我有一个关于序列的文件。每个序列都有一些行。序列由五条白线隔开。我想把这个文件改成一个列表,然后按5行换行。所以我有一个列表,每个序列都是一个元素。然后我想删除不包含正则表达式的序列。最后,我想要一个列表,只包含包含正则表达式的序列。你知道吗
现在我有了这个。有人能帮我进一步吗?你知道吗
import re
def main():
ReadFile()
file = open ("filename.txt", "r")
CreateList(file, data)
RegEx(file, data)
def ReadFile()
try:
file = open ("filename.txt", "r")
except IOError:
print ("Can't open the file")
except:
print ("Something went wrong.")
def CreateList(file, data)
data = file.readlines()
data = data.split('\n\n\n\n\n')
def RegEx(file, data)
regex = ("[AG].{4}GK[ST]")
for element in data:
if regex not in element:
data.remove(element)
print (data)
main()
文件看起来像:
Hits for PS00017|ATP_GTP_A (pattern) ATP/GTP-binding site motif A (P-loop) : [occurs frequently]
Pattern: [AG]-x(4)-G-K-[ST]
Approximate number of expected random matches in ~ 100'000 sequences (50'000'000 residues): 3371
>sp|Q6GZX2|003R_FRG3G (438 aa)
Uncharacterized protein 3R. [Frog virus 3 (isolate Goorha) (FV-3)]
MARPLLGKTSSVRRRLESLSACSIFFFLRKFCQKMASLVFLNSPVYQMSNILLTERRQVDRAMGGSDDDGVMVVALSPSD
FKTVLGSALLAVERDMVHVVPKYLQTPGILHDMLVLLTPIFGEALSVDMSGATDVMVQQIATAGFVDVDPLHSSVSWKDN
VSCPVALLAVSNAVRTMMGQPCQVTLIIDVGTQNILRDLVNLPVEMSGDLQVMAYTKDPLGKVPAVGVSVFDSGSVQKGD
AHSVGAPDGLVSFHTHPVSSAVELNYHAGWPSNVDMSSLLTMKNLMHVVVAEEGLWTMARTLSMQRLTKVLTDAEKDVMR
AAAFNLFLPLNELRVMGTKDSNNKSLKTYFEVFETFTIGALMKHSGVTPTAFVDRRWLDNTIYHMGFIPWGRDMRFVVEY
DLDGTNPFLNTVPTLMSVKRKAKIQEMFDNMVSRMVTS
2 - 9: ArpllGKT
>sp|Q6GZX1|004R_FRG3G (60 aa)
Uncharacterized protein 004R. [Frog virus 3 (isolate Goorha) (FV-3)]
MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY
33 - 40: GyyydGKT
>sp|Q6GZW0|015R_FRG3G (322 aa)
Uncharacterized protein 015R. [Frog virus 3 (isolate Goorha) (FV-3)]
MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDSKRHIIPCAVVISGSEEANGFYKGVVPDLFI
YHQFSPSIIDRIHRRQVKAKAEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYVMDLTPDLRSS
VDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQNYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSY
WKYACSKTGEEMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGPSDDEEGLSKDGVSEYYQSDL
DD
34 - 41: GkpgsGKS',
>sp|P32234|128UP_DROME (368 aa)
GTP-binding protein 128up. [Drosophila melanogaster (Fruit fly)]
MSTILEKISAIESEMARTQKNKATSAHLGLLKAKLAKLRRELISPKGGGGGTGEAGFEVAKTGDARVGFVGFPSVGKSTL
LSNLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFMVLDCLKPLGHKKL
LEHELEGFGIRLNKKPPNIYYKRKDKGGINLNSMVPQSELDTDLVKTILSEYKIHNADITLRYDATSDDLIDVIEGNRIY
IPCIYLLNKIDQISIEELDVIYKIPHCVPISAHHHWNFDDLLELMWEYLRLQRIYTKPKGQLPDYNSPVVLHNERTSIED
FCNKLHRSIAKEFKYALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKKV
71 - 78: GfpsvGKS
数据应该是(但仅包含RegEx的蛋白质):
['>sp|Q6GZX2|003R_FRG3G (438 aa)
Uncharacterized protein 3R. [Frog virus 3 (isolate Goorha) (FV-3)]
MARPLLGKTSSVRRRLESLSACSIFFFLRKFCQKMASLVFLNSPVYQMSNILLTERRQVDRAMGGSDDDGVMVVALSPSD
FKTVLGSALLAVERDMVHVVPKYLQTPGILHDMLVLLTPIFGEALSVDMSGATDVMVQQIATAGFVDVDPLHSSVSWKDN
VSCPVALLAVSNAVRTMMGQPCQVTLIIDVGTQNILRDLVNLPVEMSGDLQVMAYTKDPLGKVPAVGVSVFDSGSVQKGD
AHSVGAPDGLVSFHTHPVSSAVELNYHAGWPSNVDMSSLLTMKNLMHVVVAEEGLWTMARTLSMQRLTKVLTDAEKDVMR
AAAFNLFLPLNELRVMGTKDSNNKSLKTYFEVFETFTIGALMKHSGVTPTAFVDRRWLDNTIYHMGFIPWGRDMRFVVEY
DLDGTNPFLNTVPTLMSVKRKAKIQEMFDNMVSRMVTS
2 - 9: ArpllGKT',
'>sp|Q6GZX1|004R_FRG3G (60 aa)
Uncharacterized protein 004R. [Frog virus 3 (isolate Goorha) (FV-3)]
MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY
33 - 40: GyyydGKT',
'>sp|Q6GZW0|015R_FRG3G (322 aa)
Uncharacterized protein 015R. [Frog virus 3 (isolate Goorha) (FV-3)]
MEQVPIKEMRLSDLRPNNKSIDTDLGGTKLVVIGKPGSGKSTLIKALLDSKRHIIPCAVVISGSEEANGFYKGVVPDLFI
YHQFSPSIIDRIHRRQVKAKAEMGSKKSWLLVVIDDCMDNAKMFNDKEVRALFKNGRHWNVLVVIANQYVMDLTPDLRSS
VDGVFLFRENNVTYRDKTYANFASVVPKKLYPTVMETVCQNYRCMFIDNTKATDNWHDSVFWYKAPYSKSAVAPFGARSY
WKYACSKTGEEMPAVFDNVKILGDLLLKELPEAGEALVTYGGKDGPSDNEDGPSDDEDGPSDDEEGLSKDGVSEYYQSDL
DD
34 - 41: GkpgsGKS',
'>sp|P32234|128UP_DROME (368 aa)
GTP-binding protein 128up. [Drosophila melanogaster (Fruit fly)]
MSTILEKISAIESEMARTQKNKATSAHLGLLKAKLAKLRRELISPKGGGGGTGEAGFEVAKTGDARVGFVGFPSVGKSTL
LSNLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFMVLDCLKPLGHKKL
LEHELEGFGIRLNKKPPNIYYKRKDKGGINLNSMVPQSELDTDLVKTILSEYKIHNADITLRYDATSDDLIDVIEGNRIY
IPCIYLLNKIDQISIEELDVIYKIPHCVPISAHHHWNFDDLLELMWEYLRLQRIYTKPKGQLPDYNSPVVLHNERTSIED
FCNKLHRSIAKEFKYALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKKV
71 - 78: GfpsvGKS']
更新(再次)以满足新的要求
Regex1(将文本文件拆分为蛋白质列表:)https://regex101.com/r/gU0gX5/1
Regex2(显示它们都匹配的regex)https://regex101.com/r/nZ0pD6/1
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