如何从python的fasta文件中提取标头

Question

我有一个包含序列的fasta文件。我只想提取标题信息并显示它。

我是python编码的新手

Answer 1

即

# 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)

输出：
>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

===

您也可以选择不使用循环或'with'。 
f = open("/home/rightmire/Downloads/fastafile", "r")
line  = f.readline() # reads one line
print(line)
f.close() # Closes the open file. 

===

最后，您可以将整个文件读入内存，在这里您可以将整个文件作为一个整体进行操作，可以对各个行进行操作，甚至可以逐个字符地解析文件。但是，这可能不是最好的主意，因为文件可能很大！
# 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) 

输出：

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

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