awk to split one field and print the last two fields within the split part.
Hello;
I have a file consists of 4 columns separated by tab. The problem is the third fields. Some of the them are very long but can be split by the vertical bar "|". Also some of them do not contain the string "UniProt", but I could ignore it at this moment, and sort the file afterwards. Here is the input file like (>100k rows!!!):
I want the output file with the truncated field-3, which is like following:
What I did is by matching the "UniProt" string in the third field, split this field and only print the last two columns of the split fields, the original 3 fields ($1, $2, $4) need to be printed untouched.
Here is my code:
Have struggled for a while, but did not work out. Appreciate your expertise to help me out. Thanks a lot! Yifang
Hi all,
I have a field in the line, let's say argument $6, which is in the format 00.00
If i want to split the field to get rid of the "." in between of the amount, how can i do that i awk script?
I have it like this
split($6,a,".")
but it will get rid of the last 2 digits after the... (4 Replies)
I am trying to pull data out of a file to execute a series of repetitive commands. One of the fields is a {hex number}.{hex number} pattern. I need the first part of that structure to pass into the command. The file structure is like this:
A 2007/10/20 09:50:00 li text ef6da.1 name ... (6 Replies)
Hi,
I have a comma delimited text file where character fields (as opposed to numeric and date fields) are always enclosed with double quotes. Records are separated by the newline character. In a shell script I would like to split a particular field into two separate fields (enclosed with double... (4 Replies)
Hi there I have a text file with several fields separated by ";" as follow :
5466-43;5466;JOAN;LIGA;LIGA ESPANOLA;43;DEP LA CORUNA - OSASUNA;10/01/10 17:00
5466-44;5466;CARLES;LIGA;LIGA ESPANOLA;44;MALAGA - ATHL BILBAO;10/01/10 17:00
5466-45;5466;FAB;LIGA;LIGA ESPANOLA;45;REAL MADRID -... (4 Replies)
Hi all,
I have a .vcf file which contains 8 coulmns and the data under each column as shown below,
CHROM POS ID REF ALT QUAL FILTER INFO
1 3000012 . A G 126 ... (6 Replies)
I want to use awk to split fields and put them into a file
but I don't know the number of fields
for example, in the following line
Ports: 22/filtered/tcp//ssh///, 53/open/tcp//tcpwrapped///, 111/filtered/tcp//rpcbind///, 543/filtered/tcp//klogin///, 544/filtered/tcp//kshell///,... (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)
I am trying to split a tab-delimeted file using awk after the second _ in bold. The awk below is close but splits on the first _, and I am not sure how to use the second _. Thank you :).
file
chr1 92145889 92149424 NM_001195684_exon_0_10_chr1_92145900_r 0 -
chr1 92161218 ... (4 Replies)
In the tab-delimited input below I am trying to use awk to -10 from $2 and +10 to $3. Something like
awk -F'\t' -v OFS='\t' -v s=10 '{split($4,a,":"); print $1,$2-s,$3+s,a,$5,$6} | awk {split(a,b,"-"); print $1,$2-s,$3+s,b-s,b+s,$5,$6}' input
should do that. I also need to -10 from $4... (2 Replies)
In the awk I am splitting on the : into array a, then splitting on the - into element b. I can not seem to duplicate b if there is no - after it. Lines 1,2,4 are examples. If there is a - after the number in b then the value to the right of it is $3 in the ouput. Thank you :).
awk... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
probalign
PROBALIGN(1) User Commands PROBALIGN(1)NAME
probalign - Align sequences in MFAFILE(s) and print result to standard output
DESCRIPTION
PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and
Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein).
PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.
See the README file for details.
Usage:
probalign [OPTION]... [MFAFILE]...
Description:
Align sequences in MFAFILE(s) and print result to standard output
-clustalw
use CLUSTALW output format instead of MFA
-v, --verbose
report progress while aligning (default: off)
-a, --alignment-order
print sequences in alignment order rather than input order (default: off)
-T, -temperature
Sets the thermodynamic temperature parameter
(default: 5 (for protein data mode), 1 ( for nucleotide data mode)).
-score_matrix, --score_matrix
Sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer
README for details)
-go, --gap-open
This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix)
is 4.
-ge, --gap-extension
This option can be used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple
matrix) is 0.25.
-nuc
Specify this option to indicate that inputted sequences are nucleotide sequences
-prot
Specify this option to indicate that inputted sequences are protein sequences [DEFAULT]
-showPP
Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are
scaled to be between integers between 0 and 9).
probalign 1.4 May 2011 PROBALIGN(1)