from Bio import SeqIO

list_file = "/srv/projects3/human_plasmids/georgina/16_Host_Linkage/1_Blast/Outv2/MAGS_plasmidA_list.txt"

# open list text file

f = open(list_file, 'r')

# set mag directory

mag_dir = "/srv/projects3/human_plasmids/georgina/7_coverm/reformatted_mags/"

# set cluster directory

n = 0

for line in f.readlines():

subject = line.split("\t")[1].strip("\n\t")

print("Subject:", subject)

assemblyname = "f."+subject.split("_")[0]

print("Assembly:", assemblyname)

assembly = list(SeqIO.parse("{}/{}".format(mag_dir, assemblyname), 'fasta'))

print("Opening Assembly {} of length {}".format(assemblyname, len(assembly)))

new = []

for seq_record in assembly:

if seq_record.id != subject:

new.append(seq_record)

elif seq_record.id == subject:

n = n+1

SeqIO.write(new, "{}/{}".format(mag_dir, assemblyname), 'fasta')

print("Done! Deleted ", n, " contigs.")