grep has various options.
I frequently use -v option to filter lines without the keyword.
grep -v human data.txt
where data.txt is a bunch of data to be greped.
We can filter out lines with keyword human.
Other example is to filter the lines which have a value …
It turned out that the command I regularly use to search a bunch of data is not known to others.
I frequently use fgrep to grep against a list of keywords (i.e. IDs).
fgrep -f keywords.txt data.txt
where keywords.txt contains a list of keywords ('one keyword …
When we submit relatively large entries to DDBJ, we use Mass Submission System (MSS). We will use MSS for submitting transcriptome sequence assembly (TSA) to DDBJ.
After extracting the list of IDs from header lines of FASTA by command like
% perl -nle 'print $1 if(/^\>(\S+)/) hoge.fasta > id.txt' …
Identifiers (IDs) in public databases often contain version information.
For example, .16 in ENSG00000100644.16 from Ensembl and .1 in NM_001243084.1 from RefSeq.
Such version information can be an obstacle to join entries from different databases.
So, version information should be trimmed before joining.
The file that contains such …
To get reverse complement for specific DNA string is frequently needed in molecular biology. There were some web interface to do that, but it is not secure. Calculating reverse complement locally is ideal solution for that issue.
In the search of an example code with practical usefulness in GitHub, I …
As there was a mechanical trouble in my main machine, MacBookPro, I am moving to new MacBookPro with cleanly installed High Sierra (10.13.6). Below is a log for my future replication...
First of all, default shell was changed with chsh command to /bin/zsh.
After installing Homebrew, coreutils …
When we want to join two files by a same key into one file, we can use join command. We can join lines by a first column value of tab-delimited files.
join -j 1 file1 file2
Indeed, join command itself is very useful, default output is not tab-delimited text, but …
Joining two files by key in the first column of files can be easily done by using UNIX command below.
join -j 1 file1.txt file2.txt
This is very useful command, but the output is space-delimited by default. In order to get the output by tab-delimited, following option for …
In order to extract a set of sequence from FASTA-formatted file (both in nucleotides and peptides), several commands can be used to do so.
In recent years, I regularly use blastdbcmd in NCBI BLAST suite. To run this command, the file must be indexed by makeblastdb with the option below …
When I want to count the number of redundant words in a file (hoge.txt), I have used simple Perl code like this(count.pl).
1 2 3 4 5 6 7 8 | #!/usr/bin/perl
while(<>) {
my($word) = split;
$num{$word}++;
}
foreach (sort keys %num) {
print "$_\t$num … |