how to print a loop output in a table format using python

Question

My script is working but I have not been able to print output in a table format. I have two files - I read file1 sequences and see if any of them binds with any sequence in file2.

file1.fa

>seq1
ACCGG
>seq2
AATTTC

file2.fa

>seq3
CCGGT
>seq9
GGGGGGCCC

current output:

---
file1.seq
>seq1
ACCGG
file2.seq
>seq3
CCGGT

Based on the files only seq1 binds with seq3 and the current output based on my code is correct but then I have to get the output I want in a format showing every sequence ids against each other - marked with 1 if they interact and marked with 0 if they do not.

I need help to fix the print part to get output in a table format as below:

    file2   seq3   seq9
file1 

seq1          1         0

seq2          0         0

My code:

from Bio import SeqIO
from Bio.Seq import Seq

records=list(SeqIO.parse("file1.fa","fasta"))

window_size = 5
step_size = 1

target_records=list(SeqIO.parse("file2.fa","fasta"))

for i in records:
    for j in range(0, len(i.seq)-window_size+1):
        for k in (i.seq.reverse_complement()[j: j+5].split()):
            for l in target_records:
                if l.seq.find(k)!=-1:
                    print('---\n{}\n>{}\n{}\n{}\n>{}\n{}'.format ("file1.seq", i.id,i.seq, "file2.seq", l.id,l.seq))

Thank you

Answer 1

i'd like to uses pandas when i want get the table format:
for example:

from Bio import SeqIO
import pandas as pd


def same_seq(a_record, brecord):
    window_size = 5
    step_size = 1
    for j in range(0, len(a_record.seq) - window_size + 1):
        for k in (a_record.seq.reverse_complement()[j: j + 5].split()):
            return brecord.seq.find(k) != -1


if __name__ == '__main__':
    records = list(SeqIO.parse("file1.fa", "fasta"))
    target_records = list(SeqIO.parse("file2.fa", "fasta"))
    rows_list = []
    for target_record in target_records:
        new_row = {'name': target_record.name}
        for record in records:
            if same_seq(record, target_record):
                new_row[record.name] = 1
            else:
                new_row[record.name] = 0
        rows_list.append(new_row)
    df = pd.DataFrame(rows_list)
    df = df.set_index(["name"])
    print(df)

      seq1  seq2
name            
seq3     1     0
seq9     0     0

if you wana change the compare of seq:
you should use seq[j: j+5].reverse_complement() but seq.reverse_complement()[j: j+5] I'm not sure if I understand it right
file1.fa

>seq1
ACCGG
>seq2
AATTTC
>seqtest1
NNNACCGTGCNN

file1.fa

>seq1
ACCGG
>seq2
AATTTC
>seqtest1
NNNACCGTGCNN

file2.fa

>seq3
CCGGT
>seq9
GGGGGGCCC
>seqtest2
NNCACGGTNN

from Bio import SeqIO
import pandas as pd



def same_seq_window(a_record, b_record, window_size):
    for i in range(len(a_record.seq)- window_size + 1):
        a_seq = a_record.seq[i: i + window_size]
        if b_record.seq.find(a_seq.reverse_complement()) != -1:
            return True
    return False

def same_seq(a_record, b_record):
    window_sizes = range(5, len(a_record.seq)+1)
    for window_size in window_sizes:
        if same_seq_window(a_record, b_record, window_size):
            return True
    return False

if __name__ == '__main__':
    records = list(SeqIO.parse("file1.fa", "fasta"))
    target_records = list(SeqIO.parse("file2.fa", "fasta"))
    rows_list = []
    for target_record in target_records:
        new_row = {'name': target_record.name}
        for record in records:
            if same_seq(record, target_record):
                new_row[record.name] = 1
            else:
                new_row[record.name] = 0
        rows_list.append(new_row)
    df = pd.DataFrame(rows_list)
    df = df.set_index(["name"])
    print(df)

          seq1  seq2  seqtest1
name                          
seq3         1     0         0
seq9         0     0         0
seqtest2     0     0         1