cgeb2001's DokuWiki!

You've loaded an old revision of the document! If you save it, you will create a new version with this data.

upcoming

Here's a list of commands to retrieve deleted text in vi:

<code>
u	Undoes the last change
U	Undoes changes to current line
p	"Puts" last delete after cursor
P	"Puts" last delete before cursor
1p	"Puts" next-to-last delete after cursor
2p	"Puts" second-to-last delete after cursor
</code>

Multiple FASTA seqeunces into one line https://www.biostars.org/p/9262/
<code>
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < file.fa

</code>

Yield the mega FASTA file with each the sequence ID as the file name (linearised FASTA) https://www.biostars.org/p/455915/

<code>
#split.sh

numseqs=$(grep -c ">" "$1");
numlines=$(wc -l < "$1");
if (( "$numlines" > $(( 2*$numseqs )) )); then
    echo "The fasta file needs to be linearised before this function will work.";
    return 1;
fi;

while read line; do
    if [ "${line:0:1}" == ">" ]; then
        header="$line";
        filename=$(echo "${line#>}" | sed 's/\ .*//g');
        touch "$filename".fasta
        echo "$header" >> "${filename}".fasta;
    else
        seq="$line";
        echo "$seq" >> "${filename}".fasta;
    fi;
done < $1

#usage: ./split.sh test.fasta
</code>

Speed up the script running after chopping the input files (applicable for any scripts)
<code>
#interproscan.sh

while read line
do

/scratch2/software/interproscan-5.52-86.0/interproscan.sh -i data/$line.fasta -f tsv -dp -goterms -pa -o results/$line.tsv

done <$1

# usage: ./interproscan.sh gene_id.txt
# note:must leave extra line break for gene_id.txt
</code>

<code>
#Remove duplicates in fasta file based on ID

https://www.biostars.org/p/321641/

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' 1.fa|sort -t $'\t' -k1,1 -u |tr "\t" "\n"

https://www.biostars.org/p/143617/

awk '/^>/{f=!d[$1];d[$1]=1}f' 
</code>

Please fill all the letters into the box to prove you're human. G U R J I Please keep this field empty:

Edit summary

Note: By editing this page you agree to license your content under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International