The below bash (though not optimized), yields the desired result for one entry. That is depending on the digits in the file manually selected in the first process, the second file used is automatically selected using the matching digits along with the full path. The problem is this seems to work for the first file but not for others. Thank you .
file manually selected: 123_base_counts.txt
Code:
123_base_counts.txt
456_base_counts.txt
file selected automatically using the matching digits in (/home/user)
# manual selection of file
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools
ANNOVARDIR=/home/user
PS3="please select a file to analyze with a panel: " # specify file1
select file1 in $(cd ${FILESDIR};ls);do break;done
file1=`basename ${FILESDIR}/${file1}`
printf "FILE is: ${file1} and will be used
# automatic file based on match
FILESDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools # match directory
ANNOVARDIR=/home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar # search directory
printf "\n\n"
printf "These are all vcf files in the directory: \n"
ls ${ANNOVARDIR}
file1=`basename ${FILESSDIR}/${file1}` # file matched
file2=(${ANNOVARDIR}/${file1%%_*}*)
printf "file2 is: ${file2} and will be used
output
Code:
1) 123_base_counts.txt
2) 456_base_counts.txt
please select a file to analyze with a panel: 1
FILE is: 123_base_counts.txt and will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, calculate 20x and 30x coverage, and filter the vcf for the 98 gene epilepsy panel
These are all files in the new directory:
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/cmccabe/Desktop/NGS/API/5-14-2016/vcf/overall/annovar/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used
second time results
1) 123_base_counts.txt
2) 456_base_counts.txt
please select a file to analyze with a panel: 2
FILE is: 456_base_counts.txt and will be used
These are all files in the new directory:
123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
456_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt
file2 is: /home/user/123_variant_strandbias_readcount.vcf.hg19_multianno_removed_final.txt and will be used
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$GREP '\(\)\(\)\(\)\3\2\1'I
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e1000g123001
e1000g0
nge11101
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In the below portion of a bash script the user selects a file from a directory.
select file in $(cd /home/cmccabe/Desktop/NGS/API/5-14-2016/bedtools;ls);do break;done
files in directory
123_base_counts.txt
456_base_counts.txt
789_base_counts.txt
second portion of bash currently (user... (4 Replies)
As part of a bash the below line strips off a numerical prefix from directory 1 to search for in directory 2.
for file in /home/cmccabe/Desktop/comparison/missing/*.txt
do
file1=${file##*/} # Strip off directory
getprefix=${file1%%_*.txt}
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Hey everyone,
I am trying to extract column values from a column in a tab-delimited text file and overlay them in a 2nd tab-delimited text file using a V-lookup type script in Unix bash.
These are the 1st few rows of the 1st input file IN1:
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Discussion started by: Geneanalyst
10 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)
07-26-2016
.