I have a file with 1000 rows in it
For example:
chr1 Cufflinks transcript 34611 36081 1000 - . gene_id "FAM138A"; transcript_id "uc001aak.3"; FPKM "1.2028600217"; frac "1.000000"; conf_lo "0.735264"; conf_hi "1.670456"; cov "0.978610";
I want to search file and extract the values after string FPKM, like
"1.2028600217"
Can I do it using awk?
if you don't care which column does the FPKM show in, you could:
grep -Po '(?<=FPKM )"[^"]*"' file
You can use awk, but this is a simple substitution on a single line so sed is better suited:
$ cat file
chr1 Cufflinks transcript 34611 36081 1000 - . gene_id "FAM138A"; transcript_id "uc001aak.3"; FPKM "1.2028600217"; frac "1.000000"; conf_lo "0.735264"; conf_hi "1.670456"; cov "0.978610";
$ sed 's/.*FPKM *"\([^"]*\)".*/\1/' file
1.2028600217
Related
I have this tab separated file:
gene 1 A 6 gene_name TP53 B
exon 6 B 2 2 A gene_name MYC2 10.0 B
transcript 3 B B 4 gene_name ORF1
How can I print the first column plus the next column after gene_name column? As you can see, gene_name do not exist always in the same column.
I am not sure about how to get the last part of this:
awk 'BEGIN{OFS="\t"} {print $1, ??}' myFile.tsv
So, my expected output is:
gene TP53
exon MYC2
transcript ORF1
Thanks!
With your shown samples, please try following.
1st solution: In case you have multiple gene_name values in single line then following may help.
awk 'BEGIN{FS=OFS="\t"} {for(i=1;i<=NF;i++){if($i=="gene_name"){print $1,$(i+1);i++}}}' Input_file
2nd solution: In case you have only 1 gene_name then use following.
awk 'BEGIN{FS=OFS="\t"} {for(i=1;i<=NF;i++){if($i=="gene_name"){print $1,$(i+1);next}}}' Input_file
3rd solution: With your very specific case where gene_name always coming on 3rd field we could try this one, for Generic ones try 1st or 2nd solutions.
awk 'BEGIN{FS=OFS="\t"} $3=="gene_name"{print $1,$4}' Input_file
OR if you want to check 2nd last field and print last field value then use:
awk 'BEGIN{FS=OFS="\t"} $(NF-1)=="gene_name"{print $(NF-1),$NF}' Input_file
4th solution: With sed please try following.
sed -E 's/(\S+).*gene_name\s+(\S+).*/\1\t\2/' Input_file
You may use this gnu awk solution:
awk '{print gensub(/^(\S+).*\tgene_name\t(\S+).*/, "\\1\t\\2", "1")}' file
gene TP53
exon MYC2
transcript ORF1
Using GNU grep:
grep -oP '(^\S+)|(\bgene_name\s+\K\S+)' myFile.tsv | paste - -
$ awk -v OFS='\t' '{v=$1; sub(/.* gene_name /,""); print v, $1}' file
gene TP53
exon MYC2
transcript ORF1
And also with awk:
awk -v FS=' .*gene_name | ' '{print $1,$2}' file
gene TP53
exon MYC2
transcript ORF1
I would like to modify a file where both tabs and spaces are used as field separators.
At the beginning we have a file with this type of structure:
chr1 Cufflinks gene_id "XLOC_000001"; oId "XR_003076322.1";
chr1 Cufflinks gene_id "XLOC_000012"; oId "XR_001548508";
Doing awk -F' ' '$4=$6 {print $0}' performs what I am looking for (changing the value of the "gene_id" by the value in "oId"):
chr1 Cufflinks gene_id "XR_003076322.1"; oId "XR_003076322.1";
chr1 Cufflinks gene_id "XR_001548508"; oId "XR_001548508";
The problem is that it changes the line structure: the tabs \t between chr1, Cufflinks and gene_id disappeared. I tried adding -v OFS=\t but it puts tabs in the gene_id "XLOC_000012"; oId "XR_001548508"; part (which should stay separated by spaces). I also tried with sed something like sed -i 's/ /\t/' but it also put tabs everywhere.
How could I change the field separator of column 1 to 3 (and do not change columns 3 to 6) ?
A possibility with awk:
awk -F '[ ]' '{$2 = $4; print}' file
By using the space character for the input field separator (as opposed to spaces and tabs), a field can be assigned to without changing the tab characters to spaces.
For more complex cases, there is split (but no "join"):
awk 'BEGIN {FS=OFS="\t"} {n = split($3, a, " "); a[2] = a[4]; for (i=1; i<=n; ++i)
$3 = (i == 1 ? "" : $3 " ") a[i]
} 1' file
You may use this sed that preserves your whitespaces:
sed -E $'s/^([ \t]*([^ \t]+[ \t]+){3})[^ \t]+([ \t]+)(([^ \t]+[ \t]+){1})([^ \t]+)/\\1\\6\\3\\4\\6/' ff
chr1 Cufflinks gene_id "XR_003076322.1"; oId "XR_003076322.1";
chr1 Cufflinks gene_id "XR_001548508"; oId "XR_001548508";
Explanation for copying 6th field to 4th field:
^: # match start
([ \t]*([^ \t]+[ \t]+){3}): # match first 4-1 fields and capture in group #1
[^ \t]+: # match 4th field
([ \t]+): # match whitespace after 4th field and capture in group #3
(([^ \t]+[ \t]+){1}): # match next (6-4-1) fields and capture in group #4
([^ \t]+): # match 6th field and capture in group #6
\\1\\6\\3\\4\\6: Place back-reference back in substitution
Alternatively this awk also creates a tabular aligned output:
awk '$4=$6' file | column -t
chr1 Cufflinks gene_id "XR_003076322.1"; oId "XR_003076322.1";
chr1 Cufflinks gene_id "XR_001548508"; oId "XR_001548508";
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 two files. I would like to replace a certain string in file 1, with the contents of file 2 based on a common string.
file 1
Chr5 psl2gff exon 15907715 15907933 . + . NM_001046410
Chr2 psl2gff exon 8898358 8898394 . + . NM_001192190
file 2
NM_001046410 gene_id TUBA1D; transcript_id tubulin, alpha 3d
NM_001192190 gene_id BOD1L1; transcript_id biorientation of chromosomes in cell division 1 like 1
output
Chr5 psl2gff exon 15907715 15907933 . + . gene_id TUBA1D; transcript_id tubulin, alpha 3d
Chr2 psl2gff exon 8898358 8898394 . + . gene_id BOD1L1; transcript_id biorientation of chromosomes in cell division 1 like 1
in file 1 there are multiple instances of the same string, however, file 2 only has it once. I would like all instances of the NM_**** etc. to be replaced by the contents of file 2 when the first column matches. following this, I would like to completely remove the NM_**** from the file.
I am very new to bash etc. I have looked all over the place for a way to do this, but none so far have worked. Also, there are over 5000 lines in file 2, many more in file 1.
Any help would be much appreciated!
Thanks.
this is a join operation. If the files are sorted on the join key, and if the white space is not significant the easiest will be
$ join -19 -21 file1 file2 | cut -d' ' -f2-
Chr5 psl2gff exon 15907715 15907933 . + . gene_id TUBA1D; transcript_id tubulin, alpha 3d
Chr2 psl2gff exon 8898358 8898394 . + . gene_id BOD1L1; transcript_id biorientation of chromosomes in cell division 1 like 1
if the files are not sorted and white space is important awk will be a better solution
$ awk 'NR==FNR {k=$1; $1=""; a[k]=$0; next}
$NF in a {sub(FS $NF"$",a[$NF])}1' file2 file1
Chr5 psl2gff exon 15907715 15907933 . + . gene_id TUBA1D; transcript_id tubulin, alpha 3d
Chr2 psl2gff exon 8898358 8898394 . + . gene_id BOD1L1; transcript_id biorientation of chromosomes in cell division 1 like 1
exercise for you is to understand the code. There are many examples (>100) on this site exactly for this question and with many commented scripts, some of which are written by me.
I have a large file with lines like so
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
I want to extract ENSG00000223972.5, DDX11L1, chr1, 11869 and 14409.
I have succeeded in the first two by:
awk 'BEGIN {FS="\""}; {print $2"\t"$6}' file.txt
I'm struggling to now extract the chr1, 11869 and 14409 as this will need a different feild seperator? How is this done on the same ;line??
Try to use following command to extract what you want,
awk 'BEGIN {FS="\"";OFS="\t"}; {split($1,a,/[\ ]*/); print a[1],a[4],a[5],$2,$6}' file.txt
Brief explanation,
split($1,a,/[\ ]*/: split $1 into the array a, and the separators would be regex /[\ ]*/
Print the split content stored in a as you desired.
$ awk -F'[ "]+' -v OFS='\t' '{print $1, $4, $5, $10, $16}' file
chr1 11869 14409 ENSG00000223972.5 DDX11L1