如何从 python 中的 fasta 文件中提取 header

Question

I have a fasta file containing a sequence. I just want to extract the header information and display it.

I am new in coding with python

Answer 1

According to the Fasta format, the header is always the first line in the file. So you just need to open the file, read one line, and you have it.

Ie

# The with open will open the file using "f" as the file handle. 
with open("/home/rightmire/Downloads/fastafile", "r") as f: 
    for line in f: # Creates a for loop to read the file line by line
        print(line) # This is the first line
        # If you comment out the break, the file will continue to be read line by line
        # If you want just the first line, you can break the loop
        break 

# even though the loop has ended, the last contents of the variable 'line' is remembered    
print("The data retained in the variable 'line' is: ", line)

OUTPUT:

>gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase

 The data retained in the variable 'line' is:  >gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase

===

You can also do it without the loop or 'with', should you choose.

f = open("/home/rightmire/Downloads/fastafile", "r")
line  = f.readline() # reads one line
print(line)
f.close() # Closes the open file. 

===

Finally, you can read the entire file into memory, where you can manipulate the entire file as a whole, manipulate individual lines, or even parse the file character by character. This may not be the best idea however because the files can get HUGE!

# The with open will open the file using "f" as the file handle. 
f = open("/home/rightmire/Downloads/fastafile", "r")
# Read the entire file into the variable 'lines'
lines  = f.read()
# Split 'lines' by the newline character to get individual lines. 
for line in lines.split("\n"): 
    print("--------")
    print(line)

# or even read it out character by character, which can be handy for parsing the genome data. 
for c in lines:
    print(c) 

OUTPUT:

--------
>gi|186681228|ref|YP_001864424.1| phycoerythrobilin:ferredoxin oxidoreductase
--------
MNSERSDVTLYQPFLDYAIAYMRSRLDLEPYPIPTGFESNSAVVGKGKNQEEVVTTSYAFQTAKLRQIRA
--------
AHVQGGNSLQVLNFVIFPHLNYDLPFFGADLVTLPGGHLIALDMQPLFRDDSAYQAKYTEPILPIFHAHQ
--------
QHLSWGGDFPEEAQPFFSPAFLWTRPQETAVVETQVFAAFKDYLKAYLDFVEQAEAVTDSQNLVAIKQAQ
--------
LRYLRYRAEKDPARGMFKRFYGAEWTEEYIHGFLFDLERKLTVVK
--------

>
g
i
|
1
(snip)

M
N
S
E
(snip)