I am trying to modify an awkkindly provided by #karakfa to update all the unknown values in $6 of file2, if the $4 value in file2 is within the range of $1 of file1. If there is already a value in $6 other then unknown, it is skipped and the next line is processed. In my awk attempt below the final output is 6 tab-delimited fields. Currently the awk runs but the unknown vales are not updated and I can not seem to solve this. Thank you :)
file1 (space delimited)
chr1:4714792-4852594 AJAP1
chr1:4714792-4837854 AJAP1
chr1:9160364-9189229 GPR157
chr1:9160364-9189229 GPR157
chr1:15783223-15798586 CELA2A
chr1:15783224-15798586 CELA2A
file2 (tab-delimited)
chr1 3649533 3649653 chr1:3649533-3649653 . TP73
chr1 4736396 4736516 chr1:4736396-4736516 . unknown
chr1 5923314 5923434 chr1:5923314-5923434 . NPHP4
chr1 9161991 9162111 chr1:9161991-9162111 . unknown
chr1 9162050 9162051 chr1:9162050-9162051 . rs6697376
desired output
--- the second and fourth unknown values are updated based on the range that they fall in $1 of file1
chr1 3649533 3649653 chr1:3649533-3649653 . TP73
chr1 4736396 4736516 chr1:4736396-4736516 . AJAP1
chr1 5923314 5923434 chr1:5923314-5923434 . NPHP4
chr1 9161991 9162111 chr1:9161991-9162111 . unknown
chr1 9162050 9162051 chr1:9162050-9162051 . rs6697376
current output with awk
awk -v OFS='\t' 'NR==FNR{
rstart[a[1]]=a[2]
rend[a[1]]=a[3]
value[a[1]]=$2
next}
$6~/unknown/ && $2>=rstart[$1] && $3<=rend[$1] {sub(/unknown/,value[$1],$6)}1' hg19.txt input | column -t
chr1 3649533 3649653 chr1:3649533-3649653 . TP73
chr1 4736396 4736516 chr1:4736396-4736516 . unknown
chr1 5923314 5923434 chr1:5923314-5923434 . NPHP4
chr1 9161991 9162111 chr1:9161991-9162111 . unknown
chr1 9162050 9162051 chr1:9162050-9162051 . rs6697376
edit:
awk -v OFS='\t' 'NR==FNR{split($1,a,/[:-]/)
rstart[a[1]]=a[2]
rend[a[1]]=a[3]
value[a[1]]=$2
next}
$6~/unknown/ && $2>=rstart[$1] && $3<=rend[$1] {sub(/unknown/,value[$1],$6)}1' hg19.txt input | column -t
possible solution to issue 2:
----- matching $2 values in file1 are combined with the first lines rstart[a[1]]=a[2] being the start and the last lines rend[a[1]]=a[3] being the end
chr1:4714792-4837854 AJAP1
chr1:9160364-9189229 GPR157
chr1:15783223-15798586 CELA2A
here is another script (it's inefficient since does a linear scan instead of more efficient search approaches) but works and simpler.
$ awk -v OFS='\t' 'NR==FNR{split($1,a,"[:-]"); k=a[1]; c[k]++;
rstart[k,c[k]]=a[2];
rend[k,c[k]]=a[3];
value[k,c[k]]=$2;
next}
$6=="unknown" && ($1 in c) {k=$1;
for(i=1; i<=c[k]; i++)
if($2>=rstart[k,i] && $3<=rend[k,i])
{$6=value[k,i]; break}}1' file1 file2 |
column -t
since it's possible to have more than one match, this one uses the first found.
chr1 3649533 3649653 chr1:3649533-3649653 . TP73
chr1 4736396 4736516 chr1:4736396-4736516 . AJAP1
chr1 5923314 5923434 chr1:5923314-5923434 . NPHP4
chr1 9161991 9162111 chr1:9161991-9162111 . GPR157
chr1 9162050 9162051 chr1:9162050-9162051 . rs6697376
note that the fourth record also matches based on the rules.
Related
I have a text file like this small example:
small example:
chr1 HAVANA exon 13221 13374
chr1 HAVANA exon 13453 13670
chr1 HAVANA gene 14363 29806
I am trying to filter the rows base on the 3rd column. in fact if the 3rd column is gene i will keep the entire row and filter out the other rows. here is the expected output:
expected output:
chr1 HAVANA gene 14363 29806
I am trying to do that in awk using the following command but the results is empty. do you know how to fix it?
awk '{ if ($3 == 'gene') { print } }' infile.txt > outfile.txt
Use double quotes in the script:
$ awk '{ if ($3 == "gene") { print } }' file
chr1 HAVANA gene 14363 29806
or:
$ awk '{ if ($3 == "gene") print }' file
but you could just:
$ awk '$3 == "gene"'
i have a tab separated text file like this small example:
chr1 100499714 100499715 1
chr1 100502177 100502178 10
chr1 100502181 100502182 2
chr1 100502191 100502192 18
chr1 100502203 100502204 45
in the new file that I will make:
1- I want to select the rows based on the 4th column meaning in the value of 4th column is at least 10, I will keep the entire row otherwise will be filtered out.
2- in the next step the 4th column will be removed.
the result will look like this:
chr1 100502177 100502178
chr1 100502191 100502192
chr1 100502203 100502204
to get such results I have tried the following code in awk:
cat input.txt | awk '{print $1 "\t" $2 "\t" $3}' > out.txt
but I do not know how to implement the filtering step. do you know how to fix the code?
Just put the condition before output:
cat input.txt | awk '$4 >= 10 {print $1 "\t" $2 "\t" $3}' > out.txt
here is another, might work better if you have many more fields
$ awk '$NF>=10{sub(/\t\w+$/,""); print}' file
In the below awk I am trying to match $2 in file1 up until the ., with $4 in file2 up to the first undescore _. If a match is found then that portion of file2 is up dated with the matching $1 value in file1. I think it is close but not sure how to account for the . in file1. In my real data there are thousands of lines, but they are all in the below format and a match may not always be found. The awk as is does execute but file2 is not updated, I think because the . is not matching. Thank you :).
file 1 space delimited
TGFBR1 NM_004612.3
TGFBR2 NM_003242.5
TGFBR3 NM_003243.4
file 2 tab-delimited
chr1 92149295 92149414 NM_003243_cds_0_0_chr1_92149296_r
chr1 92161228 92161336 NM_003243_cds_1_0_chr1_92161229_r
chr1 92163645 92163687 NM_003243_cds_2_0_chr1_92163646_r
chr3 30648375 30648469 NM_003242_cds_0_0_chr3_30648376_f
chr3 30686238 30686407 NM_003242_cds_1_0_chr3_30686239_f
chr9 101867487 101867584 NM_004612_cds_0_0_chr9_101867488_f
chr9 101904817 101904985 NM_001130916_cds_3_0_chr9_101904818_f
desired output tab-delimited
chr1 92149295 92149414 TGFBR3_cds_0_0_chr1_92149296_r
chr1 92161228 92161336 TGFBR3_cds_1_0_chr1_92161229_r
chr1 92163645 92163687 TGFBR3_cds_2_0_chr1_92163646_r
chr3 30648375 30648469 TGFBR2_cds_0_0_chr3_30648376_f
chr3 30686238 30686407 TGFBR2_cds_1_0_chr3_30686239_f
chr9 101867487 101867584 TGFBR1_cds_0_0_chr9_101867488_f
awk
awk 'FNR==NR {A[$1]=$1; next} $4 in A {sub ($4, $4 "_" A[$4]) }1' OFS='\t' file1 FS='\t' file2
Following awk may help you on same. Also you could change you FS field separator as per your Input_file(s) too, eg--> Input_file1 is space delimited then use FS=" " before it and Input_file2 is TAB delimited then use FS="\t" before its name.
awk '
FNR==NR{
val=$2;
sub(/\..*/,"",val);
a[val]=$1;
next
}
{
split($4,array,"_")
}
((array[1]"_"array[2]) in a){
sub(/.*_cds/,a[array[1]"_"array[2]]"_cds",$4);
print
}
' Input_file1 Input_file2
Output will be as follows:
chr1 92149295 92149414 TGFBR3_cds_0_0_chr1_92149296_r
chr1 92161228 92161336 TGFBR3_cds_1_0_chr1_92161229_r
chr1 92163645 92163687 TGFBR3_cds_2_0_chr1_92163646_r
chr3 30648375 30648469 TGFBR2_cds_0_0_chr3_30648376_f
chr3 30686238 30686407 TGFBR2_cds_1_0_chr3_30686239_f
chr9 101867487 101867584 TGFBR1_cds_0_0_chr9_101867488_f
I have an awk that seemed straight-forward, but I seem to be having a problem. In the file below if $5 starts with a ( then to that string a ) is added at the end. However if$5does not start with a(then nothing is done. The out is separated by a tab. Theawkis almost right but I am not sure how to add the condition to only add a)if the field starts with a(`. Thank you :).
file
chr7 100490775 100491863 chr7:100490775-100491863 ACHE
chr7 100488568 100488719 chr7:100488568-100488719 ACHE;DJ051769
chr1 159174749 159174770 chr1:159174749-159174770 (ACKR1
chr1 159175223 159176240 chr1:159175223-159176240 (ACKR1
awk tried
awk -v OFS='\t' '{print $1,$2,$3,$4,""$5")"}' file
current output
chr7 100490775 100491863 chr7:100490775-100491863 ACHE)
chr7 100488568 100488719 chr7:100488568-100488719 ACHE;DJ051769)
chr1 159174749 159174770 chr1:159174749-159174770 (ACKR1)
chr1 159175223 159176240 chr1:159175223-159176240 (ACKR1)
desired output (line 1 and 2 nothing is done but line 3 and 4 have a ) added to the end)
chr7 100490775 100491863 chr7:100490775-100491863 ACHE
chr7 100488568 100488719 chr7:100488568-100488719 ACHE;DJ051769
chr1 159174749 159174770 chr1:159174749-159174770 (ACKR1)
chr1 159175223 159176240 chr1:159175223-159176240 (ACKR1)
$ awk -v OFS='\t' '{p = substr($5,1,1)=="(" ? ")" : ""; $5=$5 p}1' mp.txt
chr7 100490775 100491863 chr7:100490775-100491863 ACHE
chr7 100488568 100488719 chr7:100488568-100488719 ACHE;DJ051769
chr1 159174749 159174770 chr1:159174749-159174770 (ACKR1)
chr1 159175223 159176240 chr1:159175223-159176240 (ACKR1)
Check the first character of the 5th field. If it is ( append a ) to the end, otherwise append the empty string.
By appending something (where one of the somethings is "nothing" :) in all cases, we force awk to reconstitute the record with the defined (tab) output separator, which saves us from having to print the individual fields. The trailing 1 acts as an always-true pattern whose default action is simply to print the reconstituted line.
I have a file with 5 columns and I want to separate the columns using number range as a criteria: example:
chr1 2120987 2144159 NM_001282670 0.48106
chr1 2123333 2126214 NM_001256946 2.71647
chr1 4715104 4837854 NM_001042478 0
chr1 4715104 4843851 NM_018836 0
chr1 3728644 3773797 NM_014704 4.61425
chr1 3773830 3801993 NM_004402 4.39674
chr1 3773830 3801993 NM_001282669 0
chr1 6245079 6259679 NM_000983 75.1769
chr1 6304251 6305638 NM_001024598 0
chr1 6307405 6321035 NM_207370 0.273874
chr1 6161846 6240194 NM_015557 0.0149477
chr1 6266188 6281359 NM_207396 0
chr1 6281252 6296044 NM_012405 14.0752
I want to remove 0 from the list , then would like to sort out numbers between 0.01 and 0.27 and so on....
I am new to shell programming....can someone help with awk ?
Thanks.
As you are new to shell programming, you may not be aware of grep and sort which would be simpler for this job.
If you are hell-bent on awk as your tool of choice, please just disregard my answer.
I would do it like this:
grep -v '\s0$' file | sort -k 5,5 -g
chr1 6161846 6240194 NM_015557 0.0149477
chr1 6307405 6321035 NM_207370 0.273874
chr1 2120987 2144159 NM_001282670 0.48106
chr1 2123333 2126214 NM_001256946 2.71647
chr1 3773830 3801993 NM_004402 4.39674
chr1 3728644 3773797 NM_014704 4.61425
chr1 6281252 6296044 NM_012405 14.0752
chr1 6245079 6259679 NM_000983 75.1769
The grep with -v inverts the search and looks for lines not containing the sequence space followed by a zero followed by end of line. The sort sorts the data on column 5, and does a general numeric sort because of the -g.
If you are trying to select the rows in which $5 is non-zero and within a certain range, then indeed awk makes sense, and the following may be close to what you're after:
awk -v min=0.01 -v max=0.27 '
$5 == 0 { next }
min <= $5 && $5 <= max { print }'
Here, the call to awk has been parameterized to suggest how these few lines can be adapted for more general usage.