Re: [Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
You should probably look into Biopython: http://biopython.org/wiki/Main_Page Your question should involve fairly straightforward use of the Seq methods of Biopython. You should not try to write your own FASTA parser: Biopython comes with a good one already. Note that the tutor mailing list is not entirely general: the questions here are expected to be beginner-level. Bioinformatics questions are a bit out of scope for tutor @python.org, since they involve a specialized domain that our participants here won't probably be very familiar with. The last times I participated, the Biopython forums were very active. You should check them out: http://biopython.org/wiki/Mailing_lists Good luck! ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
On 08/03/16 12:19, syed zaidi wrote:
One thing. This is a plain text mailing list and because Python is space
dependant you need to post in plain text not HTML/RTF or the layout gets
lost in the mail system. (as you see below).
The main things you need to tell us are what libraries you are
using to read the FASTA data, which OS, and which Python version.
> Well, fasta is a file format used by biologists to store
> biological sequencesthe format is as under
> sequence information (sequence name, sequence length etc)genomic sequence>
> sequence information (sequence name, sequence length etc)genomic sequenceI
> want to match the name of sequence with another list of sequence names and
> splice the sequence by the provided list of start and end sites for each
> sequenceso the pseudo code could beif line starts with '>':match the
> header name with sequence name:if sequence name found:
> splice from the given start and end positions of that sequencethe
> code I have devised so far is:import oswith open('E:/scaftig.sample -
> Copy.scaftig','r') as f:header = f.readline()header =
> header.rstrip(os.linesep)sequence = ''
>for line in f:line = line.rstrip('\n')if line[0] == '>':
> header = header[:]print headerif
> line[0] != '>':sequence+= line
> print sequence, len(sequence)I would appreciate if you can
> helpThanksBest RegardsAli
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Re: [Tutor] how to receive messages form a server?
On 08/03/16 11:56, Paul Z wrote: > There is AP with UDP-Server(sending UDP messages). > My computer has connected the AP. How did you do that? Via a socket? From Python? > I know how to receive messages form a client via socket. Your terminology confuses me. You send messages from a client to a server. So are you saying you know how to write a server? > But, Now, how to receive messages from a server? Servers don't generally send messages, they send responses to requests from clients. I'm not sure what exactly you are trying to do? Is this a multi-tier application with your code in the middle interacting with clients and servers? Or are you a client accessing a server? Or is it a peer to peer set up? Do you have any code you can share with us? That might clarify things. Also it will definitely help if you tell us which OS and Python version you are using. -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.amazon.com/author/alan_gauld Follow my photo-blog on Flickr at: http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] how to receive messages form a server?
Hi, There is AP with UDP-Server(sending UDP messages). My computer has connected the AP. I know how to receive messages form a client via socket. But, Now, how to receive messages from a server? Thanks! ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
Well, fasta is a file format used by biologists to store biological
sequencesthe format is as under> sequence information (sequence name, sequence
length etc)genomic sequence> sequence information (sequence name, sequence
length etc)genomic sequenceI want to match the name of sequence with another
list of sequence names and splice the sequence by the provided list of start
and end sites for each sequenceso the pseudo code could beif line starts with
'>':match the header name with sequence name:if sequence name
found:splice from the given start and end positions of that
sequencethe code I have devised so far is:import oswith
open('E:/scaftig.sample - Copy.scaftig','r') as f:header = f.readline()
header = header.rstrip(os.linesep)sequence = ''for line in f:
line = line.rstrip('\n')if line[0] == '>':header =
header[:]print headerif line[0] != '>':
sequence+= line
print sequence, len(sequence)I would appreciate if you can
helpThanksBest RegardsAli
> Date: Tue, 8 Mar 2016 03:11:42 -0500
> Subject: Re: [Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
> From: wolfrage8...@gmail.com
> To: syedzaid...@hotmail.co.uk
>
> What is FASTA? This seems very specific. Do you have any code thus far
> that is failing?
>
> On Tue, Mar 8, 2016 at 2:33 AM, syed zaidi wrote:
> > Hello all,
> > I am stuck in a problem, I hope someone can help me out. I have a FASTA
> > file with multiple sequences and another file with the gene coordinates.
> > SAMPLEFASTA FILE:
> >>EBM_revised_C2034_1
> >>length=611GCAGCAGTAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTAGTACGGCCGCAAGGTTCTCAAATGAATTGACGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT>EBM_revised_C2104_1
> >>
> >>length=923TCCGAGGGCGGTGGGATGTTGGTGCTGCAGCGGCTTTCGGATGCGCGGCGGTTGGGTCATCCGGTGTTGGCGGTGGTGGTCGGGTCGGCGGTTAATCAGGATCGTCGAATGGGTTGACCGCGCCTAATGGTCCTTCGCAGCAGCGGGTGGTGCGGGCGGCGTTGGCCAATGCCGGGTTGAGCGCGGCCGAGGTGGATGTGGTGGACATGGGACCGGGACCACGTTGATCCGATTGAGGCTCAGGCGTTGTTGGCCACTTATGGGCAAGATCGGAGCCGGGAGAACCTTTGTGGTTTCGGT
GAA
> >
> > GTCGAATATGGGTCATACGCAGGCCGCGGCGTGGCCTGATCAAGATGGTGTTGGCGATGCGCCATGAGCTGTTGCCGGCGACGTTGCACGTGGATGTGCCTAGCCCGCATGTGGATTGGTCGGCGCGGTGGAGTTGTTGACCGCGCCGCGGGTGTGGCCTGCTGGTGCTCGGACGCGTCGTGCGTGTCGTCGTTTGGGATTAGTGGCACTAATGCGCATGTGATTATCGAGGCGGTGCCGGTGGTGCCGCGGCGGGAGGCTGGTTGGGCCCGGTGGTGCCGTGGGTGGTGTCGGCGAAGTCGGAGTCGGCGTTGCGCAGGCGGCTCGGTTGGCCGCGTACGTGCGTGGCGATGATGGCCTCGATGTTGCCGATGTTGGTCGTTGGCGGGTCGTTCGGTGAGCATCGGGCGGTGGTGGTTGGCACCGTGATCGGTTGTTGGCCGGGCTCGATGAGCTGGCGGGTGACCAGTTGGGCGGCTCGGTTGTTCCACGGCGACTGCGGCGGGTAAGACGGTGTTCGTCTTGGCCAAGGCTCCCAATGGCTGGGCATGGGAAT
> > GENE COORD FILEScaf_nameGene_name DS_St
> > DS_EnEBM_revised_C2034_1gene1_1 33 99EBM_revised_C2034_1
> > gene1_1 55 100EBM_revised_C2034_1 gene1_1 111
> > 150EBM_revised_C2104_1 gene1_1 44 70
> > I want to perform the following steps:compare the scaf_name with the header
> > of fasta sequenceif header matches then process the sequence and extract
> > the sequence by the provided start and end positions.
> >
> > I would appreciate if someone can help
> > Thanks
> > Best Regards
> >
> > Ali
> >
> >> ___
> >> Tutor maillist - Tutor@python.org
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Re: [Tutor] simulating key presses
On 08/03/16 10:00, Benjamin Fishbein wrote: > Despite scouring stack overflow and other places, I can’t figure out how to > simulate key presses. > I’m using Mac 10.10.5. > Most answers to this involve sending keys to an element, but my problem is > that I have no element to send to; I’m trying to automate key presses for > choosing (browsing) a file in the Finder window. > Any help is much appreciated. This is specific to your GUI toolkit, in your case Cocoa. You will need to look in the Apple documentation for Cocoa on the Apple develop site then see if the required functionality is made available in the Python Cocoa bindings available from the MacPython community. From my ObjectiveC Cocoa books it looks like you need to create a Key event using the +(NSEvent*)keyEventWithType: (NSEventType) type method. Another approach would be to use AppleScript via osascript as a subprocess. You can certainly automate the finder via that route. It might be easier than going in via Cocoa. I think there's a Python wrapper for osascript too. Not much direct help but maybe a pointer in the right direction... HTH -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.amazon.com/author/alan_gauld Follow my photo-blog on Flickr at: http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] Fasta Identy
Dear Ali, I suggest your best way is to use the resource at the EMBL or the National Library of Congress, NIH, resources. There you can compare your FASTA sequences with authentic databases. The programs know about FASTA and will recognise the format. It will identify the gene for you. And it will give you a link to all the available data on that gene. -- Sydney ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] simulating key presses
Despite scouring stack overflow and other places, I can’t figure out how to simulate key presses. I’m using Mac 10.10.5. Most answers to this involve sending keys to an element, but my problem is that I have no element to send to; I’m trying to automate key presses for choosing (browsing) a file in the Finder window. Any help is much appreciated. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
On 08/03/16 07:33, syed zaidi wrote: > Hello all, Hello, For future reference, please do not hijack an old thread for a new topic - a) it messes up0 the archives for searching b) it means those using threaded readers will probably not see your message > I am stuck in a problem, I hope someone can help me out. I have a FASTA file There are specialist libraries for reading processing fasta data. Are you using one of those, if so which? Thee are also general purpose Bio science libraries within the SciPy and SciKit bundles that may help you. Their support forums are also much more likely to have the specialist knowledge on how to use these tools. This forum is concerned with core Python language issues. It will also help if you tell us which OS and Python version you are using. > > I want to perform the following steps: > compare the scaf_name with the header of fasta sequence > if header matches then process the sequence > and extract the sequence by the provided start and end positions. OK, There are three clear steps there. Have you written any code for any of them? If so show us, along with any error messages. Do you have a specific issue where you need help? -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.amazon.com/author/alan_gauld Follow my photo-blog on Flickr at: http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
Hello all, I am stuck in a problem, I hope someone can help me out. I have a FASTA file with multiple sequences and another file with the gene coordinates. SAMPLEFASTA FILE: >EBM_revised_C2034_1 >length=611GCAGCAGTAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTAGTACGGCCGCAAGGTTCTCAAATGAATTGACGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT>EBM_revised_C2104_1 > >length=923TCCGAGGGCGGTGGGATGTTGGTGCTGCAGCGGCTTTCGGATGCGCGGCGGTTGGGTCATCCGGTGTTGGCGGTGGTGGTCGGGTCGGCGGTTAATCAGGATCGTCGAATGGGTTGACCGCGCCTAATGGTCCTTCGCAGCAGCGGGTGGTGCGGGCGGCGTTGGCCAATGCCGGGTTGAGCGCGGCCGAGGTGGATGTGGTGGACATGGGACCGGGACCACGTTGATCCGATTGAGGCTCAGGCGTTGTTGGCCACTTATGGGCAAGATCGGAGCCGGGAGAACCTTTGTGGTTTCGGTGAA GTCGAATATGGGTCATACGCAGGCCGCGGCGTGGCCTGATCAAGATGGTGTTGGCGATGCGCCATGAGCTGTTGCCGGCGACGTTGCACGTGGATGTGCCTAGCCCGCATGTGGATTGGTCGGCGCGGTGGAGTTGTTGACCGCGCCGCGGGTGTGGCCTGCTGGTGCTCGGACGCGTCGTGCGTGTCGTCGTTTGGGATTAGTGGCACTAATGCGCATGTGATTATCGAGGCGGTGCCGGTGGTGCCGCGGCGGGAGGCTGGTTGGGCCCGGTGGTGCCGTGGGTGGTGTCGGCGAAGTCGGAGTCGGCGTTGCGCAGGCGGCTCGGTTGGCCGCGTACGTGCGTGGCGATGATGGCCTCGATGTTGCCGATGTTGGTCGTTGGCGGGTCGTTCGGTGAGCATCGGGCGGTGGTGGTTGGCACCGTGATCGGTTGTTGGCCGGGCTCGATGAGCTGGCGGGTGACCAGTTGGGCGGCTCGGTTGTTCCACGGCGACTGCGGCGGGTAAGACGGTGTTCGTCTTGGCCAAGGCTCCCAATGGCTGGGCATGGGAAT GENE COORD FILEScaf_nameGene_name DS_St DS_EnEBM_revised_C2034_1gene1_1 33 99EBM_revised_C2034_1 gene1_1 55 100EBM_revised_C2034_1 gene1_1 111 150EBM_revised_C2104_1 gene1_1 44 70 I want to perform the following steps:compare the scaf_name with the header of fasta sequenceif header matches then process the sequence and extract the sequence by the provided start and end positions. I would appreciate if someone can help Thanks Best Regards Ali > ___ > Tutor maillist - Tutor@python.org > To unsubscribe or change subscription options: > https://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
