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Full Discussion: Beginner Questions.
Homework and Emergencies Homework & Coursework Questions Beginner Questions. Post 302426764 by curleb on Wednesday 2nd of June 2010 10:02:43 PM
Old 06-02-2010
You might want to post a sample of the file layout next time, rather than ask we download your whole file. Otherwise, the following should answer most, if not all in succession, but just so you're aware: there's always more than one way to do it.

It's now up to you to actually deconstruct them per your study guide(s) or texts. HTH.

Code:
mv Test_Data.snp Test_Data.txt

Code:
awk ' $2 ~ /A/ || $3 ~ /A/ { print $0;} ' Test_Data.snp

Code:
awk '{print $9;}' Test_Data.snp >Reference_length.txt

Code:
sort -n -k4 <Test_Data.snp

Code:
awk ' $2 !~ /\./ && $3 !~ /\./ { print $0; }' Test_Data.snp >snp_report.txt

In case anyone else might want to offer something:

Code:
$ head -20 Test_Data.snp #|tail +6 |awk ' $2 !~ /\./ && $3 !~ /\./ { print $0; }'

NUCMER

    [P1]  [SUB]  [P2]      |   [BUFF]   [DIST]  |  [LEN R]  [LEN Q]  | [FRM]  [TAGS]
========================================================================================
       7   A .   1892597   |        7        7  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     140   C T   1892730   |        2       90  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     142   T A   1892732   |        2       88  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     153   A G   1892743   |       11       77  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     213   A G   1892803   |       17       17  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     630   T C   401       |      175      401  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
     805   G A   576       |      175      576  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    1054   C T   825       |      249      825  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    2960   . G   2732      |       77     2732  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    3037   G A   2809      |       77     2809  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    3329   A C   3101      |      104     3101  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    4354   A G   1832816   |       67     4354  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    4421   C A   1832883   |       27     4421  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    4448   T C   1832910   |       27     4448  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella
    4539   A G   1833001   |       17     4539  |  1895994  1892819  |  1  1  LVS_Francisella   SchuS4_Francisella

Last edited by curleb; 06-02-2010 at 11:15 PM..
This User Gave Thanks to curleb For This Post:
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