l-modolo

#!/bin/sh
# compute reads length distribution from a fastq file
awk 'NR%4 == 2 {lengths[length($0)]++} END {for (l in lengths) {print l, lengths[l]}}'  file.fastq

l-modolo

#PBS -q q1day
#PBS -j oe
#PBS -o $HOME/working_directory/task.log
#PBS -N task
#PBS -m n
#PBS -l mem=memory_sizegb,nodes=1:ppn=core_number
#PBS -S /bin/bash
# if more than 65gb:
# -l nodes=1:ppn=1:bigmem

l-modolo

#!/bin/sh
cat file.hit.clstr | awk '{if ($1 == ">Cluster") {clusterNumber = $2} else {print(clusterNumber"\t"$0)}}'

l-modolo

#!/bin/sh
# split fastq file in two file for cases where paired-end are concatened (not interlaced)
(gzip -dc  intput.fastq.gz) | awk -F"=" 'BEGIN {OFS = "\n"} {name = $0; getline seq; getline name2; getline phred; print name, substr(seq,0,int(length(seq)/2)), name2, substr(phred,0,int(length(seq)/2)) >> "intput-1.fastq"; print name, substr(seq,int(length(seq)/2)+1,length(seq)), name2, substr(phred,int(length(seq)/2)+1,length(seq)) >> "intput-2.fastq"}'

l-modolo

awk 'BEGIN {OFS = "\n"} {header = $0 ; getline seq ; getline qheader ; getline qseq ; if (length(seq) >= 20){print header, seq, qheader, qseq}}' < input.fastq > output.fastq

l-modolo

#!/bin/sh
# count number of base in a fastq.gz
(gzip -dc $0) | awk 'NR%4 == 2 {basenumber += length($0)} END {print basenumber}'

l-modolo

#!/bin/sh
# return a list of sequence_id sequence_length from a fasta file

awk 'BEGIN {OFS = "\n"}; /^>/ {print(substr(sequence_id, 2)" "sequence_length); sequence_length = 0; sequence_id = $0}; /^[^>]/ {sequence_length += length($0)}; END {print(substr(sequence_id, 2)" "sequence_length)}' file.fasta

l-modolo

#!/bin/sh
# convert fasta sequence to uppercase, usefull for nhmmer
awk '/^>/ {print($0)}; /^[^>]/ {print(toupper($0))}' file.fasta > file_upper.fasta

l-modolo

#!/bin/sh
# remove all non ASCII character from file/folder names in a file tree
convmv -f utf8 -t ASCII -r . 2>&1 | grep ascii |  perl -pe "s/ascii doesn't cover all needed characters for: //g" | awk '{system("mv "$0" \"$(echo "$0" | uconv -t ASCII -x nfd -c )\"")}'

l-modolo

#!/bin/sh
# alternative to renaming old file with a .back
# usage : back.sh file_name
mv "$1" "$1"$(date +".%m-%d-%y_%T")