extracting subsequence from the sequence

[parijat24]

hey, thanks to all of them who helps me in learning this language,
again there is one text file
file 1.txt

>sp|P81928[/B]|140U_DROME

67 198 Tim17 8.9e-19 No_clan

>sp|P20905|5HT1R_DROME

179 507 7tm_1 1.1e-97 CL0192

>sp|P28285|5HT2A_DROME

243 805 7tm_1 3.2e-73 CL0192

>sp|P28286|5HT2B_DROME

107 588 7tm_1 7.2e-82 CL0192

* here the number represents the start and ending of subsequence which has to be extracted.

the next file is sequence file2.txt

>sp|P81928|140U_DROME RPII140-upstream gene protein OS=Drosophila melanogaster GN=140up PE=2 SV=2
MNFLWKGRRFLIAGILPTFEGAADEIVDKENKTYKAFLASKPPEETGLERLKQMFTIDEF
GSISSELNSVYQAGFLGFLIGAIYGGVTQSRVAYMNFMENNQATAFKSHFDAKKKLQDQF
TVNFAKGGFKWGWRVGLFTTSYFGIITCMSVYRGKSSIYEYLAAGSITGSLYKVSLGLRG
MAAGGIIGGFLGGVAGVTSLLLMKASGTSMEEVRYWQYKWRLDRDENIQQAFKKLTEDEN
PELFKAHDEKTSEHVSLDTIK
>sp|P20905|5HT1R_DROME 5-hydroxytryptamine receptor 1 OS=Drosophila melanogaster GN=5-HT7 PE=2 SV=1
MALSGQDWRRHQSHRQHRNHRTQGNHQKLISTATLTLFVLFLSSWIAYAAGKATVPAPLV
EGETESATSQDFNSSSAFLGAIASASSTGSGSGSGSGSGSGSGSGSYGLASMNSSPIAIV
SYQGITSSNLGDSNTTLVPLSDTPLLLEEFAAGEFVLPPLTSIFVSIVLLIVILGTVVGN
VLVCIAVCMVRKLRRPCNYLLVSLALSDLCVALLVMPMALLYEVLEKWNFGPLLCDIWVS
FDVLCCTASILNLCAISVDRYLAITKPLEYGVKRTPRRMMLCVGIVWLAAACISLPPLLI
LGNEHEDEEGQPICTVCQNFAYQIYATLGSFYIPLSVMLFVYYQIFRAARRIVLEEKRAQ
THLQQALNGTGSPSAPQAPPLGHTELASSGNGQRHSSVGNTSLTYSTCGGLSSGGGALAG
HGSGGGVSGSTGLLGSPHHKKLRFQLAKEKKASTTLGIIMSAFTVCWLPFFILALIRPFE
TMHVPASLSSLFLWLGYANSLLNPIIYATLNRDFRKPFQEILYFRCSSLNTMMRENYYQD
QYGEPPSQRVMLGDERHGARESFL
>sp|P28285|5HT2A_DROME 5-hydroxytryptamine receptor 2A OS=Drosophila melanogaster GN=5-HT1A PE=2 SV=2
MAHETSFNDALDYIYIANSMNDRAFLIAEPHPEQPNVDGQDQDDAELEELDDMAVTDDGQ
LEDTNNNNNSKRYYSSGKRRADFIGSLALKPPPTDVNTTTTTAGSPLATAALAAAAASAS
VAAAAARITAKAAHRALTTKQDATSSPASSPALQLIDMDNNYTNVAVGLGAMLLNDTLLL
EGNDSSLFGEMLANRSGQLDLINGTGGLNVTTSKVAEDDFTQLLRMAVTSVLLGLMILVT
IIGNVFVIAAIILERNLQNVANYLVASLAVADLFVACLVMPLGAVYEISQGWILGPELCD
IWTSCDVLCCTASILHLVAIAVDRYWAVTNIDYIHSRTSNRVFMMIFCVWTAAVIVSLAP
QFGWKDPDYLQRIEQQKCMVSQDVSYQVFATCCTFYVPLLVILALYWKIYQTARKRIHRR
RPRPVDAAVNNNQPDGGAATDTKLHRLRLRLGRFSTAKSKTGSAVGVSGPASGGRALGLV
DGNSTNTVNTVEDTEFSSSNVDSKSRAGVEAPSTSGNQIATVSHLVALAKQQGKSTAKSS
AAVNGMAPSGRQEDDGQRPEHGEQEDREELEDQDEQVGPQPTTATSATTAAGTNESEDQC
KANGVEVLEDPQLQQQLEQVQQLQKSVKSGGGGGASTSNATTITSISALSPQTPTSQGVG
IAAAAAGPMTAKTSTLTSCNQSHPLCGTANESPSTPEPRSRQPTTPQQQPHQQAHQQQQQ
QQQLSSIANPMQKVNKRKETLEAKRERKAAKTLAIITGAFVVCWLPFFVMALTMPLCAAC
QISDSVASLFLWLGYFNSTLNPVIYTIFSPEFRQAFKRILFGGHRPVHYRSGKL

i want to extract the subsequence from this sequences with respect to the proteins id

[jcao219]

I see you are working with Drosophila genetics.
I'm not sure what you are trying to do.. can you explain it further?

[ultimatebuster]

wow that's some huge geek cred for knowing what that is.

Anyhow i don't exactly know what you want either so yeah.

[TrustyTony]

For example that first line of first file looks different format (bold finishing tag before but no starting tag), otherwise, is it so that yo want to pick identifier between > and | psoition 1:9, (>sp|P20905| > id = sp|P20905) and when it is found take start and end indexes of two lines down of start and end index (0 or 1 based?)

Something like this for file1:

inp=open('file1.txt').read()

sep='>'
data= []
while sep:
    part,sep, inp = inp.partition(sep)
    if sep and part: data.append(part.strip().split('\n\n'))

idend = len('sp|P81928')-1
info = [( id[:idend],)+tuple(loc.split(' ',2)[:2])
        for id,loc in data if id.startswith('s')
         ]
print info
info = [(a, int(b), int (c)) for a,b,c in info]
print info

[parijat24]

no it not like that sorry ,

i just want that from given sequence of lengh 400 , i have two cut the sequence ranging from one index to another index

[TrustyTony]

If those where not right ids and indexes, I am afraid I can not help you.

[jcao219]

wow that's some huge geek cred for knowing what that is.

Anyhow i don't exactly know what you want either so yeah.

Heh, I'm great at Biology (got first place in a state competition), so Drosophila melanogaster is very familiar to me. It's a fruitfly. I've helped raise them before.

Anyways, OP, can you provide us with some kind of desired output, so that we know exactly what you want?