如何解决比较fasta文件与充满序列ID的txt文件
我需要帮助,因为我被卡住了。 我有一个带有序列ID的txt文件,它 看起来像这样->
tr|K9RTD0|K9RTD0_SYNP3
tr|K9RSV3|K9RSV3_SYNP3
tr|K9RRE8|K9RRE8_SYNP3
tr|K9RMU9|K9RMU9_SYNP3
>sp|P00115|CYC6_SYNP3 Cytochrome c6 OS=Synechococcus sp. (strain ATCC 27167 / PCC 6312) OX=195253 GN=petJ PE=1 SV=2
MKTLLTILALTLVTLTTWLSTPAFAADIADGAKVFSANCAACHMGGGNVVMANKTLKKEA
LEQFGMNSADaimYQVQNGKNAMPAFGGRLSEAQIENVAAYVLDQSSKNWAG
>tr|K9RTH7|K9RTH7_SYNP3 N-acyl-D-glucosamine 2-epimerase OS=Synechococcus sp. (strain ATCC 27167 / PCC 6312) OX=195253 GN=Syn6312_2130 PE=4 SV=1
MAPQINFPFSDLIAGYVTSYDTETDIFGLKTSDGREFPVKLSPMAYAKVIQNFDEGYPDA
TSTMRAWLTPGRFLFVYGVFYPDTDVFDAKQVVFAGKKEDDYVFEKQDWWIQQINALGKF
YVKAQFGQEEIDYRNYRTDLSVSGERSSVKFRQETDTISRLVYGFATAFMMTGDEVFLEA
AEKGTEYLRDHMRFVDRDEDIIYWYHGIDVQGEKELKIFASEFGDDYDAIPAYEQIYALA
GPIQTYRCTGDPRILSDAEQTIKLFDKFFLDQSEYGGYFSHIdplMLDPRSDSLGRNKAR
KNWNSVGDHAPAYLINLWLATGEQKYADMLEYTFDTIEKYFPDYENSPFVQERFYEDWSH
DTTWGWQQNRAVVGHNLKIAWNLMRMQSLKPKEQYVGLAQKIADLMPSVGSDQQRGGWSD
TVERLLTNNSKFHQFVWHDRKAWWQQEQAILAYLILGGILEHDDYHRLGREAAAFYNAWF
LDLEDGGVYFNVLANGISYLARGNERAKGSHSMSGYHSFELCYLAAVYTNFLITKHPMDF
YFKPLPNGFPDRILRVSPDILPPGSILLEsveIDGKAYTDFDSQALTVKLPETKERVKVK
VRLAPKS
>tr|K9RXQ9|K9RXQ9_SYNP3 Uncharacterized protein OS=Synechococcus sp. (strain ATCC 27167 / PCC 6312) OX=195253 GN=Syn6312_3008 PE=4 SV=1
MKVEILKKRLNKECPMTTTRMPEDVIQELKQIAsllVFWGYQPLIGADIGQglrTDLEQL
EDDKVSALVASLKRHRVSDEVLQTALMETTIN
我需要比较这两个文件,并根据ID查找序列的描述并打印出来。 我的代码:
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import sys
p = "proteome.fasta"
file = "reference.txt"
out = "jopik.txt"
with open(out,"w") as o:
sys.stdout = o
for seq_record in SeqIO.parse(open(p,mode = "r"),"fasta"):
seq_record.description=' '.join(seq_record.description.split()[1:])
with open(file,"r") as f:
line = f.readlines()
print(line)
if (seq_record.id == line):
i = seq_record.description
print(i)
解决方法
此外,您只是缺少某种循环for x in y:
,文件处理程序在Python中是可迭代的(对于非二进制模式逐行迭代),这将使您不必将整个文件加载到内存中在开始迭代之前(例如.readlines()
)
# load first file and create a helpful structure
compare_dict = {}
with open("reference.txt") as fh:
for line in fh:
if line: # throw out empty lines,could do a stricter compare
compare_dict[line.strip()] = None
# form a tuple of possible prefixes
compare_tuple = tuple(">" + a for a in compare_dict.keys())
with open("proteome.fasta") as fh:
for line_no,line in enumerate(fh,1): # lines start at 1,not 0
if line.startswith(compare_tuple)
key,value = line.split(" ",1)
key = key[1:] # strip ">" from prefix
compare_dict[key] = value
print("found {} on L{}: {}".format(key,line_no,value))
# optionally display keys which were not in your .fasta file
for key,value in compare_dict.items():
if value is None:
print("failed to find a definition for {}".format(key))
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