Sorry about that I was leaving for a weekend trip. Anyway here are the files:
file that is updated:
Code:
Missing in IDP but found in Reference:
2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5139C>T]+[=] 52.94 Not low
12 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 c.[5070A>C]+[=] 20.97 Not low
13 77570076 - A exonic CLN5 2762 26.6 2060;702 0;0 0;0 0;0 2050;696 0;0 c.526_527insA 99.42 TP Not low
7 148106478 - GT intronic CNTNAP2 4051 28.5 0;1 0;0 0;0 2220;1829 1085;887 0;1 rs60451214 c.3716-5_3716-4insGT 48.68 Not low
9 138678036 TGCCC - intronic KCNT1 834 23.1 0;0 0;0 0;31 0;1 0;0 0;802 rs141359570 c.3178-7_3178-3delTGCCC 96.16 Not low
7 148106476 - TT intronic CNTNAP2 4052 28.8 0;0 5;0 0;0 2221;1826 1081;884 0;0 rs61232377 c.3716-7_3716-6insTT 48.49 Not low
2 166245425 C T exonic SCN2A 49 12.6 0;0 13;9 0;0 18;9 0;0 0;0 c.[5109C>T]+[=] 55.1 Not low
current output:
Code:
Missing in IDP but found in Reference: has no . so fields shift when blank
CHR POS REF ALT FUNC GENE COVERAGE PHRED A[#F,#R] C[#F,#R] G[#F,#R] T[#F,#R] INS[#F,#R] DEL[#F,#R] SNP MUT FREQ SANGER REGION
TVC
2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 c.[5139C>T]+[=] 52.94 Not low found
12 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 c.[5070A>C]+[=] 20.97 Not low Not found
13 77570076 - A exonic CLN5 2762 26.6 2060;702 0;0 0;0 0;0 2050;696 0;0 c.526_527insA 99.42 TP Not low Not found
7 148106478 - GT intronic CNTNAP2 4051 28.5 0;1 0;0 0;0 2220;1829 1085;887 0;1 rs60451214 c.3716-5_3716-4insGT 48.68 Not low Not found
9 138678036 TGCCC - intronic KCNT1 834 23.1 0;0 0;0 0;31 0;1 0;0 0;802 rs141359570 c.3178-7_3178-3delTGCCC 96.16 Not low Not found
7 148106476 - TT intronic CNTNAP2 4052 28.8 0;0 5;0 0;0 2221;1826 1081;884 0;0 rs61232377 c.3716-7_3716-6insTT 48.49 Not low Not found
2 166245425 C T exonic SCN2A 49 12.6 0;0 13;9 0;0 18;9 0;0 0;0 c.[5109C>T]+[=] 55.1 Not low found
desired output: tab-delimited with . if the field is blank
Code:
Missing in IDP but found in Reference:
CHR POS REF ALT FUNC GENE COVERAGE PHRED "A[#F,#R]" "C[#F,#R]" "G[#F,#R]" "T[#F,#R]" "INS[#F,#R]" "DEL[#F,#R]" SNP MUT FREQ SANGER REGION TVC
2 166848646 G A exonic SCN1A 68 13 16;20 0;0 17;15 0;0 0;0 0;0 . c.[5139C>T]+[=] 52.94 . Not low found
12 52200340 A C exonic SCN8A 4129 28.3 1560;1672 413;453 0;0 0;0 0;2 31;0 . c.[5070A>C]+[=] 20.97 . Not low Not found
13 77570076 - A exonic CLN5 2762 26.6 2060;702 0;0 0;0 0;0 2050;696 0;0 . c.526_527insA 99.42 TP Not low Not found
7 148106478 - GT intronic CNTNAP2 4051 28.5 0;1 0;0 0;0 2220;1829 1085;887 0;1 rs60451214 c.3716-5_3716-4insGT 48.68 . Not low Not found
9 138678036 TGCCC - intronic KCNT1 834 23.1 0;0 0;0 0;31 0;1 0;0 0;802 rs141359570 c.3178-7_3178-3delTGCCC 96.16 . Not low Not found
7 148106476 - TT intronic CNTNAP2 4052 28.8 0;0 5;0 0;0 2221;1826 1081;884 0;0 rs61232377 c.3716-7_3716-6insTT 48.49 . Not low Not found
2 166245425 C T exonic SCN2A 49 12.6 0;0 13;9 0;0 18;9 0;0 0;0 . c.[5109C>T]+[=] 55.1 Not low found
I updated the code with:
Code:
{for(i=1;i<=19;i++)
{if($i == "")$i = "."}
}
but that seemed to remove the last 6 fields from the output. Thank you .
Hi,
I have the following data in the format as shown (note: there are more than 1 blank spaces between each field and the spaces are not uniform, meaning there can be one blank space between field1 and field2 and 3 spaces between field3 and field4, in this example, # are the spaces in between... (19 Replies)
I'm working on formatting some attendance data to meet a vendors requirements to upload to their system. With some help on the forums here, I have the data close. But they've since changed what they want.
The vendor wants me to submit three fields to them. Field 1 is the studentid field,... (4 Replies)
Hi Friends,
I have large volume of data file as shown below.
Beganing or end of each filed, there are some blank spaces.
How do I remove those spaces?
AAA AAA1 | BBB BB1 BB2 |CC CCCC
DDDD DD | EEEEEEE EEEEEEEE | FFF FFFFFF FFFF
GG GGGGGG |HH HH ... (3 Replies)
Hi experts,
I need to print the first field first then last two fields should come next and then i need to print rest of the fields.
Input :
a1,abc,jsd,fhf,fkk,b1,b2
a2,acb,dfg,ghj,b3,c4
a3,djf,wdjg,fkg,dff,ggk,d4,d5
Expected output:
a1,b1,b2,abc,jsd,fhf,fkk... (6 Replies)
Hello All,
I am trying a one liner for finding the number of null columns in every line of my flat file.
The format of my flat file is like this
a|b|c|d||||e|f|g|
a|b|c|d||||e|f|g|
I want to count the number of fields delimited by "|" which are blank.
In above case the count should be... (6 Replies)
Sample txt file :
OK00001111112|
OK00003443434|skjdaskldj
OK32812983918|asidisoado
OK00000000001|
ZM02910291029|sldkjaslkjdasldjk
what would be the shell script to figure out the blank space (if any) after the pipe sign? (4 Replies)
I have a tab delimited file with some fields potentially containing no data. In ksh 'read' though treats multiple tabs as a single delimiter. Is there any way to change that behavior so I could have blank data too? I.e. When encountering 2 tabs it would take it as a null field? Or do I have to... (3 Replies)
Hi
I have a file as below
<field1> <field2> <field3> ... <field_num1> <field_num2>
Trying to sort based on difference of <field_num1> and <field_num2> in desceding order and print all fields.
I tried this and it doesn't sort on the difference field .. Appreciate your help.
cat... (9 Replies)
The below code runs and creates an output file with three sections. The first 2 sections are ok, but the third section doesn't seem to put a . in all the fields that are blank. I don't know if this is what causes the last two fields in the current output to shift to a newline, but I can not seem... (3 Replies)
Hi,
Below are the sample files. x.txt is from an Excel file that is a list of users from Windows and y.txt is a list of database account.
$ head -500 x.txt y.txt
==> x.txt <==
TEST01 APP_USER_PROFILE
USER03 APP_USER_PROFILE
TEST02 APP_USER_EXP_PROFILE
TEST04 APP_USER_PROFILE
USER01 ... (3 Replies)
10-24-2016
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