I have a file which has these columns:
chr1 1397031 1445511 360 chr1 1436533 1436893
chr1 3558988 3639716 9837 chr1 3565359 3575196
chr1 9634389 9711556 1958 chr1 9635273 9637231
chr1 10657207 10657742 535 chr1 10629864 10676549
chr1 12590100 12594553 4453 chr1 12550526 12600407
chr1 14599424 14601321 1897 chr1 14590538 14619056
chr1 15352815 15419459 7429 chr1 15363278 15370707
The fourth column represents the overlap between the 2nd, 3rd, 6th and the 7th columns.
So,the smaller one between the 7th column and the 3rd is the end position of the overlapping region. And the bigger one between the 2nd column and the 6th is the start position.
Can anyone help with an awk script ?
well your question is not that clear.. you described your data, but didn't mention what do you want to get..
I guess you want to list the start/end of your "overlapping" right?
awk '{s=$2>=$6?$2:$6;e=$3<=$7?$3:$7;print $1,s,e,$4}' file
the output would be:
chr1 1436533 1436893 360
chr1 3565359 3575196 9837
chr1 9635273 9637231 1958
chr1 10657207 10657742 535
chr1 12590100 12594553 4453
chr1 14599424 14601321 1897
chr1 15363278 15370707 7429
columns:
col1 is the text
col2 is the overlapping start
col3 is the overlapping end
col4 is the overlap
a magic answer to magic question...:)
Related
I am trying to use awk to check if each $2 in file1 falls between $2 and $3 of the matching $4 line of file2. If it does then in $5 of file2, exon if it does not intron. I think the awk below will do that, but I am struggling trying to is add a calculation that if the difference is less than or equal to 10, then $5 is splicing. I have added an example of line 1 as well.
The 6th line is an example of the splicing, because the $2 value in file1 is 2 away from the $2 value in file2. My actual data is very large with file2 always being several hundreds of thousand lines. File 1 will be variable but usually ~100 lines. The files are hardcoded in this example but will be gotten from a bash for loop. That will provide the input. Thank you :).
file1 tab-delimited with whitespace after $3 and $4
chr1 17345304 17345315 SDHB
chr1 17345516 17345524 SDHB
chr1 93306242 93306261 RPL5
chr1 93307262 93307291 RPL5
chrX 153295819 153296875 MECP2
chrX 153295810 153296830 MECP2
file2 tab-delimited
chr1 17345375 17345453 SDHB_cds_0_0_chr1_17345376_r 0 -
chr1 17349102 17349225 SDHB_cds_1_0_chr1_17349103_r 0 -
chr1 17350467 17350569 SDHB_cds_2_0_chr1_17350468_r 0 -
chr1 17354243 17354360 SDHB_cds_3_0_chr1_17354244_r 0 -
chr1 17355094 17355231 SDHB_cds_4_0_chr1_17355095_r 0 -
chr1 17359554 17359640 SDHB_cds_5_0_chr1_17359555_r 0 -
chr1 17371255 17371383 SDHB_cds_6_0_chr1_17371256_r 0 -
chr1 17380442 17380514 SDHB_cds_7_0_chr1_17380443_r 0 -
chr1 93297671 93297674 RPL5_cds_0_0_chr1_93297672_f 0 +
chr1 93298945 93299015 RPL5_cds_1_0_chr1_93298946_f 0 +
chr1 93299101 93299217 RPL5_cds_2_0_chr1_93299102_f 0 +
chr1 93300335 93300470 RPL5_cds_3_0_chr1_93300336_f 0 +
chr1 93301746 93301949 RPL5_cds_4_0_chr1_93301747_f 0 +
chr1 93303012 93303190 RPL5_cds_5_0_chr1_93303013_f 0 +
chr1 93306107 93306196 RPL5_cds_6_0_chr1_93306108_f 0 +
chr1 93307322 93307422 RPL5_cds_7_0_chr1_93307323_f 0 +
chrX 153295817 153296901 MECP2_cds_0_0_chrX_153295818_r 0 -
chrX 153297657 153298008 MECP2_cds_1_0_chrX_153297658_r 0 -
chrX 153357641 153357667 MECP2_cds_2_0_chrX_153357642_r 0 -
desired output tab-delimited
chr1 17345304 17345315 SDHB intron
chr1 17345516 17345524 SDHB intron
chr1 93306242 93306261 RPL5 intron
chr1 93307262 93307291 RPL5 intron
chrX 153295819 153296875 MECP2 exon
chrX 153295810 153296800 MECP2 splicing
awk
awk '
FNR==NR{
a[$4];
min[$4]=$2;
max[$4]=$3;
next
}
{
split($4,array,"_");
print $0,(array[1] in a) && ($2>=min[array[1]] &&
$2<=max[array[1]])?"exon":"intron"
}' file1 OFS="\t" file2 > output
example of line 1
a[$4] = SDHB
min[$4] = 17345304
max[$4] = 17345315
array[1] = SDHB, 17345304 >= 17345375 && array[1] = SDHB, 17345315 <= 17345453 ---- intron
I have a tab separated text file and want to do some math operation on one column and make a new tab separated text file.
this is an example of my file:
chr1 144520803 144520804 12 chr1 144520813 58
chr1 144520840 144520841 12 chr1 144520845 36
chr1 144520840 144520841 12 chr1 144520845 36
chr1 144520848 144520849 14 chr1 144520851 32
chr1 144520848 144520849 14 chr1 144520851 32
i want to change the 4th column. in fact I want to divide every single element in the 4th column by sum of all elements in the 4th column and then multiply by 1000000 . like the expected output.
expected output:
chr1 144520803 144520804 187500 chr1 144520813 58
chr1 144520840 144520841 187500 chr1 144520845 36
chr1 144520840 144520841 187500 chr1 144520845 36
chr1 144520848 144520849 218750 chr1 144520851 32
chr1 144520848 144520849 218750 chr1 144520851 32
I am trying to do that in awk using the following command but it does not return what I want. do you know how to fix it:
awk '{print $1 "\t" $2 "\t" $3 "\t" $4/{sum+=$4}*1000000 "\t" $5 "\t" $6 "\t" $7}' myfile.txt > new_file.txt
you need two passes, one to compute the sum and then to scale the field
something like this
$ awk -v OFS='\t' 'NR==FNR {sum+=$4; next}
{$4*=(1000000/sum)}1' file{,} > newfile
Input: A tab-separated input file with 15 columns where column 15 is an integer.
Output: The number of lines that satisfy the conditional.
My code:
$ closest-features --closest --no-overlaps --delim '\t' --dist --ec megatrans_enhancers.sorted.bed ../../data/alu_repeats.sorted.bed | awk -v OFS='\t' '{if ($15 <= 1000 || $15 >= -1000) print $0}' | wc -l
1188
The || conditional in this case is failing to work (the total number of lines in the file are 1188 and I know for certain at least some lines do not satisfy the condition), because if I remove the OR conditional then suddenly it works:
$ closest-features --closest --no-overlaps --delim '\t' --dist --ec megatrans_enhancers.sorted.bed ../../data/alu_repeats.sorted.bed | awk -v OFS='\t' '{if ($15 <= 1000) print $0}' | wc -l
926
Not sure what i'm doing wrong. Any advice?
Example Input to Awk command:
chr1 378268 378486 chr1-798_Enhancer 17.2 + chr1 375923 376219 AluY|SINE|Alu-HOMER529 0 + E:375923 0.044 -2050
chr1 1079471 1079689 chr1-929_Enhancer 14.6 - chr1 1071271 1071563 AluSx1|SINE|Alu-HOMER1669 0 - E:1071271 0.13 -7909
chr1 1080259 1080477 chr1-830_Enhancer 16.7 - chr1 1071271 1071563 AluSx1|SINE|Alu-HOMER1669 0 - E:1071271 0.13 -8697
chr1 6611744 6611962 chr1-241_Enhancer 46.6 + chr1 6611431 6611723 AluSc|SINE|Alu-HOMER10257 0 + E:6611431 0.089 -22
chr1 6959639 6959857 chr1-58_Enhancer 100.1 - chr1 6966612 6966911 AluSx|SINE|Alu-HOMER11041 0 - E:6966612 0.137 6756
chr1 6960593 6960811 chr1-202_Enhancer 51.6 - chr1 6966612 6966911 AluSx|SINE|Alu-HOMER11041 0 - E:6966612 0.137 5802
chr1 7447888 7448106 chr1-2_Enhancer 181.9 - chr1 7449489 7449799 AluSz|SINE|Alu-HOMER11879 0 + E:7449489 0.119 1384
chr1 10752461 10752679 chr1-131_Enhancer 65.4 - chr1 10752754 10753065 AluSq2|SINE|Alu-HOMER19455 0 + E:10752754 0.106 76
chr1 12485694 12485912 chr1-353_Enhancer 36.7 + chr1 12487328 12487634 AluSx3|SINE|Alu-HOMER23581 0 + E:12487328 0.085 1417
chr1 12486469 12486687 chr1-141_Enhancer 63.6 + chr1 12487328 12487634 AluSx3|SINE|Alu-HOMER23581 0 + E:12487328 0.085 642
Try to put && condition because a digit should be greater than -1000 and lesser than 1000.
Your_command | awk '$15<=1000 && $15>=-1000{count++} END{print count}'
Add -F"\t" in above awk in case your Input to it is coming TAB delimited too. Also there is no need to use wc -l after awk. I have written logic for that so give the count of lines which are satisfying the condition by creating a variable named count and printing it at very last of Input_file.
Also for your provided samples output is coming as 3 which I believe is correct one.
This is a similar question to what has been previously asked (see below for link) but this time I would like to output the common strings into rows instead of columns as shown below:
I have two files, each with one column that look like this:
File 1
chr1 106623434
chr1 106623436
chr1 106623442
chr1 106623468
chr1 10699400
chr1 10699405
chr1 10699408
chr1 10699415
chr1 10699426
chr1 10699448
chr1 110611528
chr1 110611550
chr1 110611552
chr1 110611554
chr1 110611560
File 2
chr1 1066234
chr1 106994
chr1 1106115
I want to search file 1 and pull out all lines that are an exact match with line 1 of file 2 and output all matches on it's own line. Then I want to do the same for line 2 of file 2 and so on until all matches of file 2 have been found in file 1 and output to it's own row. Also I am working with very large files so something that won't require file 2 to be completely stored in memory, otherwise it will not run to completion. Hopefully the output will look something like this:
chr1 106623434 chr1 106623436 chr1 106623442 chr1 106623468
chr1 10699400 chr1 10699405 chr1 10699408 chr1 10699415 chr1 10699426 chr1 10699448
chr1 110611528 chr1 110611550 chr1 110611552 chr1 110611554 chr1 110611560
Similar question at:
How to move all strings in one file that match the lines of another to columns in an output file?
as long as your patterns don't overlap completely this should work
$ while read p; do grep "$p" file1 | tr '\n' '\t'; echo ""; done < file2
chr1 106623434 chr1 106623436 chr1 106623442 chr1 106623468
chr1 10699400 chr1 10699405 chr1 10699408 chr1 10699415 chr1 10699426 chr1 10699448
chr1 110611528 chr1 110611550 chr1 110611552 chr1 110611554 chr1 110611560
You could do this as it uses close to zero memory but it'll be very slow since it reads the whole of "file1" once for every line of "file2":
$ cat tst.awk
{
ofs = ors = ""
while ( (getline line < "file1") > 0) {
if (line ~ "^"$0) {
printf "%s%s", ofs, line
ofs = "\t"
ors = "\n"
}
}
printf ors
close("file1")
}
$ awk -f tst.awk file2
chr1 106623434 chr1 106623436 chr1 106623442 chr1 106623468
chr1 10699400 chr1 10699405 chr1 10699408 chr1 10699415 chr1 10699426 chr1 10699448
chr1 110611528 chr1 110611550 chr1 110611552 chr1 110611554 chr1 110611560
you can try
awk -vOFS="\t" '
NR==FNR{ #only file2
keys[++i]=$0; #'keys' store pattern to search ('i' contains number of keys)
next; #stop processing the current record and
#go on to the next record
}
{
for(j=1; j<=i; ++j)
#if line start with key then add
if($0 ~ "^"keys[j])
a[keys[j]] = a[keys[j]] (a[keys[j]]!=""?OFS:"") $0;
}
END{
for(j=1; j<=i; ++j) print a[keys[j]]; #print formating lines
}' file2 file1
you get,
chr1 106623434 chr1 106623436 chr1 106623442 chr1 106623468
chr1 10699400 chr1 10699405 chr1 10699408 chr1 10699415 chr1 10699426 chr1 10699448
chr1 110611528 chr1 110611550 chr1 110611552 chr1 110611554 chr1 110611560
I have a file (test.bed) that looks like this (which might not be tab-seperated):
chr1 10002 10116 id=1;frame=0;strand=+; 0 +
chr1 10116 10122 id=2;frame=0;strand=+; 0 +
chr1 10122 10128 id=3;frame=0;strand=+; 0 +
chr1 10128 10134 id=4;frame=0;strand=+; 0 +
chr1 10134 10140 id=5;frame=0;strand=+; 0 +
chr1 10140 10146 id=6;frame=0;strand=+; 0 +
chr1 10146 10182 id=7;frame=0;strand=+; 0 +
chr1 10182 10188 id=8;frame=0;strand=+; 0 +
chr1 10188 10194 id=9;frame=0;strand=+; 0 +
chr1 10194 10200 id=10;frame=0;strand=+; 0 +
I want to produce the following output (which should be tab-seperated):
chr1 10002 10116 id=1 0 +
chr1 10116 10122 id=2 0 +
chr1 10122 10128 id=3 0 +
chr1 10128 10134 id=4 0 +
chr1 10134 10140 id=5 0 +
chr1 10140 10146 id=6 0 +
chr1 10146 10182 id=7 0 +
chr1 10182 10188 id=8 0 +
chr1 10188 10194 id=9 0 +
chr1 10194 10200 id=10 0 +
I have tried with the following code:
awk 'OFS="\t" split ($0, a, ";"){print a[1],$5,$6}' test.bed
But then I get:
chr1 10002 10116 id=1 40 4+
chr1 10116 10122 id=2 40 4+
chr1 10122 10128 id=3 40 4+
chr1 10128 10134 id=4 40 4+
chr1 10134 10140 id=5 40 4+
chr1 10140 10146 id=6 40 4+
chr1 10146 10182 id=7 40 4+
chr1 10182 10188 id=8 40 4+
chr1 10188 10194 id=9 40 4+
chr1 10194 10200 id=10 40 4+
What am I doing wrong? Somehow the number '4' is added to the last two fields. I thought the number '4' somehow might have something to do with splitting in the 4th field, however, I tried producing a similar file where it was the 3rd field that was split, and still got the number '4' added to the last two fields. I am rather new to 'awk' so I guess it is an error in the syntax. Any help would be appreciated.
If you set your field separator as whitespace or semi-columns you won't have to handle the splitting yourself:
$ awk '{print $1,$2,$3,$4,$8,$9}' FS='[[:space:]]+|;' OFS='\t' file
chr1 10002 10116 id=1 0 +
chr1 10116 10122 id=2 0 +
chr1 10122 10128 id=3 0 +
chr1 10128 10134 id=4 0 +
chr1 10134 10140 id=5 0 +
chr1 10140 10146 id=6 0 +
chr1 10146 10182 id=7 0 +
chr1 10182 10188 id=8 0 +
chr1 10188 10194 id=9 0 +
chr1 10194 10200 id=10 0 +
As for what you are doing wrong in:
awk 'OFS="\t" split ($0, a, ";"){print a[1],$5,$6}'
The syntax of awk is condition{block} and setting the value of OFS and splitting is not a conditional. They are statements that should be inside the block.
However you really don't need to set the value of OFS on every line so it should be initialized only once. You can do this using the -v option, in the BEGIN block or after the script.
Valid alternatives:
$ awk -v OFS='\t' '{split($0,a,";");print a[1],$5,$6}' file
$ awk 'BEGIN{OFS="\t"}{split($0,a,";");print a[1],$5,$6}' file
$ awk '{split ($0,a,";");print a[1],$5,$6}' OFS='\t' file
Try this :
awk -F\; '{print $1,$4}' test.bed