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
glam2-purge
GLAM2-PURGE(1) glam2 Manual GLAM2-PURGE(1)NAME
glam2-purge - Removes redundant sequences from a FASTA file
SYNOPSIS
glam2-purge file score [options]
DESCRIPTION
glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended
in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates
an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output
file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA.
Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.
OPTIONS -n
Sequences are DNA (default: protein).
-b
Use blast heuristic method (default for protein).
-e
Use an exhaustive method (default for DNA).
-q
Keep first sequence in the set.
-x
Use xnu to mask protein tandem repeats.
SEE ALSO glam2(1), glam2format(1), glam2mask(1), glam2scan(1), xnu(1)
The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in
/usr/share/doc/glam2/.
REFERENCES
Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer
membrane protein repeats", Protein Science, 4:1618-1632, 1995. Please cite it if you use Purge.
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and
deletions, PLoS Computational Biology (in press).
AUTHORS
Andrew Neuwald
Author of purge, renamed glam2-purge in Debian.
Martin Frith
Modified purge to be ANSI standard C and improved the user interface.
Timothy Bailey
Modified purge to be ANSI standard C and improved the user interface.
Charles Plessy <plessy@debian.org>
Formatted this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
The source code and the documentation of Purge and GLAM2 are released in the public domain.
GLAM2 1056 05/19/2008 GLAM2-PURGE(1)