = df.transpose()
df_list.append(df)
Expand All @@ -73,8 +73,8 @@ def main(args):
sample = node.get_node_str().strip("'")
sample = sample.replace(' ', '_')
sample = sample.replace(args['string_to_remove'], '')
prefixes = [prefix for prefix in
['k__', 'p__', 'c__', 'o__',
prefixes = [prefix for prefix in
['k__', 'p__', 'c__', 'o__',
'f__', 'g__', 's__'] \
if prefix in sample]

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48 changes: 24 additions & 24 deletions strainphlan_src/build_tree_single_strain.py
View file
Expand Up @@ -6,9 +6,9 @@
__version__ = '0.1'
__date__ = '17 Sep 2015'

import sys
# import sys
import os
import argparse
import argparse
import numpy
from Bio import SeqIO
import glob
Expand All @@ -17,34 +17,34 @@
def read_params():
p = argparse.ArgumentParser()
p.add_argument(
'--ifn_alignments',
'--ifn_alignments',
nargs='+',
required=True,
default=None,
required=True,
default=None,
type=str,
help='The alignment file.')
p.add_argument(
'--log_ofn',
required=True,
default=None,
'--log_ofn',
required=True,
default=None,
type=str,
help='The log file.')
p.add_argument(
'--nprocs',
required=True,
default=None,
'--nprocs',
required=True,
default=None,
type=int,
help='Number of processors.')
p.add_argument(
'--bootstrap_raxml',
required=False,
default=0,
'--bootstrap_raxml',
required=False,
default=0,
type=int,
help='The number of runs for bootstraping when building the tree. '\
'Default 0.')
p.add_argument(
'--verbose',
required=False,
'--verbose',
required=False,
dest='quiet',
action='store_false',
help='Show all information. Default "not set".')
Expand Down Expand Up @@ -84,15 +84,15 @@ def main(args):

if len(sample2polrate):
log_line = '%s\t%d\t%d\t%f\n'%\
(os.path.basename(ifn_polymorphic).replace('.polymorphic', ''),
len(singles),
len(sample2polrate),
(os.path.basename(ifn_polymorphic).replace('.polymorphic', ''),
len(singles),
len(sample2polrate),
float(len(singles)) / len(sample2polrate))
else:
log_line = '%s\t%d\t%d\t%f\n'%\
(os.path.basename(ifn_polymorphic).replace('.polymorphic', ''),
len(singles),
len(sample2polrate),
(os.path.basename(ifn_polymorphic).replace('.polymorphic', ''),
len(singles),
len(sample2polrate),
0)
lfile.write(log_line)

Expand All @@ -116,7 +116,7 @@ def main(args):
cmd += '-N %d '%(args.bootstrap_raxml)
cmd += '-s %s '%os.path.abspath(ifn_alignment2)
cmd += '-w %s '%os.path.abspath(os.path.dirname(ifn_alignment2))
cmd += '-n %s '%output_suffix
cmd += '-n %s '%output_suffix
cmd += '-p 1234 '
else:
cmd = 'raxmlHPC-PTHREADS-SSE3 '
Expand All @@ -136,7 +136,7 @@ def main(args):
'''
run(cmd)
lfile.close()




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36 changes: 18 additions & 18 deletions strainphlan_src/compute_distance.py
View file
Expand Up @@ -15,17 +15,17 @@

from mixed_utils import dist2file, statistics
import argparse as ap
from Bio import SeqIO, Seq, SeqRecord
from collections import defaultdict
from Bio import SeqIO#, Seq, SeqRecord
# from collections import defaultdict
import numpy
from ooSubprocess import ooSubprocess


'''
SUBST = {
'A':{'A':0.0, 'C':1.0, 'G':1.0, 'T':1.0, '-':1.0},
'C':{'A':1.0, 'C':0.0, 'G':1.0, 'T':1.0, '-':1.0},
'G':{'A':1.0, 'C':1.0, 'G':0.0, 'T':1.0, '-':1.0},
'C':{'A':1.0, 'C':0.0, 'G':1.0, 'T':1.0, '-':1.0},
'G':{'A':1.0, 'C':1.0, 'G':0.0, 'T':1.0, '-':1.0},
'T':{'A':1.0, 'C':1.0, 'G':1.0, 'T':0.0, '-':1.0},
'-':{'A':1.0, 'C':1.0, 'G':1.0, 'T':1.0, '-':0.0}}
'''
Expand All @@ -35,14 +35,14 @@ def read_params():
p = ap.ArgumentParser()
p.add_argument('--ifn_alignment', required=True, default=None, type=str)
p.add_argument('--ofn_prefix', required=True, default=None, type=str)
p.add_argument('--count_gaps',
p.add_argument('--count_gaps',
required=False,
dest='ignore_gaps',
dest='ignore_gaps',
action='store_false')
p.set_defaults(ignore_gaps=True)
p.add_argument('--overwrite',
p.add_argument('--overwrite',
required=False,
dest='overwrite',
dest='overwrite',
action='store_true')
p.set_defaults(overwrite=False)

Expand Down Expand Up @@ -72,7 +72,7 @@ def get_dist(seq1, seq2, ignore_gaps):
rel_sim = 1.0 - rel_dist
rel_snp = abs_snp / float(len(seq1))
return abs_dist, rel_dist, abs_sim, rel_sim, abs_snp, rel_snp


def compute_dist_matrix(ifn_alignment, ofn_prefix, ignore_gaps, overwrite):
ofn_abs_dist = ofn_prefix + '.abs_dist'
Expand Down Expand Up @@ -101,30 +101,30 @@ def compute_dist_matrix(ifn_alignment, ofn_prefix, ignore_gaps, overwrite):

for i in range(len(recs)):
for j in range(i, len(recs)):
abs_d, rel_d, abs_s, rel_s, abs_sp, rel_sp = get_dist(recs[i].seq,
abs_d, rel_d, abs_s, rel_s, abs_sp, rel_sp = get_dist(recs[i].seq,
recs[j].seq,
ignore_gaps)

abs_dist[i][j] = abs_d
abs_dist[j][i] = abs_d
abs_dist_flat.append(abs_d)

rel_dist[i][j] = rel_d
rel_dist[j][i] = rel_d
rel_dist_flat.append(rel_d)

abs_sim[i][j] = abs_s
abs_sim[j][i] = abs_s
abs_sim_flat.append(abs_s)

rel_sim[i][j] = rel_s
rel_sim[j][i] = rel_s
rel_sim_flat.append(rel_s)

abs_snp[i][j] = abs_sp
abs_snp[j][i] = abs_sp
abs_snp_flat.append(abs_sp)

rel_snp[i][j] = rel_sp
rel_snp[j][i] = rel_sp
rel_snp_flat.append(rel_sp)
Expand Down Expand Up @@ -198,7 +198,7 @@ def compute_dist_matrix(ifn_alignment, ofn_prefix, ignore_gaps, overwrite):
'--flabel_size', '5',
'--slabel_size', '5',
'--max_flabel_len', '200'])
'''
'''

ofn_abs_snp = ofn_prefix + '.abs_snp'
dist2file(abs_snp, labels, ofn_abs_snp)
Expand All @@ -208,17 +208,17 @@ def compute_dist_matrix(ifn_alignment, ofn_prefix, ignore_gaps, overwrite):
dist2file(rel_snp, labels, ofn_rel_snp)
with open(ofn_rel_snp + '.info', 'w') as ofile:
ofile.write(statistics(rel_snp_flat)[1])




def main(args):
compute_dist_matrix(
args['ifn_alignment'],
args['ifn_alignment'],
args['ofn_prefix'],
args['ignore_gaps'],
args['overwrite'])
args['overwrite'])

if __name__ == "__main__":
args = read_params()
main(args)
18 changes: 9 additions & 9 deletions strainphlan_src/compute_distance_all.py
View file
Expand Up @@ -13,9 +13,9 @@
os.environ['PATH'] += ':%s'%MAIN_DIR
sys.path.append(MAIN_DIR)
import argparse as ap
from Bio import SeqIO, Seq, SeqRecord
from collections import defaultdict
import numpy
from Bio import SeqIO#, Seq, SeqRecord
# from collections import defaultdict
# import numpy
from compute_distance import compute_dist_matrix
from ooSubprocess import parallelize

Expand All @@ -24,9 +24,9 @@ def read_params():
p = ap.ArgumentParser()
p.add_argument('--ifn_alignments', nargs='+', required=True, default=None, type=str)
p.add_argument('--nprocs', required=True, default=None, type=int)
p.add_argument('--count_gaps',
p.add_argument('--count_gaps',
required=False,
dest='ignore_gaps',
dest='ignore_gaps',
action='store_false')
p.set_defaults(ignore_gaps=True)

Expand All @@ -37,19 +37,19 @@ def read_params():

def compute_dist_matrix_wrapper(args):
compute_dist_matrix(
args['ifn_alignment'],
args['ifn_alignment'],
args['ofn_prefix'],
args['ignore_gaps'],
overwrite=True)
overwrite=True)



def main(args):
args_list = []
for i in range(len(args['ifn_alignments'])):
args_list.append({})
args_list[i]['ifn_alignment'] = args['ifn_alignments'][i]
args_list[i]['ofn_prefix'] = args['ifn_alignments'][i]
args_list[i]['ofn_prefix'] = args['ifn_alignments'][i]
if not args['ignore_gaps']:
args_list[i]['ofn_prefix'] += '.count_gaps'
args_list[i]['ignore_gaps'] = args['ignore_gaps']
Expand Down
4 changes: 2 additions & 2 deletions strainphlan_src/extract_markers.py
View file
Expand Up @@ -6,8 +6,8 @@
__version__ = '0.1'
__date__ = '1 Sep 2014'

import sys
import os
# import sys
# import os
import argparse as ap
import pickle
import bz2
Expand Down
20 changes: 10 additions & 10 deletions strainphlan_src/ooSubprocess.py
View file
Expand Up @@ -8,12 +8,12 @@
import multiprocessing
from multiprocessing.pool import ThreadPool
import sys
import cStringIO
from tempfile import NamedTemporaryFile
# import cStringIO
from tempfile import NamedTemporaryFile
import which
import functools
import traceback
import numpy
# import numpy


class ooSubprocessException(Exception):
Expand Down Expand Up @@ -62,8 +62,8 @@ def ex(
elif get_out_pipe:
tmp_file = NamedTemporaryFile(dir=self.tmp_dir)
p = subprocess.Popen(
cmd,
stdin=in_pipe,
cmd,
stdin=in_pipe,
stdout=tmp_file,
**kwargs)
p.wait()
Expand All @@ -74,15 +74,15 @@ def ex(
elif out_fn:
ofile = open(out_fn, 'w') if out_fn else None
result = subprocess.check_call(
cmd,
stdin=in_pipe,
stdout=ofile,
cmd,
stdin=in_pipe,
stdout=ofile,
**kwargs)
ofile.close()
else:
result = subprocess.check_call(
cmd,
stdin=in_pipe,
cmd,
stdin=in_pipe,
**kwargs)
return result

Expand Down

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