Here is the top of the Master file I'm trying to grep out of
Chr1 3658 A 1 ^M. C
Chr1 3659 A 1 . C
Chr1 3660 A 1 . C
Chr1 3661 C 2 .^M. F@
Chr1 3662 A 2 .. F@
Chr1 3663 A 2 .. F@
Chr1 3664 A 2 .. F@
Chr1 3665 T 2 .. FD
Chr1 3666 A 2 .. HD
Chr1 3667 C 2 .. HD
Chr1 3668 A 4 ..^K,^K. H:.$
Chr1 3669 T 4 ..,. GA1*
Chr1 3670 A 4 ..,. HCD9
Chr1 3671 A 4 ..,. GDDJ
Chr1 3672 T 4 ..,. JFBI
Chr1 3673 C 4 ..,. JBDJ
Chr1 3674 G 6 ..,.^:,^:. IBDJ?=
Chr1 3675 G 6 ..,.,. J8DHDJ
So I have a 12GB file and I want to pull out the lines that correspond to about 350,000 specific positions on the chromosomes. Each is a separate line.
I'm using Ubuntu. The Master file is a .bcf made with samtools and the coordinates (pattern file) was made from a table in a paper and is tab delimited. I added a third column with just a tab so as not to pull out multiple entries beginning with the search pattern eg only want Chr1 3675 pulling not other entries like Chr1 367567 for example.
This starts to ouput the lines with the correct patterns to the terminal within a few seconds:
But this just greps indefinately, creates the output file but it stays empty. After about 10 min I kill the command.
I tried the script command to copy the terminal to a file but it has all kinds if formatting info in it as well. Must be an easier way.
---------- Post updated at 01:29 AM ---------- Previous update was at 01:21 AM ----------
Should I let it run overnight? Its just the non-write to file version only takes a few seconds!!
I'm wondering if it scans the whole 12 GB file before writing to file whereas if it finds something it may instantly display it in the terminal?
I 'm trying to grep 2 fieldds on 2 differnt lines. Like this:
psit > file
egrep -e '(NS|ES)' $file. Not working. If this succeeds then run next cmd else exit. Pls Help
Gundu (13 Replies)
Hey guys:
I've been meaning to post this question for awhile...it is regarding grep. Let's say for example that the following entry is in logxx:
Wed Feb 2 07:44:11 <vsm> 91030 Line 5 Severity 1 Vps 6
Call Answered - DN:8753101 CLID:5164665761 PI:83
If I do a grep 91030... (27 Replies)
Hi.
I have this format on a textfile:
VG Name /dev/vg00
PV Name /dev/dsk/c16t0d0
PV Name /dev/dsk/c18t0d0
PV Name /dev/dsk/c16t4d0
VG Name /dev/vg01
PV Name ... (6 Replies)
Guys I am having a problem with being able to find missing monitors in a configuration check script I am trying to create for accountability purposes for managing a large number of systems. What I am trying to do is run a script that will look at the raw config data in a file and pull all the pool... (7 Replies)
I want to search files (basically .cc files) in /xx folder and subfolders.
Those files (*.cc files) must contain #include "header.h" AND x() function.
I am writing it another way to make it clear,
I wanna list of *.cc files that have 'header.h' & 'x()'. They must have two strings, header.h... (2 Replies)
hi
i have kind of below text in a file.
I want to get a complete paragraph starting with START and ending with before another START) which has a particular string say XYZ or ABC
START XYZ hshjghkjh 45 ljkfd
fldjlj d jldf
START 3493u ABC 454
4545454
4545454 45454
4545454
START ...... (3 Replies)
How do you grep 'select * from table_name' string from a script if the select * and from table_name are on 2 different lines ? like
select *
from table_name
Any help would be greatly appreciated !!!
Thanks
RDR (4 Replies)
I have 1300 files (SearchFiles0001.txt, SearchFiles0002.txt, etc.) , each with 650,000 lines, tab-delimited data.
I have a pattern file, with about 1000 lines with a single word. Each single word is found in the 1300 files once.
If I grep -f PatternFile.txt SearchFiles*.txt >OutputFile.txt... (2 Replies)
I want to grep multiple lines from a text file. I want to grep all lines containing X,Y and NA in a single command. How do I go about doing that?
This is what my text files look like:
rs1983866 0.0983 10 100016313
rs1983865 0.5994 X 100016339
rs1983864 0.3272 11 100017453
rs7077266... (2 Replies)
Hi Everyone,
Im currently using the below code to pull data from a large CSV file and put it into smaller files with just the data associated with the number that I "grep".
grep 'M053' test.csv > test053.csv
Is there a way that I can use grep to run through my file like the example below... (6 Replies)
Discussion started by: TheStruggle
6 Replies
LEARN ABOUT V7
zgrep
ZGREP(1) General Commands Manual ZGREP(1)NAME
zgrep - search possibly compressed files for a regular expression
SYNOPSIS
zgrep [ grep_options ] [ -e ] pattern filename...
DESCRIPTION
Zgrep invokes grep on compressed or gzipped files. These grep options will cause zgrep to terminate with an error code:
(-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*). All other options specified are passed directly to grep. If no file is specified, then the
standard input is decompressed if necessary and fed to grep. Otherwise the given files are uncompressed if necessary and fed to grep.
If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.
EXIT CODE
2 - An option that is not supported was specified.
AUTHOR
Charles Levert (charles@comm.polymtl.ca)
SEE ALSO grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)ZGREP(1)