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--- unix_shell [2021/10/06 09:31] – created 38.20.199.40
+++ unix_shell [2022/06/23 10:21] (current) – 134.190.232.106
@@ Line 1: / Line 1: @@
-upcoming
+The commonly used scripts collected from previous Github page and course materials.
+.How to set up timer for specific script run?
+<code>
+#!/bin/bash
+# Twosday.sh
+while true;
+do
+    DATE=`date | cut -d' ' -f4`
+    #echo $DATE
+    if [[ $DATE == "22:22:22" ]]
+    then
+            echo "this is a test program" >> xyz.log
+            qrsh
+            sleep 1s
+    fi
+done
+</code>
+<code>
+#stopwatch
+#https://superuser.com/questions/611538/is-there-a-way-to-display-a-countdown-or-stopwatch-timer-in-a-terminal
+while true; do echo -ne "`date`\r"; done
+#nanoseconds:
+while true; do echo -ne "`date +%H:%M:%S:%N`\r"; done
+</code>
+.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
+p	"Puts" next-to-last delete after cursor
+p	"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[$1]=1}f'
+</code>
+<code>
+https://github.com/brentp/pyfasta
+# To install python2 version
+pip install pyfasta
+# To install python3 version
+pip3 install pyfasta
+#split a fasta file into 6 new files of relatively even size:
+pyfasta split -n 6 original.fasta
+</code>
+Rename file name with the one user wanted https://linuxgazette.net/18/bash.html
+https://unix.stackexchange.com/questions/580506/renaming-multiple-files-using-a-loop
+<code>
+for i in *; do -- mv "$i" "${i/%.fasta/.fa}"; done
+for f in *; do mv "$f" "${f#*_}";done
+for i in chr*
+do
+  mv -- "$i" "${i/%.fasta/.fa}"
+done
+or
+for i in chr*
+do
+  NEWNAME="${i/%.fasta/.fa}"
+  mv -- "$i" "$NEWNAME"
+done
+The "%{var/%pat/replacement}" looks for pat only at the end of the variable and replaces it with replacement.
+</code>
+<code>
+Usage:
+    rename [ -h|-m|-V ] [ -v ] [ -n ] [ -f ] [ -e|-E perlexpr]*|perlexpr
+    [ files ]
+</code>
+How to use sort in linux, especially ignore the header to sort special col?
+<code>
+(head -n 1 all.txt && tail -n +2 all.txt| sort -n -r -k2) > 123.txt
+# sort -n
+#sort -r
+#sort -k
+https://shapeshed.com/unix-sort/; https://stackoverflow.com/questions/14562423/is-there-a-way-to-ignore-header-lines-in-a-unix-sort
+</code>
+<Last updated by Xi Zhang on Oct 6th,2021> <June 23th,2022>