Both awk command below execute but I do not get the intended result:
I added some more comments to both as well. Thank you .
awk 1
Code:
awk '
# BEGIN runs before any of the input files is opened
BEGIN { FS=OFS="\t" }
# The input files are processed one by one and the following code runs for each line
# FNR is equal to NR when processing file1
# a[ ] is indexed by the one letter code, its value is the three letter code
FNR==NR { a[$1]=$2; next }
# The next goes to the next input cycle
# The following code runs for file2 (and further files)
$12 ~ /:NM_/{ # search $12 for pattern :NM_
match($12,/p..*/) # using match the regex will match in $12 from the p. to the
VAL=substr($12,RSTART+1,RLENGTH-2) # Put the values of substring whose value starts from RSTART+1 to RSTART-2
# update one letter code to three letter by storing the value of $12 in array then updating if it matches file1
{ if(a[$12]){$12=a[$12] };
}
print}' file1 file2 > out
out
Code:
4 chr1 949597 949597 C T exonic ISG15 . . synonymous SNV ISG15:NM_005101:exon2:c.237C>T:p.D79D rs61766284
5 chr1 949654 949654 A G exonic ISG15 . . synonymous SNV ISG15:NM_005101:exon2:c.294A>G:p.V98V rs8997
awk 2
Code:
# store value of $2 in file1 in array A and update each sub-patter of p. matching $12 in file2
awk 'FNR==NR {A[$1]=$2; next} $12 in A {sub ($12, $12 "p." A[$12]) }1' OFS="\t" file1 FS='\t' file2 > out
out
Code:
R_Index Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene Inheritence ExonicFunc.refGene AAChange.refGene avsnp147
1 chr1 948846 948846 - A upstream ISG15 dist=1 . . . rs3841266
2 chr1 948870 948870 C G UTR5 ISG15 NM_005101:c.-84C>G . . . rs4615788
3 chr1 948921 948921 T C UTR5 ISG15 NM_005101:c.-33T>C . . . rs15842
4 chr1 949597 949597 C T exonic ISG15 . . synonymous SNV ISG15:NM_005101:exon2:c.237C>T:p.D79D rs61766284
5 chr1 949654 949654 A G exonic ISG15 . . synonymous SNV ISG15:NM_005101:exon2:c.294A>G:p.V98V rs8997
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
g1111.b1 Lucy russia 126 (6 Replies)
Hi, I have 2 files that I have modified to basically match each other, however I want to determine what (if any) line in file 1 does not exist in file 2. I need to match column $1 and $2 as a single string in file1 to $1 and $2 in file2 as these two columns create a match.
I'm stuck in an AWK... (9 Replies)
Help needed urgently please.
I have a large file - a few hundred thousand lines.
Sample
CP START ACCOUNT
1234556
name 1
CP END ACCOUNT
CP START ACCOUNT
2224444
name 1
CP END ACCOUNT
CP START ACCOUNT
333344444
name 1
CP END ACCOUNT
I need to split this file each time "CP START... (7 Replies)
Hi,
I need help with this-
input.txt :
L B white
X Y white
A B brown
M Y black
Read this input file and if 3rd column is "white", then add specific lines to another file insert.txt.
If 3rd column is brown, add different set of lines to insert.txt, and so on.
For example, the given... (6 Replies)
If $1 in file1 matches $2 in file2. Then the value in $2 of file2 is updated to $1"."$2 of file2. The awk seems to only match the two files but not update. Thank you :).
awk
awk 'NR==FNR{A ; next} $1 in A { $2 = a }1' file1 file2
file1
name version
NM_000593 5
NM_001257406... (3 Replies)
I am trying to match $1 in file1 with $2 in file2. If a match is found then $3 and $4 of file2 are copied to file1. Both files are tab-delimeted and I am getting a syntax error and would also like to update file1 in-place without creating a new file, but am not sure how. Thank you :).
file1
... (19 Replies)
I am trying to use awk to match two files that are tab-delimited. When a match is found between file1 $1 and file2 $4, $4 in file2 is updated using the $2 value in file1. If no match is found then the next line is processed. Thank you :).
file1
uc001bwr.3 ADC
uc001bws.3 ADC... (4 Replies)
I am trying to create a cronjob that will run on startup that will look at a list.txt file to see if there is a later version of a database using database.txt as the source. The matching lines are written to output.
$1 in database.txt will be in list.txt as a partial match. $2 of database.txt... (2 Replies)
In the perl below I am trying to set/update the value of $14 (last field) in file2, using the matching NM_ in $12
or $9 in file2 with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern will always be NM_ and the end pattern is always
;... (4 Replies)
Trying to use awk to store the value of $5 in file1 in array x. That array x is then used to search $4 of file1 to find aa match (I use x to skip the header in file1). Since $4 can have multiple strings in it seperated by a , (comma), I split them and iterate througn each split looking for a match.... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
h5diff
h5diff(1) General Commands Manual h5diff(1)NAME
h5diff - Compares two HDF5 files and reports the differences.
SYNOPSIS
h5diff file1 file2 [OPTIONS] [object1 [object2 ] ]
DESCRIPTION
h5diff is a command line tool that compares two HDF5 files, file1 and file2, and reports the differences between them.
Optionally, h5diff will compare two objects within these files. If only one object, object1, is specified, h5diff will compare object1 in
file1 with object1 in file2. In two objects, object1 and object2, are specified, h5diff will compare object1 in file1 with object2 in
file2. These objects must be HDF5 datasets.
object1 and object2 must be expressed as absolute paths from the respective file's root group.
Additional information, with several sample cases, can be found in the document H5diff Examples.
OPTIONS
file1 file2
The HDF5 files to be compared.
-h Print all differences.
-r Print only the names of objects that differ; do not print the differences. These objects may be HDF5 datasets, groups, or named
datatypes.
-n count
Print difference up to count differences, then stop. count must be a positive integer.
-d delta
Print only differences that are greater than the limit delta. delta must be a positive number. The comparison criterion is whether
the absolute value of the difference of two corresponding values is greater than delta (e.g., |a-b| > delta, where a is a value in
file1 and b is a value in file2).
-p relative
Print only differences that are greater than a relative error. relative must be a positive number. The comparison criterion is
whether the absolute value of the difference 1 and the ratio of two corresponding values is greater than relative (e.g., |1-(b/a)| >
relative where a is a value in file1 and b is a value in file2).
object1 object2
Specific object(s) within the files to be compared.
EXAMPLES
The following h5diff call compares the object /a/b in file1 with the object /a/c in file2:
h5diff file1 file2 /a/b /a/c
This h5diff call compares the object /a/b in file1 with the same object in file2:
h5diff file1 file2 /a/b
And this h5diff call compares all objects in both files:
h5diff file1 file2
SEE ALSO h5dump(1), h5ls(1), h5repart(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1)h5diff(1)
09-06-2017
.