# Coronavirus Exploration

We are still impacted by Covid19. Let's see how Biopython can help us explore and understand these coronaviruses.

* 1\. we search PubMed for papers in order to access the timely coronavirus findings. In this way, we will have a good idea what people already know and still do not know about coronaviruses.

```
search PubMed for coronavirus information:
In [1]: import Bio
In [2]: Bio.__version__
In [3]: from Bio import Entrez
In [4]: handle=Entrez.esearch(db="pubmed",retmax=10,term="coronavirus")
In [5]: record=Entrez.read(handle)
In [6]: record["IdList"]
Out[6]: ['32526774', '32526763', '32526759', '32526746', '32526627', 
'32526560', '32526559', '32526545', '32526541', '32526530']
```

* 2\. we look into specific terms. We will use '32526774' as an example

```
In [1]: import Bio
In [2]: Bio.__version__
In [3]: from Bio import Entrez
In [4]: handle=Entrez.efetch(db='pubmed',id='32526774')
In [5]: print(handle.read())
```

* 3\. we mine nucleotide database to start bioinformatics study

```
In [1]: import Bio
In [2]: Bio.__version__
In [3]: from Bio import Entrez,SeqIO
In [4]: handle=Entrez.esearch(db="nucleotide",retmax=10,term="coronavirus")
In [5]: record=Entrez.read(handle)
In [6]: record["IdList"]
```

* 4\. we retrieve individual coronavirus genome sequences. Here, we use '1850952228' as an example

```
In [1]: import Bio
In [2]: Bio.__version__
In [3]: from Bio import Entrez,SeqIO
In [4]: handle=Entrez.efetch(db='nucleotide',id='1850952228',rettype='gb',retmode='text')
In [5]: record=SeqIO.read(handle,'genbank')
In [6]: handle.close()
##writing genBank file
In [7]: SeqIO.write(record,open("MT578017.gb","w"),"gb")
##converting GenBank to FASTA
In [8]: SeqIO.convert("MT578017.gb", "genbank", "MT578017.fna", "fasta")
```

* 5\. Identifying open reading frames from genomic sequence. Here, we use '1850952228' as an example

The code is from ["Cookbook: Translating a FASTA file of CDS entries"](https://biopython.org/docs/latest/Tutorial/chapter_cookbook.html)

```
from Bio import SeqIO
record = SeqIO.read("MT578017.fna", "fasta")
table = 1
min_pro_len = 100
for strand, nuc in [(+1, record.seq), (-1, record.seq.reverse_complement())]:
    for frame in range(3):
        length = 3 * ((len(record)-frame) // 3) #Multiple of three
        for pro in nuc[frame:frame+length].translate(table).split("*"):
            if len(pro) >= min_pro_len:
                print("%s...%s - length %i, strand %i, frame %i" \
                      % (pro[:30], pro[-3:], len(pro), strand, frame))
```

* 6\. build up a list of the candidate proteins and keep track of where the proteins are. Here, we use '1850952228' as an example

The code is from ["Cookbook 20.1.13 Identifying open reading frames"](http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec379)

```
from Bio import SeqIO

record = SeqIO.read("MT578017.gb", "genbank")
table = 1
min_pro_len = 100

def find_orfs_with_trans(seq, trans_table, min_protein_length):
    answer = []
    seq_len = len(seq)
    for strand, nuc in [(+1, seq), (-1, seq.reverse_complement())]:
        for frame in range(3):
            trans = str(nuc[frame:].translate(trans_table))
            trans_len = len(trans)
            aa_start = 0
            aa_end = 0
            while aa_start < trans_len:
                aa_end = trans.find("*", aa_start)
                if aa_end == -1:
                    aa_end = trans_len
                if aa_end - aa_start >= min_protein_length:
                    if strand == 1:
                        start = frame + aa_start * 3
                        end = min(seq_len, frame + aa_end * 3 + 3)
                    else:
                        start = seq_len - frame - aa_end * 3 - 3
                        end = seq_len - frame - aa_start * 3
                    answer.append((start, end, strand, trans[aa_start:aa_end]))
                aa_start = aa_end + 1
    answer.sort()
    return answer


orf_list = find_orfs_with_trans(record.seq, table, min_pro_len)
for start, end, strand, pro in orf_list:
    print(
        "%s...%s - length %i, strand %i, %i:%i"
        % (pro[:30], pro[-3:], len(pro), strand, start, end)
    )                    
```

Now we have coronavirus protein sequences. There is so much more that we can do. I will leave it to you to do great jobs using Biopython.


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