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Diverse fixes #1

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Diverse fixes #1

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d6bca17
Whitespace fixes
flying-sheep May 9, 2017
2c28ca5
use subprocess instead of deprecated commands
May 9, 2017
17b4bbe
wrapped it all into functions
May 9, 2017
60067d5
allow importing
May 9, 2017
92d4780
also converted index and taxtbl
May 9, 2017
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200 changes: 106 additions & 94 deletions taxMaps
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env python
#!/usr/bin/env python

################################################################################
### COPYRIGHT ##################################################################
Expand All @@ -23,7 +23,7 @@
### MODULES ####################################################################

from optparse import OptionParser, OptionGroup
import sys, os, errno, commands, uuid
import sys, os, errno, subprocess, uuid

################################################################### /MODULES ###
################################################################################
Expand All @@ -34,12 +34,12 @@ import sys, os, errno, commands, uuid
### FUNCTIONS ##################################################################

def mkdir_p(path):
try:
os.makedirs(path)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else: raise
try:
os.makedirs(path)
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else: raise

def rp(path,start):
return os.path.relpath(path, start)
Expand Down Expand Up @@ -332,91 +332,93 @@ parser_misc.add_option(

parser.add_option_group(parser_misc)

(opt, args) = parser.parse_args()
def parse_args(args=None):
if args is None:
args = sys.argv
opt, args = parser.parse_args(args)


### check options
error_list = []
warning_list = []
### check options
error_list = []
warning_list = []

# input
input_list = []
if not opt.i_comm and not opt.i_fq and not opt.i_bam and (not opt.i_fq_1 or not opt.i_fq_2):
error_list.append('ERROR: Missing valid input [-i | -b | -f | (-1 & -2)]')
if opt.i_comm:
input_list.append('-i')
if opt.i_fq:
if missing_files(opt.i_fq):
error_list.append('ERROR: File(s) not found in [-f ' + opt.i_fq + ']')
else:
input_list.append('-f')
if opt.i_bam:
if missing_files(opt.i_bam):
error_list.append('ERROR: File(s) not found in [-b ' + opt.i_bam + ']')
else:
input_list.append('-b')
if opt.i_fq_1 and opt.i_fq_2:
if len(opt.i_fq_1.split(',')) != len(opt.i_fq_2.split(',')):
error_list.append('ERROR: Different number of R1 an R2 files [-1 ' + opt.i_fq_1 + ' -2 ' + opt.i_fq_2 + ']')
else:
if missing_files(opt.i_fq_1) or missing_files(opt.i_fq_2):
error_list.append('ERROR: File(s) not found in [-1 ' + opt.i_fq_1 + ' -2 ' + opt.i_fq_2 + ']')
# input
input_list = []
if not opt.i_comm and not opt.i_fq and not opt.i_bam and (not opt.i_fq_1 or not opt.i_fq_2):
error_list.append('ERROR: Missing valid input [-i | -b | -f | (-1 & -2)]')
if opt.i_comm:
input_list.append('-i')
if opt.i_fq:
if missing_files(opt.i_fq):
error_list.append('ERROR: File(s) not found in [-f ' + opt.i_fq + ']')
else:
input_list.append('(-1 & -2)')
if len(input_list) > 1:
error_list.append('ERROR: Too many inputs [' + ' & '.join(input_list) + ']')
input_list.append('-f')
if opt.i_bam:
if missing_files(opt.i_bam):
error_list.append('ERROR: File(s) not found in [-b ' + opt.i_bam + ']')
else:
input_list.append('-b')
if opt.i_fq_1 and opt.i_fq_2:
if len(opt.i_fq_1.split(',')) != len(opt.i_fq_2.split(',')):
error_list.append('ERROR: Different number of R1 an R2 files [-1 ' + opt.i_fq_1 + ' -2 ' + opt.i_fq_2 + ']')
else:
if missing_files(opt.i_fq_1) or missing_files(opt.i_fq_2):
error_list.append('ERROR: File(s) not found in [-1 ' + opt.i_fq_1 + ' -2 ' + opt.i_fq_2 + ']')
else:
input_list.append('(-1 & -2)')
if len(input_list) > 1:
error_list.append('ERROR: Too many inputs [' + ' & '.join(input_list) + ']')



# mapping
n_indexes = 0
if opt.m_indices:
if missing_files(opt.m_indices):
error_list.append('ERROR: File(s) not found in [-d ' + opt.m_indices + ']')
else:
n_indexes = len(opt.m_indices.split(','))
if not n_indexes:
error_list.append('ERROR: Missing valid index(es) [-d]')

n_dist = len(opt.m_edits.split(','))
if n_dist != n_indexes and n_indexes:
if n_dist == 1 :
warning_list.append('WARNING: Setting the maximum edit distance for all indexes [-e ' + ','.join([opt.m_edits]*n_indexes) + ']')
else:
error_list.append('ERROR: ' + str(n_dist) + ' distances specified [-e ' + opt.m_edits + '], incompatible with ' + str(n_indexes) + ' indexes [-d ' + opt.m_indices + ']')
# mapping
n_indexes = 0
if opt.m_indices:
if missing_files(opt.m_indices):
error_list.append('ERROR: File(s) not found in [-d ' + opt.m_indices + ']')
else:
n_indexes = len(opt.m_indices.split(','))
if not n_indexes:
error_list.append('ERROR: Missing valid index(es) [-d]')

n_dist = len(opt.m_edits.split(','))
if n_dist != n_indexes and n_indexes:
if n_dist == 1 :
warning_list.append('WARNING: Setting the maximum edit distance for all indexes [-e ' + ','.join([opt.m_edits]*n_indexes) + ']')
else:
error_list.append('ERROR: ' + str(n_dist) + ' distances specified [-e ' + opt.m_edits + '], incompatible with ' + str(n_indexes) + ' indexes [-d ' + opt.m_indices + ']')

n_cpus = len(opt.m_cpus.split(','))
if n_cpus != n_indexes and n_indexes:
if n_cpus == 1 :
warning_list.append('WARNING: Setting the number of CPUs for all indexes [-c ' + ','.join([opt.m_cpus]*n_indexes) + ']')
n_cpus = len(opt.m_cpus.split(','))
if n_cpus != n_indexes and n_indexes:
if n_cpus == 1 :
warning_list.append('WARNING: Setting the number of CPUs for all indexes [-c ' + ','.join([opt.m_cpus]*n_indexes) + ']')
else:
error_list.append('ERROR: ' + str(n_cpus) + ' CPU specifications [-c ' + opt.m_cpus + '], incompatible with ' + str(n_indexes) + ' indexes [-d ' + opt.m_indices + ']')


# taxonomy
if opt.t_table:
if missing_files(opt.t_table):
error_list.append('ERROR: File not found [-t ' + opt.t_table + ']')
else:
error_list.append('ERROR: ' + str(n_cpus) + ' CPU specifications [-c ' + opt.m_cpus + '], incompatible with ' + str(n_indexes) + ' indexes [-d ' + opt.m_indices + ']')
error_list.append('ERROR: Missing taxonomic table [-t]')


# taxonomy
if opt.t_table:
if missing_files(opt.t_table):
error_list.append('ERROR: File not found [-t ' + opt.t_table + ']')
else:
error_list.append('ERROR: Missing taxonomic table [-t]')
if opt.t_mode not in ['s', 'p', 'P']:
error_list.append('ERROR: Invalid mode [-m ' + opt.t_mode + ']')


# misc
if opt.m_queue:
if opt.m_queue not in subprocess.check_output('qstat -g c | egrep "CLUSTER|\--" -v | awk \'{print $1}\'', shell=True).split('\n'):
error_list.append('ERROR: Specified queue does not exist [-q ' + opt.m_queue + ']')
ecounter += 1

sys.stderr.write('\n'.join(warning_list) + '\n')
if error_list:
raise Exception('\n'.join(error_list) + '\n\n')

if opt.t_mode not in ['s', 'p', 'P']:
error_list.append('ERROR: Invalid mode [-m ' + opt.t_mode + ']')
return opt, args


# misc
if opt.m_queue:
if opt.m_queue not in commands.getoutput('qstat -g c | egrep "CLUSTER|\--" -v | awk \'{print $1}\'').split('\n'):
error_list.append('ERROR: Specified queue does not exist [-q ' + opt.m_queue + ']')
ecounter += 1


sys.stderr.write('\n'.join(warning_list) + '\n')
if error_list:
sys.stderr.write('\n'.join(error_list) + '\n\n')
parser.print_help()
exit(-1)

######################################################### /ARGUMENTS,OPTIONS ###
################################################################################

Expand All @@ -433,9 +435,16 @@ if error_list:
################################################################################
### MAIN #######################################################################

if __name__ == '__main__':
def main(args=None):
try:
opt, args = parse_args(args)
except Exception as e:
sys.stderr.write(str(e))
parser.print_help()
sys.exit(-1)

# base dirs
module_dir = os.path.abspath(os.path.dirname(__file__))
module_dir = os.path.realpath(os.path.dirname(__file__))
start_dir = os.getcwd()

prefix = opt.m_prefix
Expand Down Expand Up @@ -490,8 +499,8 @@ if __name__ == '__main__':
q_offset = opt.p_qoff

# mapping
index_files = opt.m_indices.split(',')
len_files = ['.'.join(f.split('.')[:-1]) + '.len' for f in index_files]
index_files = opt.m_indices.split(',')
len_files = ['.'.join(f.split('.')[:-1]) + '.len' for f in index_files]

index_names = ['.'.join(os.path.basename(f).split('.')[:-1]) for f in index_files]

Expand Down Expand Up @@ -519,8 +528,8 @@ if __name__ == '__main__':

det_mode = opt.t_mode

comp_coverage = opt.r_cov
exc_taxa = opt.r_exc
comp_coverage = opt.r_cov
exc_taxa = opt.r_exc

# report
rep_cutoff = opt.r_cutoff
Expand Down Expand Up @@ -548,7 +557,7 @@ if __name__ == '__main__':
input_command = comm_str
elif opt.i_fq:
if opt.i_fq[-3:] == '.gz':
input_command = 'zcat ' + ' '.join([rp(fq_lnk, run_dir) for fq_lnk in fq_lnks])
input_command = 'zcat ' + ' '.join([rp(fq_lnk, run_dir) for fq_lnk in fq_lnks])
else:
input_command = 'cat ' + ' '.join([rp(fq_lnk, run_dir) for fq_lnk in fq_lnks])
elif opt.i_bam:
Expand Down Expand Up @@ -617,9 +626,9 @@ if __name__ == '__main__':
map_out = rp(map_dir + '/' + prefix + '.' + index_names[i] + '.map', run_dir)
out_files.append(map_out)
map_str = gem_command + ' '.join([' -I', map_index, '-m', map_dist, '-e', map_dist, '-T', map_cpus, '2>', map_log, ' \\\n\t| txM_rescore \\\n\t| '])
map_str += 'txM_mapout 2> ' + map_out
map_str += 'txM_mapout 2> ' + map_out
map_commands.append(map_str)
map_lnker = ' \\\n\t| ' + 'txM_gem2fq \\\n\t| '
map_lnker = ' \\\n\t| ' + 'txM_gem2fq \\\n\t| '
map_command = map_lnker.join(map_commands)
map_out = rp(map_dir + '/' + prefix + '.unmapped.map', run_dir)
out_files.append(map_out)
Expand All @@ -636,8 +645,8 @@ if __name__ == '__main__':
else:
tax_command = 'txM_mergintlv '
tax_command += ' '.join(out_files)
tax_command += ' 2> /dev/null \\\n\t| '
tax_command += 'txM_lca '
tax_command += ' 2> /dev/null \\\n\t| '
tax_command += 'txM_lca '
tax_command += '-t ' + rp(tax_lnk, run_dir) + ' '
tax_command += '-m ' + det_mode + ' '
tax_command += '2> ' + rp(map_dir + '/' + prefix + '.merged.map.lca', run_dir)
Expand All @@ -647,7 +656,7 @@ if __name__ == '__main__':
tax_command += '-e ' + max_edit + ' '
if comp_coverage:
tax_command += '-c '
tax_command += '-l ' + ','.join([rp(x, run_dir) for x in len_lnks]) + ' '
tax_command += '-l ' + ','.join([rp(x, run_dir) for x in len_lnks]) + ' '
if exc_taxa:
tax_command += '-x ' + exc_taxa + ' '
tax_command += '2> /dev/null > ' + rp(out_dir + '/' + prefix + '.merged.map.lca.summary', run_dir)
Expand All @@ -667,7 +676,7 @@ if __name__ == '__main__':
sh_file.write(tax_command + '\n\n')
sh_file.write('cd ' + rp(out_dir, run_dir) +'\n')
sh_file.write(rep_command + '\n')
sh_file.close()
sh_file.close()

if sge_queue:
pipe_file = open(pipe_filename, 'w')
Expand All @@ -685,3 +694,6 @@ if __name__ == '__main__':

###################################################################### /MAIN ###
################################################################################

if __name__ == '__main__':
main()
19 changes: 12 additions & 7 deletions taxMaps-index
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Original file line number Diff line number Diff line change
Expand Up @@ -115,11 +115,6 @@ parser.add_option(
help = "Dry run (default = False)"
)

(opt, args) = parser.parse_args()
if not opt.fasta_file or not opt.corr_file or not opt.tax_file:
parser.print_help()
sys.exit(-1)


######################################################### /ARGUMENTS,OPTIONS ###
################################################################################
Expand All @@ -137,7 +132,15 @@ if not opt.fasta_file or not opt.corr_file or not opt.tax_file:
################################################################################
### MAIN #######################################################################

if __name__ == '__main__':
def main(args=None):
if args is None:
args = sys.argv

opt, args = parser.parse_args(args)
if not opt.fasta_file or not opt.corr_file or not opt.tax_file:
parser.print_help()
sys.exit(-1)

module_dir = os.path.abspath(os.path.dirname(__file__))

fasta_f = opt.fasta_file
Expand All @@ -160,7 +163,7 @@ if __name__ == '__main__':
if sge_queue:
sge_f = prefix + '.sge'

dry_run = opt.dry
dry_run = opt.dry

gitax_str = ' '.join(['txM_gitax', '-i', fasta_f, '-c', gitax_f,'-t', tax_f, '2>', out_f, '>', in_f])
len_str = ' '.join(['txM_fastalen', '-i', in_f, '>', len_f])
Expand All @@ -187,3 +190,5 @@ if __name__ == '__main__':
###################################################################### /MAIN ###
################################################################################

if __name__ == '__main__':
main()
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