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run.py
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run.py
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# @copyright 2016-2023 Clarity Genomics BVBA
# @copyright 2012-2016 Bonsai Bioinformatics Research Group
# @copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
#
# SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
# This is a free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SortMeRNA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
#
# contributors: Jenya Kopylova jenya.kopylov@gmail.com
# Laurent Noé laurent.noe@lifl.fr
# Pierre Pericard pierre.pericard@lifl.fr
# Daniel McDonald wasade@gmail.com
# Mikaël Salson mikael.salson@lifl.fr
# Hélène Touzet helene.touzet@lifl.fr
# Rob Knight robknight@ucsd.edu
'''
file: run.py
created: Aug 12, 2019 Mon
conda install scikit-bio -c conda-forge <- pre-requisites
'''
import os
import sys
import subprocess
import platform
from optparse import OptionParser
import re
import time
import difflib
import shutil
import yaml
from jinja2 import Environment, FileSystemLoader
import gzip
def mock_missing(name):
def init(self, *args, **kwargs):
raise ImportError(
f'The class {name} is not importable; '
f'likely due to it not being installed. '
f'Supposed to be used on a minion running a k8s control node.')
return type(name, (), {'__init__': init})
try:
import pandas
except ImportError:
pandas = mock_missing('pandas')
is_skbio = True
try:
import skbio.io
except (ImportError, OSError) as ex:
print(f'\'import skbio.io\' failed: {ex}')
is_skbio = False
# globals
OS = None
ENV = None # WIN | WSL | LNX_AWS | LNX_TRAVIS
WRK_DIR = None
# define platform
pf = platform.platform()
IS_WIN = 'Windows' in pf
IS_WSL = 'Linux' in pf and 'Microsoft' in pf # Windows Subsystem for Linux (WSL)
IS_LNX = 'Linux' in pf and not 'Microsoft' in pf
OS = 'WIN' if IS_WIN else 'WSL' if IS_WSL else 'LNX' if IS_LNX else None
if not OS:
print(f'Unexpected platform: {pf}')
sys.exit(1)
UHOME = os.environ.get('USERPROFILE') if IS_WIN else os.environ.get('HOME') # not defined for AWS SSM
SMR = 'sortmerna'
SMR_SRC = None # source root dir
SMR_DIST = None # dist root dir
SMR_EXE = None # full path to executable
ZLIB_SRC = None
ZLIB_DIST = None
ROCKS_SRC = None
ROCKS_DIST = None
# no binaries, so always build Release only
RAPID_SRC = None
RAPID_DIST = None
DATA_DIR = None
RUN_DIR = None
OUT_DIR = None
TEST_DATA = None
# base names of the report files
ALI_NAMES = [] # get from test.jinja.yaml + fa/fa + gz/non-gz -> 7 x 4 = 28 names
OTH_NAMES = []
ALI_BASE = 'aligned'
OTH_BASE = 'other'
ALI_FWD_BASE = None # '{}_fwd'.format(ALI_BASE)
ALI_REV_BASE = None # '{}_rev'.format(ALI_BASE)
OTH_FWD_BASE = None # '{}_fwd'.format(OTH_BASE)
OTH_REV_BASE = None # '{}_rev'.format(OTH_BASE)
LOG_BASE = None # '{}.log'.format(ALI_BASE)
DENOVO_BASE = None # '{}_denovo.fasta'.format(ALI_BASE)
OTU_BASE = None # '{}_otus.txt'.format(ALI_BASE)
BLAST_BASE = None # '{}.blast'.format(ALI_BASE)
SAM_BASE = None # '{}.sam'.format(ALI_BASE)
READS_EXT = None
IS_FASTQ = False
IS_PAIRED_IN = False
IS_PAIRED_OUT = False
# output files
LOGF = None
ALIF = None
ALI_FWD = None
ALI_REV = None
OTHF = None
OTH_FWD = None
OTH_REV = None
ALI_REF = None
DENOVOF = None
OTUF = None
BLASTF = None
SAMF = None
# KVDB and index dirs
KVDB_DIR = None
IDX_DIR = None
def run(cmd, cwd=None, capture=False):
'''
'''
ST = '[run]'
ret = {'retcode':0, 'stdout':None, 'stderr':None}
# print compiler version e.g. 'Microsoft (R) C/C++ Optimizing Compiler Version 19.16.27031.1 for x86'
#"%VS_HOME%"\bin\Hostx86\x86\cl.exe
cmds = ' '.join(cmd)
msg = f'{ST} Running: {cmds} in {cwd}' if cwd else f'{ST} Running: {cmds}'
print(msg)
start = time.time()
#print('Running {} in {}'.format(' '.join('{}'.format(xx) for xx in cmd), cwd))
# cmake configure and generate
#kw = {'stdout':subprocess.PIPE, 'stderr':subprocess.PIPE} if capture else {}
try:
if cwd and not os.path.exists(cwd):
os.makedirs(cwd)
proc = subprocess.run(cmd, cwd=cwd, capture_output=capture)
else:
proc = subprocess.run(cmd, capture_output=capture)
ret['retcode'] = proc.returncode
if capture:
ret['stdout'] = proc.stdout
ret['stderr'] = proc.stderr
#proc = subprocess.run(cmd, cwd=build_dir, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
except OSError as err:
print(err)
ret['retcode'] = 1
ret['stderr'] = err
except:
for info in sys.exc_info(): print(info)
ret['retcode'] = 1
ret['stderr'] = sys.exc_info()
rt = time.time() - start
print(f"{ST} run time: {rt}")
return ret
#END cmake_run
def get_diff(fpath0, fpath1):
'''
'''
dlist = []
with open(fpath0, 'rU') as fout:
with open(fpath1, 'rU') as fexpect:
diff = difflib.unified_diff(
fout.readlines(),
fexpect.readlines(),
fromfile='fout',
tofile='fexpect',
)
for line in diff:
dlist.append(line)
if line:
print(line)
return dlist
#END get_diff
def to_lf(ddir):
'''
convert to LF line endings of the data files
NOTE: 'find . -type f -name "*.fasta" -o -name "*.fastq" | xargs dos2unix'
using 'subprocess.run' is problematic because of the pipe.
'''
ST = '[to_lf]'
CRLF = b'\r\n'
LF = b'\n'
for dpath, dnames, fnames in os.walk(ddir):
for fname in fnames:
if fname.endswith('.fasta') or fname.endswith('.fastq'):
fpath = os.path.join(dpath, fname)
print(f'{ST} converting {fpath}')
with open(fpath, 'rb') as infile:
content = infile.read()
content = content.replace(CRLF, LF)
with open(fpath, 'wb') as infile:
infile.write(content)
print('to_lf Done')
#END to_lf
def parse_log(fpath, logd={}):
'''
parse 'aligned.log' to dictionary
:param str fpath 'aligned.log' file
:param dict logd log file structure (test.jinja.yaml:aligned.log)
'''
#logd = {
# 'cmd': ['Command', None],
# 'pid': ['Process pid', None],
# 'params': {'refs': []},
# 'num_reads': ['Total reads =', 0],
# 'results': {
# 'num_hits': ['Total reads passing E-value threshold', 0],
# 'num_fail': ['Total reads failing E-value threshold', 0],
# 'num_denovo': ['Total reads for de novo clustering', 0],
# 'min_len': ['Minimum read length', 0],
# 'max_len': ['Maximum read length', 0],
# 'mean_len': ['Mean read length', 0]
# },
# 'coverage': [],
# 'num_id_cov': ['Total reads passing %%id and %%coverage thresholds', 0],
# 'num_otus': ['Total OTUs', 0],
# 'date': None
#}
with open(fpath) as f_log:
for line in f_log:
if logd['num_reads'][0] in line:
logd['num_reads'][1] = int((re.split(' = ', line)[1]).strip())
elif logd['results']['num_denovo'][0] in line:
logd['results']['num_denovo'][1] = int((re.split(' = ', line)[1]).strip())
elif logd['results']['num_hits'][0] in line:
logd['results']['num_hits'][1] = int((re.split(' = | \(', line)[1]).strip())
elif logd['results']['num_fail'][0] in line:
logd['results']['num_fail'][1] = int((re.split(' = | \(', line)[1]).strip())
elif logd['num_id_cov'][0] in line:
# line: '..thresholds = 44223 (44.22)'
val = line.split('=')[1]
if val: val = val.split()[0].strip()
logd['num_id_cov'][1] = int(val)
elif logd['num_otus'][0] in line:
logd['num_otus'][1] = int((re.split(' = ', line)[1]).strip())
return logd
#END parse_log
def process_smr_opts(args):
'''
:param args list of parameters passed to sortmerna
'''
ST = '[process_smr_opts]'
WDIR = '-workdir'
KVD = '-kvdb'
IDX = '-idx'
ALN = '-aligned'
OTH = '-other'
OUT2 = '-out2'
global KVDB_DIR
global IDX_DIR
global ALI_BASE
global OTH_BASE
global LOGF
global ALIF
global ALI_FWD
global ALI_REV
global OTHF
global OTH_FWD
global OTH_REV
global ALI_REF
global DENOVOF
global OTUF
global BLASTF
global SAMF
global READS_EXT
global IS_FASTQ
global IS_PAIRED_IN
global IS_PAIRED_OUT
global WRK_DIR
is_gz = False
psplit = os.path.splitext(args[args.index('-reads')+1]) # 1.concat.fq.gz -> [1.concat.fq, .gz]
READS_EXT = psplit[1]
if READS_EXT in ['.gz']:
#READS_EXT = os.extsep + args[args.index('-reads')+1].split(os.extsep)[1]
READS_EXT = os.path.splitext(psplit[0])[1]
is_gz = True
IS_FASTQ = READS_EXT[1:] in ['fq', 'fastq']
IS_PAIRED_IN = '-paired_in' in args
IS_PAIRED_OUT = '-paired_out' in args
if ALN in args:
aln_pfx = args[args.index(ALN) + 1]
if not os.path.basename(aln_pfx):
ALIF = os.path.join(aln_pfx, ALI_BASE + READS_EXT) # use default 'aligned'
else:
ALI_BASE = os.path.basename(aln_pfx)
ALIF = os.path.abspath(aln_pfx + READS_EXT)
elif WDIR in args:
wdir = args[args.index(WDIR) + 1]
print('{} \'-workdir\' option was provided. Using workdir: [{}]'.format(ST, os.path.realpath(wdir)))
ALIF = os.path.join(wdir, 'out', ALI_BASE + READS_EXT)
elif WRK_DIR:
ALIF = os.path.join(WRK_DIR, 'out', ALI_BASE + READS_EXT)
elif UHOME:
ALIF = os.path.join(UHOME, 'sortmerna', 'run', 'out', ALI_BASE + READS_EXT)
else:
print(f'{ST} cannot define alignment file')
if OUT2 in args:
ALI_FWD = os.path.join(os.path.dirname(ALIF), ALI_BASE + '_fwd' + READS_EXT)
ALI_REV = os.path.join(os.path.dirname(ALIF), ALI_BASE + '_rev' + READS_EXT)
if OTH in args:
idx = args.index(OTH)
# check idx + 1 no exceeds args length and other options has arg
if idx + 1 < len(args) -1 and args[idx+1][:1] != '-':
oth_pfx = args[idx + 1]
if not os.path.basename(oth_pfx):
OTHF = os.path.join(oth_pfx, OTH_BASE + READS_EXT)
else:
OTH_BASE = os.path.basename(oth_pfx)
OTHF = os.path.abspath(oth_pfx + READS_EXT)
elif ALN in args:
OTHF = os.path.join(os.path.dirname(ALIF), OTH_BASE + READS_EXT) # use the same out dir as ALN
elif WDIR in args:
wdir = args[args.index(WDIR) + 1]
print('{} \'-workdir\' option was provided. Using workdir: [{}]'.format(ST, os.path.realpath(wdir)))
ALIF = os.path.join(wdir, 'out', OTH_BASE + READS_EXT)
else:
OTHF = os.path.join(UHOME, 'sortmerna', 'run', 'out', OTH_BASE + READS_EXT)
if OUT2 in args:
OTH_FWD = os.path.join(os.path.dirname(ALIF), OTH_BASE + '_fwd' + READS_EXT)
OTH_REV = os.path.join(os.path.dirname(ALIF), OTH_BASE + '_rev' + READS_EXT)
if KVD in args:
KVDB_DIR = args[args.index(KVD) + 1]
elif WDIR in args:
KVDB_DIR = os.path.join(args[args.index(WDIR) + 1], 'kvdb')
else:
KVDB_DIR = os.path.join(UHOME, 'sortmerna', 'run', 'kvdb')
if IDX in args:
IDX_DIR = args[args.index(IDX) + 1]
elif WDIR in args:
IDX_DIR = os.path.join(args[args.index(WDIR) + 1], 'idx')
else:
IDX_DIR = os.path.join(UHOME, 'sortmerna', 'run', 'idx')
gzs = '.gz' if is_gz else ''
LOGF = os.path.join(os.path.dirname(ALIF), '{}.log'.format(ALI_BASE))
BLASTF = os.path.join(os.path.dirname(ALIF), '{}.blast{}'.format(ALI_BASE, gzs))
OTUF = os.path.join(os.path.dirname(ALIF), 'otu_map.txt')
DENOVOF = os.path.join(os.path.dirname(ALIF), '{}_denovo.fa'.format(ALI_BASE))
SAMF = os.path.join(os.path.dirname(ALIF), '{}.sam'.format(ALI_BASE))
#END process_smr_opts
def process_blast(**kwarg):
'''
# Check count of reads passing %id and %coverage threshold
# as given in aligned.blast
'''
ST = '[{}]'.format('process_blast')
vald = kwarg.get('validate')
BLAST_ID_COL = 2
BLAST_COV_COL = 13
num_hits_file = 0
n_yid_ycov = 0
n_yid_ncov = 0
n_nid_ycov = 0
n_denovo = 0
has_cov = False
BLAST_PID_PCOV = os.path.join(os.path.dirname(ALIF), 'pid_pcov.blast')
is_dbg_pid_pcov = True
cols = ['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen',
'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore', 'sseq', 'qcovs']
if os.path.exists(BLASTF):
print(f'{ST} processing : {BLASTF}')
gzs = os.path.basename(BLASTF).split(os.extsep)[-1]
is_gz = gzs == 'gz'
is_use_skbio = False
with open(BLASTF, 'rb') as f_blast:
is_gz = is_gz and (f_blast.read(2) == b'\x1f\x8b')
if is_use_skbio:
# just returns column names - not at all what's expected
for seq in skbio.io.read(BLASTF, format='blast+6', columns=cols, compression='gzip', into=pandas.DataFrame):
num_hits_file += 1
else:
with gzip.open(BLASTF, 'rb') if is_gz else open(BLASTF, 'rb') as f_blast, open(BLAST_PID_PCOV, 'w') as f_pid_pcov:
for lineb in f_blast:
num_hits_file += 1
line = lineb.decode('utf-8')
llist = line.strip().split('\t')
fid = float(llist[BLAST_ID_COL])
is_pass_id = fid >= 97.0
has_cov = len(llist) > BLAST_COV_COL
if has_cov:
fcov = float(llist[BLAST_COV_COL])
is_pass_cov = fcov >= 97.0
if is_pass_id:
if is_pass_cov:
n_yid_ycov += 1
if is_dbg_pid_pcov:
f_pid_pcov.write(line)
else:
n_yid_ncov += 1
elif is_pass_cov:
n_nid_ycov += 1
else:
n_denovo += 1
is_pass_id = False
is_pass_cov = False
bn = os.path.basename(BLASTF)
print(f'{ST} from {bn}: num_hits= {num_hits_file} n_yid_ycov= {n_yid_ycov}'
' n_yid_ncov= {n_yid_ncov} n_nid_ycov= {n_nid_ycov} n_denovo= {n_denovo}')
blastd = vald.get('files', {}).get('aligned.blast')
if blastd:
if blastd.get('n_yid_ycov'):
tmpl = '{} Testing reads passing ID threshold: {}: {} Expected: {}'
print(tmpl.format(ST, os.path.basename(BLASTF), n_yid_ycov, blastd['n_yid_ycov']))
assert n_yid_ycov == blastd['n_yid_ycov'], \
'{} not equals {}'.format(blastd['n_yid_ycov'], n_yid_ycov)
num_recs = blastd.get('num_recs')
if num_recs:
tmpl = '{} Testing num_hits: {}: {} Expected: {}'
print(tmpl.format(ST, os.path.basename(BLASTF), num_hits_file, num_recs))
assert num_hits_file == num_recs, \
'{} not equals {}'.format(num_hits_file, num_recs)
return {
'n_hits' : num_hits_file,
'yid_ycov': n_yid_ycov,
'yid_ncov': n_yid_ncov,
'nid_ycov': n_nid_ycov,
'n_denovo': n_denovo
}
#END process_blast
def dbg_blast(**kwarg):
'''
added 20210323
compare unique read IDs in two blast reports produced using different program versions
cmd: python scripts/run.py --name t0 -f dbg_blast --validate-only
'''
ST = '[{}]'.format('dbg_blast')
rdiff = None
bl_421 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-2-1/20210322/aligned.blast')
bl_431 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-3-1/20210322/aligned.blast')
srt421 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-2-1/20210322/sorted.blast')
srt431 = os.path.join(DATA_DIR, 'sortmerna/out/tests/t42/win10_8_16/4-3-1/20210322/sorted.blast')
if os.path.exists(bl_421) and os.path.exists(bl_431):
with open(bl_421) as f421, open(bl_431) as f431:
l421 = [ line.strip().split('\t')[:2] for line in f421 ]
l431 = [ line.strip().split('\t')[:2] for line in f431 ]
l421.sort(key=lambda rr: int(rr[0].split('.')[-1])) # SRR1635864.8745 -> [SRR1635864, 8745] -> 8745
l431.sort(key=lambda rr: int(rr[0].split('.')[-1]))
with open(srt421, 'w') as sr421, open(srt431, 'w') as sr431:
sr421.write('\n'.join('{}\t{}'.format(x[0], x[1]) for x in l421))
sr431.write('\n'.join('{}\t{}'.format(x[0], x[1]) for x in l431))
#l421 = [ ' '.join(line.strip().split('\t')[:2]) for line in f421 ]
#l431 = [ ' '.join(line.strip().split('\t')[:2]) for line in f431 ]
doset = False
if doset:
rdiff = set(l421) - set(l431)
print('{} rdiff.len= {}'.format(ST, len(rdiff))) # 0
[print(x) for x in list(rdiff)]
#END dbg_blast
def dbg_otu(**kwarg):
'''
'''
ST = '[{}]'.format('dbg_otu')
OTU_READSF = os.path.join(os.path.dirname(ALIF), 'otu_reads.txt')
BLAST_PID_PCOV = os.path.join(os.path.dirname(ALIF), 'pid_pcov.blast')
READS_DIFF = os.path.join(os.path.dirname(ALIF), 'reads_diff.txt')
reads = [] # list of all reads from all groups
blast_reads = []
if os.path.exists(BLAST_PID_PCOV):
with open(BLAST_PID_PCOV) as blastf:
for line in blastf:
lls = line.strip().split('\t')
blast_reads.append(lls[0]) # collect reads
# parse otu groups file
if os.path.exists(OTUF):
num_clusters_file = 0
num_reads_in_clusters_file = 0
with open(OTUF) as f_otus:
for line in f_otus:
num_clusters_file += 1
greads = line.strip().split('\t')[1:] # reads in a group
reads.extend(greads)
num_reads_in_clusters_file += len(greads)
# genreate list of reads
with open(OTU_READSF, 'w') as readsf:
reads.sort(key=lambda rr: int(rr.split('_')[-1]))
reads.sort(key=lambda rr: int(rr.split('_')[0][:-1]))
for read in reads:
readsf.write('{}\n'.format(read))
with open(READS_DIFF, 'w') as diff:
rds = set(blast_reads) - set(reads)
rdsl = list(rds)
rdsl.sort(key=lambda rr: int(rr.split('_')[-1]))
rdsl.sort(key=lambda rr: int(rr.split('_')[0][:-1]))
for rd in rdsl:
diff.write('{}\n'.format(rd))
#END dbg_otu
def validate_otu(**kwarg):
'''
:param dict kwarg test configuration see 'test.jinja.yaml'
:param dict kwarg[logd] parsed aligned.log data see 'parse_log(LOGF)'
'''
ST = '[{}]'.format('validate_otu')
vald = kwarg.get('validate')
logd = kwarg.get('logd') or parse_log(LOGF)
# parse otu groups file
if os.path.exists(OTUF):
num_clusters_file = 0
num_reads_in_clusters_file = 0
with open(OTUF) as f_otus:
for line in f_otus:
num_clusters_file += 1
num_reads_in_clusters_file += (len(line.strip().split('\t'))-1)
print('{} num groups in OTU file {} , expected {}'.format(ST, num_clusters_file, logd['num_otus'][1]))
assert logd['num_otus'][1] == num_clusters_file, \
'{} not equals {}'.format(logd['num_otus'][1], num_clusters_file)
print('{} count of reads in OTU file {} , expected {}'.format(ST, num_reads_in_clusters_file, logd['num_id_cov'][1]))
assert logd['num_id_cov'][1] == num_reads_in_clusters_file, \
'{} not equals {}'.format(logd['num_id_cov'][1], num_reads_in_clusters_file)
# verify count of groups in the aligned.log is the same as specified in configuration validate data
if logd.get('num_otus') and vald.get('num_cluster'):
assert logd['num_otus'][1] in vald['num_cluster'], \
'{} not in {}'.format(logd['num_otus'][1], vald['num_cluster'])
#END validate_otu
def validate_log(logd, ffd):
'''
:param dict logd
:param dict ffd files data as in test.jinja.yaml:<test_name>:validate:files
'''
ST = '[validate_log]'
# aligned.log :
# verify the total number of reads in aligned.log vs the number in the validation spec
n_vald = ffd.get('aligned.log', {}).get('num_reads')
n_logd = logd['num_reads'][1]
if n_vald:
print('{} testing num_reads: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify number of hits
n_vald = ffd.get('aligned.log', {}).get('num_hits')
n_logd = logd['results']['num_hits'][1]
if n_vald:
print('{} testing num_hits: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify number of misses
n_vald = ffd.get('aligned.log', {}).get('num_fail')
n_logd = logd['results']['num_fail'][1]
if n_vald:
print('{} testing num_fail: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of COV+ID
n_vald = ffd.get('aligned.log', {}).get('n_yid_ycov')
n_logd = logd['num_id_cov'][1]
if n_vald:
print('{} testing n_yid_ycov: {} Expected: {}'.format(ST, n_logd, n_vald))
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of OUT groups
n_vald = ffd.get('aligned.log', {}).get('num_groups')
n_logd = logd['num_otus'][1]
if n_vald:
print(f'{ST} testing num_groups: {n_logd} Expected: {n_vald}')
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
# verify count of de-novo reads
n_vald = ffd.get('aligned.log', {}).get('n_denovo')
n_logd = logd['results']['num_denovo'][1]
if n_vald:
print(f'{ST} testing n_denovo: {n_logd} Expected: {n_vald}')
assert n_vald == n_logd, '{} not equals {}'.format(n_vald, n_logd)
#END validate_log
def process_output(name, **kwarg):
'''
:param str name test name e.g. t0
:param dict test configuration see 'test.jinja'
'''
ST = '[process_output]'
global is_skbio
log_struct = kwarg.get('aligned.log')
vald = kwarg.get(name, {}).get('validate')
#cmdd = kwarg.get('cmd')
if not vald:
print('{} validation info not provided'.format(ST))
return
logd = parse_log(LOGF, log_struct)
ffd = vald.get('files')
if ffd and isinstance(ffd, dict):
for ff, vv in ffd.items():
print('{} {}'.format(ST, ff))
# Check aligned/other reads count
# aligned/other files only specify read count in the test validation data
if isinstance(vv, int):
ffp = os.path.join(os.path.dirname(ALIF), ff) # file path
count = 0
assert os.path.exists(ffp), '{} does not exists: {}'.format(ST, ffp)
if ff == 'otu_map.txt':
with open(ffp) as ffs:
for line in ffs:
count += 1
print('{} testing count of groups in {}: {} Expected: {}'.format(ST, ff, count, vv))
assert count == vv, '{} not equals {}'.format(count, vv)
continue
if is_skbio:
if IS_FASTQ:
for seq in skbio.io.read(ffp, format='fastq', variant=vald.get('variant')):
count += 1
else:
fmt = 'fasta' if READS_EXT[1:] in ['fasta', 'fa'] else READS_EXT[1:]
for seq in skbio.io.read(ffp, format=fmt):
count += 1
print('{} Testing count of reads in {}: {} Expected: {}'.format(ST, ff, count, vv))
assert count == vv, '{} not equals {}'.format(count, vv)
elif ff == 'aligned.log':
validate_log(logd, ffd)
elif 'aligned.blast' in ff:
test_cfg = kwarg.get(name, {})
process_blast(**test_cfg)
#END process_output
def t0(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param outd results output directory
'''
ST = '[t0:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
BLAST_EXPECTED = os.path.join(datad, 't0_expected_alignment.blast')
dlist = []
with open(BLASTF, 'r') as fout:
with open(BLAST_EXPECTED, 'r') as fexpect:
diff = difflib.unified_diff(
fout.readlines(),
fexpect.readlines(),
fromfile='fout',
tofile='fexpect',
)
for line in diff:
dlist.append(line)
if line:
print(line, end='')
assert len(dlist) == 0
print("{} Done".format(ST))
#END t0
def t2(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param kwargs validation args
Test the following case for alignment:
beginning from align_ref_start = 0 and align_que_start = X, the read finishes
before the end of the reference
ref |----------------|
que |------------------------|
LIS |-----|
^
align_que_start
'''
ST = '[t2:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
vald = kwarg['validate']
actual_alignment = []
with open(BLASTF) as afile:
for line in afile:
actual_alignment = line.strip().split('\t')
assert len(vald['expected']) == len(actual_alignment)
assert sorted(vald['expected']) == sorted(actual_alignment)
#a = set(expected_alignment) & set(actual_alignment)
print("{} Done".format(ST))
#END t2
def t3(datad, ret={}, **kwarg):
'''
:param datad Data directory
:param outd results output directory
:param kwargs validation args
test_environmental_output
Test outputting FASTA file for de novo clustering
using environmental data.
Conditions: input FASTA file is processed in
one mapped section.
'''
ST = '[t3:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
global is_skbio
logd = parse_log(LOGF)
vald = kwarg.get('validate')
cmdd = kwarg.get('cmd')
assert logd['results']['num_hits'][1] == vald['num_hits']
process_blast(**kwarg)
# sort order (descending/ascending) of candidate references (alignment.cpp)
is_refs_descending = False
# 'Total OTUs' in aligned.log has to be equal 'num_groups' in test.jinja.yaml
if is_refs_descending:
assert logd['num_otus'][1] == vald['num_groups'][0] # originally
else:
assert logd['num_otus'][1] == vald['num_groups'][1], \
'num_otus = {} != num_groups = {} expected'.format(logd['num_otus'][1], vald['num_groups'][1])
# OTU file contains one line per OTU group, so the number of lines
# has to be equal 'Total OTUs' in aligned.log
with open(OTUF) as f_otumap:
num_clusters_file = sum(1 for line in f_otumap)
assert logd['num_otus'][1] == num_clusters_file, \
'num_otus = {} != {}:num_otus = {}'.format(logd['num_otus'][1],
OTU_BASE, num_clusters_file)
# number of reads in aligned_denovo.fasta has to be equal the
# 'Total reads for de novo clustering' in aligned.log
n_denovo_file = 0
if is_skbio:
for seq in skbio.io.read(DENOVOF, format='fasta'):
n_denovo_file += 1
assert logd['results']['num_denovo'][1] == n_denovo_file, \
'num_denovo = {} != {}:num_denovo = {}'.format(\
logd['results']['num_denovo'][1], DENOVO_BASE, n_denovo_file)
print("{} Done".format(ST))
#END t3
def t4(datad, ret={}, **kwarg ):
'''
count idx files
'''
ST = '[t4:{}]'.format(kwarg.get('name'))
vald = kwarg.get('validate')
if IS_WIN:
sfx = vald.get('idx_sfx_win')
else:
sfx = vald.get('idx_sfx_lin')
idx_count = 0
idx_count_expect = vald.get('num_idx') * 3 + 1
if os.path.exists(IDX_DIR):
idx_count = len([fn for fn in os.listdir(IDX_DIR) if str(sfx) in fn])
print('{} Expected number of index files: {} Actual number: {}'.format(ST, idx_count_expect, idx_count))
assert idx_count_expect == idx_count
#END t4
def t9(datad, ret={}, **kwarg):
'''
:param datad data directory
:param dict ret results of the aignment
test_output_all_alignments_f_rc
'''
ST = '[t9:{}]'.format(kwarg.get('name'))
print(f'{ST} Validating ...')
vald = kwarg.get('validate')
sam_alignments = []
with open(SAMF) as aligned_f:
for line in aligned_f:
if line.startswith('@'):
continue
alignment = line.strip().split("\t")
sam_alignments.append(alignment)
assert len(vald['sam_alignments_expected']) == len(sam_alignments)
for alignment in vald['sam_alignments_expected']:
assert alignment in sam_alignments
print(f"{ST} done")
#END t9
def t10(datad, ret={}, **kwarg):
'''
:param str datad data directory
:param dict ret results of the aignment
test_ref_shorter_than_seed
'''
ST = '[t10:{}]'.format(kwarg.get('name'))
print(f'{ST} validating ...'.format)
vald = kwarg.get('validate')
if ret and ret.get('retcode'):
assert ret['retcode'] == 1
assert vald['err_msg'] in ret['stderr'].decode("utf-8")
print("{ST} done")
#END t10
def t11(datad, ret={}, **kwarg):
'''
@param smrexe sortmerna.exe path
@param datad Data directory
@param outd results output directory
Test on simulated data,
10000 reads with 1% error (--aligned),
10000 reads with 10% error (de novo),
10000 reads random (--other)
Conditions: reference index and input
query FASTA file both processed as one
section.
'''
ST = '[t11:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
if ret and ret.get('retcode'):
print('ERROR running alignemnt. Return code: {}'.format(ret['retcode']))
print(ret['stdout'])
print(ret['stderr'])
sys.exit(1)
else:
process_output(**kwarg)
print("{} Done".format(ST))
#END t11
def t12(datad, ret={}, **kwarg):
'''
@param smrexe sortmerna.exe path
@param datad Data directory
@param outd results output directory
Test on simulated data,
10000 reads with 1% error (--aligned),
10000 reads with 10% error (de novo),
10000 reads random (--other)
Conditions: reference index and input
query FASTA file both processed as one
section.
'''
ST = '[t12:{}]'.format(kwarg.get('name'))
print('{} Validating ...'.format(ST))
if ret and ret.get('retcode'):
print('ERROR running alignemnt. Return code: {}'.format(ret['retcode']))
print(ret['stdout'])
print(ret['stderr'])
sys.exit(1)
else:
process_output(**kwarg)
print("{} Done".format(ST))
#END t12
def t17(datad, ret={}, **kwarg):
'''
:param name sortmerna.exe path
:param datad Data directory
:param outd results output directory
:param capture Capture output
'''
ST = '[t17:{}]'.format(kwarg.get('name'))
print(f'{ST} TODO: implement')
logd = parse_log(LOGF)
print("{ST} done")
#END t17
def set_file_names(basenames, is_other=False):
'''
:param list basenames list of basenames as in test.jinja,yaml:aligned.names
:param bool is_other flag aligned (default) | other files
'''
global ALI_NAMES
if __name__ == "__main__":
'''
$env:path="$env:userprofile/a1/code/sortmerna/dist/bin;$env:path"; &python scripts/run.py -n t1
python scripts/run.py -n t1 --smr-exe=dist/bin/sortmerna.exe
python scripts/run.py -n t15 --smr-exe=dist/bin/sortmerna.exe --data-dir=../../data
python scripts/run.py -n t0 -v [--capture] [--validate-only]
python scripts/run.py --name t12 -f process_otu --validate-only -d 2
python scripts/run.py --name t0 -f dbg_blast --validate-only
python /media/sf_a01_code/sortmerna/scripts/run.py --name t6 --envn LNX_VBox_Ubuntu_1804
python /mnt/c/Users/biocodz/a01_code/sortmerna/tests/run.py --name t0 --winhome /mnt/c/Users/biocodz [--capture]
|_ on WSL
'''
ST = '[run.py:__main__]'
#import pdb; pdb.set_trace()
is_opts_ok = True
# process options
optpar = OptionParser()
optpar.add_option('-n', '--name', dest='name', help='Test to run e.g. t0 | t1 | t2 | to_lf | to_crlf | all')
optpar.add_option('-f', '--func', dest='func', help='function to run: process_otu | ')
optpar.add_option('-c', '--clean', action="store_true", help='clean Work directory and exit. Requires \'--name\'')
optpar.add_option('-d', '--dbg_level', dest="dbg_level", help='debug level 0 | 1 | 2')
optpar.add_option('--btype', dest='btype', default='release', help = 'Build type: release | debug')
optpar.add_option('--pt_smr', dest='pt_smr', default='t1', help = 'Sortmerna Linkage type t1 | t2 | t3')
optpar.add_option('--winhome', dest='winhome', help='when running on WSL - home directory on Windows side e.g. /mnt/c/Users/XX')
optpar.add_option('--capture', action="store_true", help='Capture output. By default prints to stdout')
optpar.add_option('-v', '--validate-only', action="store_true", help='Only perform validation. Assumes aligement already done')
optpar.add_option('--config', dest='config', help='Tests configuration file.')
optpar.add_option('--env', dest='envfile', help='Environment variables')
optpar.add_option('-e','--envn', dest='envname', help=('Name of environment: WIN | WSL '
'| LNX_AWS | LNX_TRAVIS | LNX_VBox_Ubuntu_1804 | ..'))
optpar.add_option('-w', '--workdir', dest='workdir', help='Environment variables')
optpar.add_option('--threads', dest='threads', help='Number of threads to use')
optpar.add_option('--index', dest='index', help='Index option 0 | 1 | 2')
optpar.add_option('-t', '--task', dest='task', help='Processing task 0 | 1 | 2 | 3 | 4')
optpar.add_option('--smr-exe', dest='smr_exe', help='path to sortmerna executable. Abs or relative')
optpar.add_option('--data-dir', dest='data_dir', help='path to the data. Abs or relative')
(opts, args) = optpar.parse_args()
# process configuration
script_dir = os.path.dirname(os.path.realpath(__file__)) # directory where this script is located
SMR_SRC = os.path.dirname(script_dir)
DATA_DIR = opts.data_dir
print(f'{ST} smr source dir: {SMR_SRC} script dir: {script_dir}')
# check env.yaml. If no env file specified, try the current directory
env_yaml = os.path.join(script_dir, 'env.jinja') if not opts.envfile else opts.envfile
if not os.path.exists(env_yaml):
print('{} No environment config file found. Please, provide one using \'--env\' option'.format(ST))
sys.exit(1)
else:
# load properties from env.yaml
print('{} Using Environment configuration file: {}'.format(ST, env_yaml))
#with open(env_yaml, 'r') as envh:
# env = yaml.load(envh, Loader=yaml.FullLoader)
env_jj = Environment(loader=FileSystemLoader(os.path.dirname(env_yaml)), trim_blocks=True, lstrip_blocks=True)
env_template = env_jj.get_template(os.path.basename(env_yaml))
# render jinja template env.jinja.yaml
vars = {'UHOME': UHOME}
if IS_WSL: vars['WINHOME'] = opts.winhome
env_str = env_template.render(vars)
env = yaml.load(env_str, Loader=yaml.FullLoader)
# check test.jinja
cfgfile = os.path.join(script_dir, 'test.jinja') if not opts.config else opts.config
if not os.path.exists(cfgfile):
print('{} No build configuration template found. Please, provide one using \'--config\' option'.format(ST))
sys.exit(1)