Rename text file with a specific pattern in directory
I am trying to rename all text files in a directory that match a pattern. The current command below seems to be using the directory path in the name and since it already exists, will not do the rename. I am not sure what I am missing? Thank you .
Files to rename in /home/cmccabe/Desktop/test/vcf/overall/annovar
Hi,
I have some ps files where I want to ectract/copy a certain number from and use that number to rename the ps file.
eg:
'file.ps' contains following text:
14 (09 01 932688 0)t
the text can be variable, the only fixed element is the '14 ('. The problem is that the fixed element can appear... (7 Replies)
How can i break a text file into parts that occur between a specific pattern?
I have text file having various xml many tags like which starts with the tag "<?xml version="1.0" encoding="utf-8"?>" . I have to break the whole file into several xmls by looking for the above pattern.
All the... (9 Replies)
Hi all,
I am working on a small prog..
i have a file.txt which contains random data...
K LINES V4 ADD CODE `COMPANY` ADD CODE `DISTRIBUTOR` SEQ NAME^K LINES V5 SEQ NAME^K LINES V6 ADD `PACK-LDATE` SEQ NAME^K^KCOMMAND END^KHEADINFO... (1 Reply)
Hi ,
i have some files of specific pattern ...i need to look for files which are having size greater than zero and move those files to another directory..
Ex...
abc_0702,
abc_0709,
abc_782
abc_1234 ...etc
need to find out which is having the size >0 and move those to target directory..... (7 Replies)
Hello
I am making a script where I need to rename the files but with different names.The file name could be change according to the product
I made a logic but that is not working properly
arr=$(echo a@b@c | tr "@" "\n")
echo $arr
output is a b c
arry=$(echo d@e@f | tr "@" "\n")
... (4 Replies)
Hi
This is my first post and I'm just a beginner. So please be nice to me.
I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file?
I have tried sed -n 241,241p... (13 Replies)
I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
I have files in a Linux directory . Some of the file is listed below
-rw-rw-r--. 1 roots roots 0 Dec 23 02:17 zzz_123_00000_A_1.csv
-rw-rw-r--. 1 roots roots 0 Dec 23 02:18 zzz_121_00000_A_2.csv
-rw-rw-r--. 1 roots roots 0 Dec 23 02:18 zzz_124_00000_A_3.csv
drwxrwxr-x. 2 roots roots 6 Dec 23... (4 Replies)
In the below file I am trying to grep or similar, all lines where only AF= is less than 0.4.. Thank you :).
grep
grep "AF=" ,+ .4 file
file
12 112036782 . T C 34.0248 PASS ... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT DEBIAN
vcf-annotate
VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1)NAME
vcf-annotate - annotate VCF file, add filters or custom annotations
SYNOPSIS
cat in.vcf | vcf-annotate [OPTIONS] > out.vcf
DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
Currently annotates only the INFO column, but it will be extended on demand.
OPTIONS -a, --annotations <file.gz>
The tabix indexed file with the annotations: CHR FROM[ TO][ VALUE]+.
-c, --columns <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
column should be ignored. If TO is not present, it is assumed that TO equals to FROM.
-d, --description <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a
file, one annotation per line.
-f, --filter <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-h, -?, --help
This help message.
Filters:
+ Apply all filters with default values (can be overridden, see the example below).
-X Exclude the filter X
1, StrandBias
FLOAT Min P-value for strand bias (given PV4) [0.0001]
2, BaseQualBias
FLOAT Min P-value for baseQ bias [1e-100]
3, MapQualBias
FLOAT Min P-value for mapQ bias [0]
4, EndDistBias
FLOAT Min P-value for end distance bias [0.0001]
a, MinAB
INT Minimum number of alternate bases [2]
c, SnpCluster
INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
D, MaxDP
INT Maximum read depth [10000000]
d, MinDP
INT Minimum read depth [2]
q, MinMQ
INT Minimum RMS mapping quality for SNPs [10]
Q, Qual
INT Minimum value of the QUAL field [10]
r, RefN
Reference base is N []
W, GapWin
INT Window size for filtering adjacent gaps [10]
w, SnpGap
INT SNP within INT bp around a gap to be filtered [10]
Example:
zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
+/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
Where descriptions.txt contains:
key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)
02-09-2017
.