Search Results

For exactly the one line FASTA example above, try
sed '/^>/ !{s/^/CTGA/; s/$/TAGTA/}' file

Wouldn't it make more sense to use the directories' suffixes for the target files' prefixes?
for FP in org*/dnaG.fasta; do TMP=${FP#org}; echo cp $FP fastconcatg/${TMP%%/*}_${FP##*/}; done
cp...

Your problem is the wrong destination in the cp command; it must be dir/file.
Together with a few improvements:
a=1
for i in */dnaG.fasta
do
cp "$i" fastcancatg/"$a"_"$i"
a=$(( a + 1 ))...

Okay, I'm sure we can help with that. A few questions for clarity though:-
Must the filename in the fastconcatg directory be the prefix of the directory that the source was found in?
What do we...

If you also want to print the >id then you can do it with perl:
perl -ne '/^>.*/ and $id=$&; /.{5}AAGC[^T].{16}AAGC[^T].{5}/ and printf "%s\n%s\n",$id,$&' gene.fasta

How about (given there are only A, C, G, T in the fasta sequences, so no test for other chars needed)
grep -oE ".{5}AAGC[^T].{16}AAGC[^T].{5}" file
ATAGAAAGCCATAGATAGTAGTAGATAAGCATATAG...

Also try:
awk -F= '/^>/{if(getline<f>0) $0=">" $2}1' f=list.txt gene1.fasta

or without the check:
awk -F= '/^>/{getline<f; $0=">" $2}1' f=list.txt gene1.fasta

For the easy case that your replacements are in lines in increasing order, try
awk 'FNR==NR {REP[NR] = $2; next} /^>/ {$0 = ">" REP[++CNT]}1' FS="=" list.txt gene1.fasta
>org5
ATGTAGC
>amylase...

$ awk ' FNR == NR { ky=$4; sub("_.*","",ky); arr[ky]=$0; next } {print arr[$1]} ' content.xls id.txt
NC_020815.1 1891831 1894692 virb4_A0A0H2X8Z4_ 1 954 1945
NC_020815.1 ...

For reading the keywords from file, try grep -f id.txt


For keeping the sequence as given in id.txt, you could write e.g. an awk or perl script. Or try this very inefficient shell (untested):...

Note that RudiC's and Scrutinizer's suggestions both depend on the fact that the orgX and orgXX strings in file2 are distinct. Had file2 also contained the line:
org2=japan
both of those...

This problem has been solved umpteen times in these fora. Did you bother to search, or look into the proposals given below under "More UNIX and Linux Forum Topics You Might Find Helpful"?

...

awk version you could try:
awk 'BEGIN{FS=RS; RS=">"; ORS=""} FNR>1{A[$1]=RS $0} END{for(i in A) print A[i]}' file1 file2

note: ensure that there are no excess trailing spaces as is the case with...

May I paraphrase your request: You want file2's sequences to prevail and file1's sequences inserted only if there's no equivalent in file2. If so, try
tr $'\n>' $' \n' <file1| grep -vf <(sed -n...

My previously posted attempt was for the provided sample files ONLY - 2 lines for each sequence: 1 header and 1 "data" lines.
Had the OP elaborated on the possible other sample data files, an...

I put my answer back as I met the scenarios:
1) when file2.fasta contains more entries than in file1.fasta and vice versa. and
2) when the sequence part can have more than one row;
awk...

not sure if I follow your samples and the desired output, but I think you might want this.

awk -f dinesh.awk file2 file1 where dinesh.awk is:

FNR==NR {
if (FNR%2)
head=$0
else
...

$ awk -F'\\]|\\[|-|:' -v RS='\n>' ' NR == FNR { gsub(" ",""); arr[$3]=1;next} arr[$2]{print ">" $0} ' f1 f2
>Contig_152:50833-51615
CGGAGTAGCTTCGATCAGCGTGACCGGTACCGAGCGACCGTCTTCAGTGAAGACGCGGCT...

No surprise "it is not working" as none of your attempts is addressing your problem if at all syntactically correct.



awk 'FNR == NR {SRCH[$3 "-" $2]; next} $2 in SRCH {print ">" $0}' FS="[]-...

I haven't seen where you mentioned anything at all about changing your sample input file format nor about changing the code RudiC suggested.

Please show us your new sample input file and the...

That is not surprising. In post #1 in this thread you said you had CSV input files and used an example that used <tab> characters as the character that separates values. The code RudiC provided...

I don't think you get very far with sort. Try instead
awk -F"\t" '
NR==FNR {for (i=1; i<=3; i++) {IX = (i-1)*3+1
split ($IX, T, "_")
...

Hello dineshkumarsrk,

Ok sure try following.

awk 'FNR==1{print;next} {for(i=1;i<=NF;i++){if($i+0>=100){$i="True"}}} 1' Input_file | column -t


Thanks,
R. Singh

sed "s/[1-9][0-9]\{2,\}/TRUE/g" file

Hello dineshkumarsrk,

Could you please try following.

awk 'FNR==1{print;next} {for(i=1;i<=NF;i++){if($i+0>100){$i="True"}}} 1' Input_file | column -t


Thanks,
R. Singh