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lel7lel7
lel7lel7
Last Activity: Jan 21 '15, 11:03 PM
Joined: Mar 22 '10
Location: Darwin
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  • lel7lel7
    started a topic Beginner!! How to convert data from 1 row to 1 column without sed??
    in Linux

    Beginner!! How to convert data from 1 row to 1 column without sed??

    Hi there,
    I have only been using linux for 2 weeks and am struggling with loops. My data is in the form...

    Code:
    [lg45@dev64-mgmt ~]$ echo $start
25293633 7393500 10578865 25293623 122206254 26797134 41906484
    Id like it to output as

    25293633
    7393500
    10578865
    25293623
    122206254
    26797134
    41906484

    In the current format, if i were to...
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    • lel7lel7
      started a topic Linux - How to call lines from a file in a for loop???
      in Linux

      Linux - How to call lines from a file in a for loop???

      Hi,

      I am new to Linux and am trying to pull several lines from one file to modify them.

      I have written a file table.txt...

      Code:
      [lg45@dev64-mgmt ~]$ cat table.txt

Angiogenin 10 25793633 25815393
Alpha-actinin 28 7893500 7941168
      I want to pull out column 3 of each line and loop through them all adding 500,000bp.

      I know that i can use awk to call...
      ...
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      • lel7lel7
        replied to How to replace multiple integers at once
        in Python
        HI Glenton,
        I understand what your saying but am having trouble working it...

        Code:
        dna = "AAATTTCCCGGG"
a = "A"
b = "T"
c = "G"
d = "C"
dd = a,b=b,a
ddd = c,d=d,c
seq = []
for x in dna.strip():
if x in "ATGC":
seq.append(dd[x]).append(ddd[x])
return dna
dnacomp = "".join(seq)
        ...
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        • lel7lel7
          replied to How to replace multiple integers at once
          in Python
          Ahh i see now. Thank-you again!!
          :)
          See more | Go to post

            Leave a comment:

          • lel7lel7
            replied to How to replace multiple integers at once
            in Python
            Basic python question

            Ok, im still learning and this is all making sense except one thing...
            Above you write "for s in dna.strip().... " I am trying to understand what 's' represents. Is 's' the dictionary? and does it always have to be this character or can i assign any random one?

            In other words, do 's' and (as below) 'l' , 'k' and 'i' have their own function?

            The reason i ask is because...
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            Last edited by bvdet; May 11 '10, 07:23 AM. Reason: Add code tags [code].........[/code]

              Leave a comment:

            • lel7lel7
              replied to How to create SQL databases in novosnp
              in MySQL
              I tried but couldnt find an appropriate one, thanks anyway i did figure it our in the end it was a formatting issue :)...
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                Leave a comment:

              • lel7lel7
                started a topic How to create SQL databases in novosnp
                in MySQL

                How to create SQL databases in novosnp

                I am not sure if anyone on this blog is familiar with novosnp but any help would be appreciated.

                Starting a new project requires opening a ref sequence and trace files. As per instructions on the ‘project creation’ help section (attached below)...

                - I added a ref seq in FASTA – this shows a directory in the top left of novosnp window. If I click this directory it says no trace selected…
                -...
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                Last edited by Niheel; May 11 '10, 03:01 AM. Reason: Minor grammar stuff :)
                • lel7lel7
                  started a topic can you open .doc or .fa in python? or how do i transfer this data to python?
                  in Python

                  can you open .doc or .fa in python? or how do i transfer this data to python?

                  Hi,

                  I am struggling to analyse a 100,000KB dna sequence file in word.... it keeps trying to 'repaginate' and freezes....

                  Is there anyway i can open this data in python so i can analyse it? I have it in .fa format and in .doc

                  Thanks in advance to anyone who can help :)
                  Lesley
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                  • lel7lel7
                    replied to How to replace multiple integers at once
                    in Python
                    Ok thanks, i dont really understand the dnacomp command but ill look back at it when im further through the training manual.
                    As a simple way ive figured out that it can be done using

                    >>>replace(repl ace(replace(rep lace(dna, 'a', "T"), 't', "A"), 'g', "C"), 'c', "G")

                    but im assuming this format will not be sufficient when im trying to write harder scripts
                    ...
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                      Leave a comment:

                    • lel7lel7
                      replied to Basic programming question on find() function
                      in Python
                      Thanks so much - your really helpful :)
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                      • lel7lel7
                        started a topic Basic programming question on find() function
                        in Python

                        Basic programming question on find() function

                        I am familiar with the notation
                        >>>dna = ....
                        >>>Ecori = "ATGATG"... .
                        >>>find(dna, Ecori)
                        >>>find(dna,Eco ri, 2)

                        My question is how to i find the second undefined base 'n'
                        ie.
                        >>>seq = 'ATGATGnATGnATG '
                        >>>find(seq, 'n')
                        6
                        >>>find(seq, 'n', 2)
                        6 Does not work - Should say 10
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                        • lel7lel7
                          started a topic How to replace multiple integers at once
                          in Python

                          How to replace multiple integers at once

                          Hi, i am new to python and having some problems...

                          I am trying to figure out how to change multiple integers at once so i can produce the complement of this DNA strand...
                          >>>dna = """tgaattctatga atggactgtccccaa agaagtaggacccac taatgcagatcctgg a
                          tccctagctaagatg tattattctgctgtg aattcgatcccacta aagat"""
                          (ie. acttaagatactt.. ...)

                          I have learnt how to remove \n character...
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