if double_stranded:
str_ec = ' -d '
else:
str_ec = ' '
#run_cmd('python ' + shannon_dir + 'extension_correction.py ' + str_ec + sample_name_input+'algo_input/k1mer.dict_org ' +sample_name_input+'algo_input/k1mer.dict ' + str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' + comp_directory_name + " " + str(comp_size_threshold))
str_ec += sample_name_input+'algo_input/k1mer.dict_org ' +sample_name_input+'algo_input/k1mer.dict ' + str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' + comp_directory_name + " " + str(comp_size_threshold) + " " + str(nJobs) + " " + reads_string
dontWriteToFile = True
k1mer_dictionary,reads = extension_correction(str_ec.split(),dontWriteToFile)
# Gets kmers from k1mers
'''if run_jellyfish or run_extension_corr:
run_cmd('python ' + shannon_dir + 'kp1mer_to_kmer.py ' + sample_name_input+'algo_input/k1mer.dict ' + sample_name_input+'algo_input/kmer.dict')'''
# Runs gpmetis to partition components of size above "partition_size" into partitions of size "partition_size"
# Gets k1mers, kmers, and reads for each partition
[components_broken, new_components, contig_weights, rps] = kmers_for_component(k1mer_dictionary,kmer_directory, reads,reads_files, base_directory_name, contig_file_extension, get_partition_kmers, double_stranded, paired_end, use_second_iteration, partition_size, overload, K, gpmetis_path, penalty, only_reads, inMem,nJobs)
k1mer_dictionary.clear() #Delete in memory
components_broken.clear()
# This counts remaining and non-remaining partitions for log.
num_remaining = 0
num_non_remaining = 0
for part in new_components:
if 'remaining' in part:
num_remaining += 1
else:
num_non_remaining += 1
# This code updates the log
if os.path.exists(comp_directory_name+"/before_sp_log.txt"):
f_log = open(comp_directory_name+"/before_sp_log.txt", 'a')
sample_name_input + 'algo_input/k1mer.dict ' +
str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' +
comp_directory_name + " " + str(comp_size_threshold))
# Gets kmers from k1mers
if run_jellyfish or run_extension_corr:
run_cmd('python ' + shannon_dir + 'kp1mer_to_kmer.py ' +
sample_name_input + 'algo_input/k1mer.dict ' + sample_name_input +
'algo_input/kmer.dict')
# Runs gpmetis to partition components of size above "partition_size" into partitions of size "partition_size"
# Gets k1mers, kmers, and reads for each partition
[components_broken, new_components
] = kmers_for_component(kmer_directory, reads_files, base_directory_name,
r1_contig_file_extension, r1_new_kmer_tag,
r1_graph_file_extension, get_og_comp_kmers,
get_partition_kmers, double_stranded, paired_end,
False, partition_size, overload, K, gpmetis_path)
# This counts remaining and non-remaining partitions for log.
num_remaining = 0
num_non_remaining = 0
for part in new_components:
if "remaining" in part:
num_remaining += 1
else:
num_non_remaining += 1
# If "use_second_partition", rerun gpmetis with a penalization for contig edges broken in old partitioning
# This to give a new partitioning for each component of size above "partition_size"
# Gets k1mers, kmers, and reads for each partition
#run_cmd('rm ' + base_directory_name+"/component*contigs.txt")
if double_stranded:
str_ec = ' -d '
else:
str_ec = ' '
run_cmd('python ' + shannon_dir + 'extension_correction.py ' + str_ec + sample_name_input+'algo_input/k1mer.dict_org ' +sample_name_input+'algo_input/k1mer.dict ' + str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' + comp_directory_name + " " + str(comp_size_threshold))
# Gets kmers from k1mers
if run_jellyfish or run_extension_corr:
run_cmd('python ' + shannon_dir + 'kp1mer_to_kmer.py ' + sample_name_input+'algo_input/k1mer.dict ' + sample_name_input+'algo_input/kmer.dict')
# Runs gpmetis to partition components of size above "partition_size" into partitions of size "partition_size"
# Gets k1mers, kmers, and reads for each partition
[components_broken, new_components] = kmers_for_component(kmer_directory, reads_files, base_directory_name, r1_contig_file_extension, r1_new_kmer_tag, r1_graph_file_extension, get_og_comp_kmers, get_partition_kmers, double_stranded, paired_end, False, partition_size, overload, K, gpmetis_path)
# This counts remaining and non-remaining partitions for log.
num_remaining = 0
num_non_remaining = 0
for part in new_components:
if "remaining" in part:
num_remaining += 1
else:
num_non_remaining += 1
# If "use_second_partition", rerun gpmetis with a penalization for contig edges broken in old partitioning
# This to give a new partitioning for each component of size above "partition_size"
# Gets k1mers, kmers, and reads for each partition
if use_second_iteration:
r2_graph_file_extension = "r2.txt"
if double_stranded:
str_ec = ' -d '
else:
str_ec = ' '
#run_cmd('python ' + shannon_dir + 'extension_correction.py ' + str_ec + sample_name_input+'algo_input/k1mer.dict_org ' +sample_name_input+'algo_input/k1mer.dict ' + str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' + comp_directory_name + " " + str(comp_size_threshold))
str_ec += sample_name_input+'algo_input/k1mer.dict_org ' +sample_name_input+'algo_input/k1mer.dict ' + str(hyp_min_weight) + ' ' + str(hyp_min_length) + ' ' + comp_directory_name + " " + str(comp_size_threshold) + " " + str(nJobs) + " " + reads_string
dontWriteToFile = True
k1mer_dictionary,reads = extension_correction(str_ec.split(),dontWriteToFile)
# Gets kmers from k1mers
'''if run_jellyfish or run_extension_corr:
run_cmd('python ' + shannon_dir + 'kp1mer_to_kmer.py ' + sample_name_input+'algo_input/k1mer.dict ' + sample_name_input+'algo_input/kmer.dict')'''
# Runs gpmetis to partition components of size above "partition_size" into partitions of size "partition_size"
# Gets k1mers, kmers, and reads for each partition
[components_broken, new_components, contig_weights, rps] = kmers_for_component(k1mer_dictionary,kmer_directory, reads,reads_files, base_directory_name, contig_file_extension, get_partition_kmers, double_stranded, paired_end, use_second_iteration, partition_size, overload, K, gpmetis_path, penalty, only_reads, inMem,nJobs)
k1mer_dictionary.clear() #Delete in memory
components_broken.clear()
# This counts remaining and non-remaining partitions for log.
num_remaining = 0
num_non_remaining = 0
for part in new_components:
if 'remaining' in part:
num_remaining += 1
else:
num_non_remaining += 1
# This code updates the log
if os.path.exists(comp_directory_name+"/before_sp_log.txt"):
f_log = open(comp_directory_name+"/before_sp_log.txt", 'a')
