Python filters a sequence based on sequence length to find the specified base sequence in a sequence

Merge all the Fasta sequences into one file first

Cat *.fasta > Result_all_sequence.fasta

Filter for more than 90bp

Then find the Gcat

From glob import globimport osos.chdir ("d:\\") File_in = open ("Result_all_ Sequences.fasta ",  ' R ')   #定义文件file_in to open file Result_all_sequences.fastafa_con = file_in.read ()            #.read () is to read all the contents of the file File_in.close ()                     #. Close () is to turn the file off Every_fas =  fa_con.split (">")     #.split (">") refers to the > Split the string into a list for the delimiter, the split list will not contain a, that is, after the split > disappear ##  write to the file Out_file = open ("Res.fasta",  ' W ')  #   w is writable for i in every_fas:    if i !=  "":         start = i.index ("\ n")          if len (I[start:])  >= 90:             out_file.write(">"  + i) out_file.close () #  read the file just filtered File_in = open ("Res.fasta",  ' R ')  # Define file file_in, open File Result_all_sequences.fastafa_con = file_in.read ()            #.read () is to read all the contents of the file File_in.close ()                    #.close () is to turn the file off every_fas =   Fa_con.split (">")    #.split (">") refers to dividing a string into a list with > as a delimiter, and the segmented list will not contain a, that is, after the split > disappears out_file  = open ("Ress.fasta",  ' W ') ##  find the gcatfor i in every_fas:   of each sequence   if i !=  "":        start =  I.index ("\ n")     #.index ("\ n") refers to the location or subscript of the display \ n               #print (I[start:])         # i[start:] is from \ n start until the end         seq_con = i[start:]               st_1 = seq_con.find ("GCAT")                  if st_1 != -1 and st_1 !=  len (Seq_con)  - 4:            out_ File.write (">"  + i[:start+1]+seq_con[st_1+4:])    out_file.close ()

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Python filters a sequence based on sequence length to find the specified base sequence in a sequence