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cut_contamination.py
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cut_contamination.py
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import os
import time
import datetime
import sys
import pprint
import pickle
def get_mag_multicopy_info_dict(mag_list,gene_copy_type,path_to_checkm_ext_file,show=False):
print(f'\n***Writing mag\'s multicopy gene accession code to mag_multicopy_info_dictionary, mag list: {mag_list} ***\n')
mag_multicopy_info={}
for i in range(len(mag_list)):
mag_multicopy_info[mag_list[i]]={}
for j in range(len(gene_copy_type)):
f=os.popen("grep -w \"%s\" %s | awk -F \"'%s': \" '{print $2}' | cut -d '[' -f2 | cut -d ']' -f1 | cut -d ',' -f1-" % (mag_list[i],path_to_checkm_ext_file,gene_copy_type[j]))#"'PF02686', 'PF01807'\n"
accessions=f.read()
mag_multicopy_info[mag_list[i]][gene_copy_type[j]]=accessions.lstrip('\"\'').rstrip('\'\n').split('\', \'')#{'CAMI_UT_6.metaspades.maxbin2.bin.2':{'GCN2': ['PF02686', 'PF01807'],'GCN3': [''],'GCN4': [''],'GCN5+': ['']}}
if show:
print("mag_multicopy_info:\n")
pprint.pprint(mag_multicopy_info)
return mag_multicopy_info
#The mag_multicopy_info_dict is look like:
# mag_multicopy_info:
# {'3HX0022.metaspades.metabat2_graphbin_dastools.bin.13': {'GCN2': ['PF01396',
# 'PF00276'],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']},
# '3HX0029.metaspades.maxbin2_graphbin_dastools.bin.17': {'GCN2': ['PF03412'],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']},
# '3HX0257.metaspades.concoct_graphbin_dastools.bin.3': {'GCN2': ['PF01396'],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']},
# '3HX0290.metaspades.maxbin2_graphbin_dastools.bin.9': {'GCN2': [''],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']},
# '3HX0296.metaspades.metabat2_graphbin_dastools.bin.17_sub': {'GCN2': ['PF02361',
# 'PF02590',
# 'PF02463'],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']},
# '3HX0451.metaspades.maxbin2_graphbin_dastools.bin.21': {'GCN2': ['PF04011',
# 'TIGR00482'],
# 'GCN3': [''],
# 'GCN4': [''],
# 'GCN5+': ['']}}
def read_in_mag_file(mag_name,mag_suffix,path_to_mag_folder):
print('\n***Reading in mag file ...***\n')
with open(f'{path_to_mag_folder}/{mag_name}.{mag_suffix}','r') as f:
mag_file=f.readlines()#['>NODE_27_length_288659_cov_40.979365\n','CGGGCTACGCATGTGTCCGTTTCCTTGGCCATGGAGAGTGCGCCATTAAA\n',...]
contigs={}#{'>NODE_27_length_288659_cov_40.979365':'CGGGCTACGCATGTGTCCGTTTCCTTGGCCATGGAGAGT...',...}
i=0
while i<len(mag_file):
if mag_file[i][0]=='>':
contig_name=mag_file[i].rstrip()[1:]
contigs[contig_name]=mag_file[i+1].rstrip()
i=i+2
else:
contigs[contig_name]=contigs[contig_name]+mag_file[i].rstrip()
i=i+1
return contigs
def append_contig_to_seq_interval_dict(cut_seq_info,hmm_result):#{'NODE_697_length_11598_cov_4.457252': [[4881, 6023], [1962, 3236], [1962, 3236]],...}
hmm_contig_name=hmm_result.pop(0)#'NODE_697_length_11598_cov_4.457252_7'
strain_type=hmm_result.pop()#'-1'
contig_length=int(hmm_contig_name.split('_')[3])#11598
contig_name='_'.join(hmm_contig_name.split('_')[0:6])#'NODE_697_length_11598_cov_4.457252'
seq_interval=[]
# if strain_type=='-1':#不管是正负链，checkm的结果都是显示正链的区间
# seq_interval.append([contig_length-int(hmm_result[1])+1,contig_length-int(hmm_result[0])+1])#5576,6718 => [11598-6718+1,11598-5576+1]
# else:
seq_interval.append([int(hmm_result[0]),int(hmm_result[1])])
if contig_name in cut_seq_info:
cut_seq_info[contig_name].extend(seq_interval)
else:
cut_seq_info[contig_name]=seq_interval
return cut_seq_info
#The cut_seq_info is look like:
# {'NODE_604_length_10964_cov_2.766235': [[8502, 9059]],
# 'NODE_499_length_13456_cov_2.127439': [[6020, 6361]]}
#The number in the list is the contamination interval of this contig
def find_min_max(internal1,internal2):#[4,6],[3,5] => [3,6]
internal1.extend(internal2)
internal1.sort()
return [internal1[0],internal1[3]]
def merge_overlap(internal_array):#[[4,7],[1,2],[3,5],[1,3],[8,10]] => [[1,7],[8,10]]
merged_interval=[]
while(internal_array):
internal1=internal_array.pop(0)
while True:
i=0
change=0
while(i<len(internal_array)):
if internal1[1]<internal_array[i][0]:
i=i+1
else:
if internal1[0]>internal_array[i][1]:
i=i+1
else:
internal1=find_min_max(internal1,internal_array[i])
change=change+1
internal_array.pop(i)
if change==0:
break
merged_interval.append(internal1)
#Bubble sort
for i in range(len(merged_interval)-1):#[[8,10],[4,5],[1,2]] => [[1,2],[4,5],[8,10]]
for j in range(len(merged_interval)-i-1):
if merged_interval[j][0]>merged_interval[j+1][0]:
temp=merged_interval[j]
merged_interval[j]=merged_interval[j+1]
merged_interval[j+1]=temp
return merged_interval
def do_cutting(raw_contigs,cut_seq_info):# raw_contigs: {'NODE_1_length_78_cov_1': 'TTAACAGCGCG...',...}, cut_seq_info: {'NODE_1_length_78_cov_1': [[1,2],[3,4]],...}
def length_check(raw_contigs,contig_name,raw_contigs_seq,head,end,split_count):
if end-head+1>=12:# smallest gene length: start codon, stop codon and two amino acid
split_count=split_count+1
raw_contigs[f'{contig_name}_cutted_{split_count}']=raw_contigs_seq[(head-1):end]
return raw_contigs,split_count
print("\n***Starting cutting process ...***\n")
for contig_name in cut_seq_info:# 'NODE_1_length_78_cov_1'
raw_contigs_seq=raw_contigs.pop(contig_name)# 'TTAA...'
contig_length=int(contig_name.split('_')[3])# 78
interval_list=cut_seq_info[contig_name]# [[1,2],[3,4]]
split_count=0
if len(interval_list)==1:
if interval_list[0][0]>1:
raw_contigs,split_count=length_check(raw_contigs,contig_name,raw_contigs_seq,1,interval_list[0][0]-1,split_count)
if interval_list[0][1]<contig_length:
raw_contigs,split_count=length_check(raw_contigs,contig_name,raw_contigs_seq,interval_list[0][1]+1,contig_length,split_count)
else:
for i in range(len(interval_list)):
if i==0:# the first interval [1,2]
if interval_list[i][0]==1:# [1,2]
continue
else:# the first interval is like [2,3]
raw_contigs,split_count=length_check(raw_contigs,contig_name,raw_contigs_seq,1,interval_list[i][0]-1,split_count)
continue
elif i==len(interval_list)-1 and interval_list[i][1]!=contig_length:# the last interval [3,4]
raw_contigs,split_count=length_check(raw_contigs,contig_name,raw_contigs_seq,interval_list[i][1]+1,contig_length,split_count)
raw_contigs,split_count=length_check(raw_contigs,contig_name,raw_contigs_seq,interval_list[i-1][1]+1,interval_list[i][0]-1,split_count)
if split_count:
print(f'The contig {contig_name} was split to {split_count} segments. Interval list of this contig\'s contaminations: {interval_list}\n')
else:
print('\n----------\n')
print(f'The contig {contig_name} was highly contaminated and thrown away! Interval list of this contig\'s contaminations: {interval_list}\n')
print('\n----------\n')
print("\n***Cutting process finished!***\n")
return raw_contigs
#The cutting process's output during running is look like:
# ***Starting cutting process ...***
# The contig NODE_604_length_10964_cov_2.766235 was split to 2 segments. Interval list of this contig's contaminations: [[8502, 9059]]
# ----------
# The contig NODE_9171_length_1093_cov_4.129921 was highly contaminated and thrown away! Interval list of this contig's contaminations: [[3, 1091]]
# ----------
# The contig NODE_499_length_13456_cov_2.127439 was split to 2 segments. Interval list of this contig's contaminations: [[6020, 6361]]
# ***Cutting process finished!***
# Cutted contigs were written to file: ./cutted_mag/3HX0451.metaspades.maxbin2_graphbin_dastools.bin.21_cutted.fa !
# Contamination cutting with 3HX0451.metaspades.maxbin2_graphbin_dastools.bin.21 finished!
# Running time: 0:00:03.716863
# ----------
def write_in_cutted_mag(cutted_contigs,mag_name,path_to_save_the_cutted_mag,mag_suffix):
if os.system(f'ls {path_to_save_the_cutted_mag}'):
os.system(f'mkdir -p {path_to_save_the_cutted_mag}')
path_to_cutted_file=f'{path_to_save_the_cutted_mag}/{mag_name}_cutted.{mag_suffix}'
with open(path_to_cutted_file,'w') as f:
for contig_name in cutted_contigs:
f.write('>'+contig_name+'\n')
base_count=0
for bases in cutted_contigs[contig_name]:
if base_count==60:
f.write('\n')
base_count=0
f.write(bases)
base_count=base_count+1
f.write('\n')
print(f'Cutted contigs were written to file: {path_to_cutted_file} !')
def main():
mag_suffix='fa'
mag_list=['CAMI_UT_0.metaspades.metabat2.graphbin2.bin.18']#CAMI_UT_6.metaspades.maxbin2.bin.2']
path_to_mag_folder='/store/yhshao/META/metapi_result_cami/link_to_mag_vamb_graphbin2'
path_to_checkm_bins_folder='/store/yhshao/META/metapi_result_cami/checkm_output/bins'
path_to_checkm_storage_folder='/store/yhshao/META/metapi_result_cami/checkm_output/storage'
path_to_checkm_ext_file='/store/yhshao/META/metapi_result_cami/checkm_output/storage/bin_stats_ext.tsv'
path_to_save_the_cutted_mag='/store/yhshao/META/cutted_mag'
gene_copy_type=['GCN2','GCN3','GCN4','GCN5+']
# Using the all_cut_mode carefully, or if you know what are you doing!
# Warning1: If the multicopy's E-value is greater than all_cut_threshold given, this kind of multicopy will escape the cutting process!
# Warning2: If the domain is not a multicopy but it's E-value is below the all_cut_threshold given, because of the all_cut_mode, you will cut them all,
# which will cause the mis-cut if this domain contain a part of sequence that are from an one-copy gene!
all_cut_mode=False
all_cut_threshold='1e-10'
mag_count=1
mag_multicopy_info=get_mag_multicopy_info_dict(mag_list,gene_copy_type,path_to_checkm_ext_file,show=True)
for mag_name in mag_multicopy_info:#'CAMI_UT_6.metaspades.maxbin2.bin.2',...
start=datetime.datetime.now()
text=f'\n<<< Starting contamination cutting process with {mag_name}({mag_count}/{len(mag_list)}) ... >>>\n'
for words in text:
sys.stdout.write(words)
sys.stdout.flush()
time.sleep(0.01)
cut_seq_info={}#{'NODE_697_length_11598_cov_4.457252': [4881, 6023, 1962, 3236, 1962, 3236],...}
print("\n***Filling contigs and contaminations seq information into the cut_seq_info dictionary ...***\n")
for multicopy_type in mag_multicopy_info[mag_name]:#'GCN2','GCN3','GCN4','GCN5+'
for domain_accession in mag_multicopy_info[mag_name][multicopy_type]:#'PF02686', 'PF01807',...
if domain_accession:
if all_cut_mode:
if all_cut_threshold:
# 'NODE_697_length_11598_cov_4.457252_7 5576 6718 -1' E-value: $7=>"1.5e-113" , cut all of the genes that E-value below the all_cut_threshold
f=os.popen("grep -w \"%s\" %s/%s/hmmer.analyze.txt | awk '{if($7<%s)print $1,$24,$26,$28}' | sed -n '2,$p'" % (domain_accession,path_to_checkm_bins_folder,mag_name,all_cut_threshold))
else:
print("Please input the all_cut_threshold!")
else:
if multicopy_type=='GCN5+':
print(f'GCN5+ exists in {mag_name}, just choosing TOP 2~5 contamination to cut!')
# 'NODE_697_length_11598_cov_4.457252_7 5576 6718 -1', Don't care about the E-value, only cut the called multicopy, e.g. GCN2 type only cut the second multicopy.
f=os.popen("grep -w \"%s\" %s/%s/hmmer.analyze.txt | awk '{print $1,$24,$26,$28}' | sed -n '2,%sp'" % (domain_accession,path_to_checkm_bins_folder,mag_name,multicopy_type[3]))
hmm_result_list=f.read().split('\n')
#'NODE_697_length_11598_cov_4.457252_7 5576 6718 -1\n' => ['NODE_697_length_11598_cov_4.457252_7 5576 6718 -1','']
#'NODE_11329_length_918_cov_1.783591_3 844 918 -1\nNODE_436_length_18290_cov_4.347993_1 1 75 1\n' => ['NODE_11329_length_918_cov_1.783591_3 844 918 -1','NODE_436_length_18290_cov_4.347993_1 1 75 1','']
hmm_result_list.pop()
for result in hmm_result_list:
hmm_result=result.split(' ')#'NODE_697_length_11598_cov_4.457252_7 5576 6718 -1' => ['NODE_697_length_11598_cov_4.457252_7','5576','6718','-1']
cut_seq_info=append_contig_to_seq_interval_dict(cut_seq_info,hmm_result)
print("\n***Filling process finished!***\n")
if cut_seq_info:
print("\n***Starting overlap merging process ...***\n")
for contig_interval_list in cut_seq_info:#{'NODE_1177_length_6645_cov_37.049635': [[4656, 5495]],...}
if len(cut_seq_info[contig_interval_list])>1:
cut_seq_info[contig_interval_list]=merge_overlap(cut_seq_info[contig_interval_list])
print("\n***Merging process finished!***\n")
raw_contigs=read_in_mag_file(mag_name,mag_suffix,path_to_mag_folder)
cutted_contigs=do_cutting(raw_contigs,cut_seq_info)
write_in_cutted_mag(cutted_contigs,mag_name,path_to_save_the_cutted_mag,mag_suffix)
else:
print(f'There are no contaminations in the MAG: {mag_name}.{mag_suffix} !')
print(f'Copy MAG to saving_folder: {path_to_save_the_cutted_mag}/{mag_name}.{mag_suffix}\n')
if os.system(f'ls {path_to_save_the_cutted_mag}'):
os.system(f'mkdir -p {path_to_save_the_cutted_mag}')
os.system(f'cp {path_to_mag_folder}/{mag_name}.{mag_suffix} {path_to_save_the_cutted_mag}')
print(f'Contamination cutting with {mag_name} finished!\n')
end=datetime.datetime.now()
running_time=end-start
print("Running time: ",running_time)
print("----------\n")
mag_count=mag_count+1
print("All processes finished!")
if __name__=='__main__':
main()