DNA TOOLS

A set of tools for to play with/analyze genomics data

• random_dna.py : creates a random sequence of DNA of length K

  usage : python random_dna.py K

• fasta_length.py : computes the length of DNA sequences in a Fasta file

  usage : python fasta_length.py file.fa

• reverse_complement.py : computes the revese complement of a DNA sequence

  usage : python reverse_complement.py CGGGTA

• faStats : compute sequence length of all sequences in a fasta file

  usage : python faStats file.fa

• melting_temp.py : compute melting temperature of a sequence

  usage : melting_temp.py DnaSequence

• entrez_specie.py : returns the specie/organism name given an ENTREZ id.

  usage : python entrez_specie.py 1567

• fastq_split.py : splits a merged paired-end Illumina {basename}.fastq (or compressed fastq.gz) file in {basename}.R1.fastq and {basename}.R2.fastq

  usage : python fastq_split.py paired_end_file.fastq

• centrifuge2krona : converts a centrifuge output file to a krona visualisation using centrifuge-kreport and ktImportTaxonomy.

  usage : centrifuge2krona centrifuge_file.out

• sam_filter : filters a sam file on identity percentage and alignment length.

  usage: sam_filter file.sam

• bam_filter : filters a bam file on identity percentage

  usage: bam_filter file.bam

• filterFastaByLength : filters a fasta file on sequence length (min and max)

  usage: filterFastaByLength -min 1 -max 66 file.fa

• krakenTometaphlan : converts a [Kraken] style report to a [Metaphlan] style report

  usage: krakenTometaphlan -o metaphlan_report.txt kraken_report.txt

• consensusMaker : creates a consensus fasta from a samtools mpileup file

  usage : consensusMaker -o myconsensus.fa infile.mpileup

• bed2coverage : computes the 10th percentile coverage for each feature in a BED file

  usage : bed2coverage infile.bed

• filterFastaByName: filters a fasta file given a list of sequence names

  usage : filterFastaByName infile.fasta seqnames_to_keep.txt -o outfile.fa

• eslfasta2fastq: Extracts the headers of fasta file formatted by Easel (hmmer toolkit) and get the matching fastq records

• usage : eslfasta2fastq fasta_input forward.fq -fq2 reverse.fq

• parallel_download: Download files from a list of files (on file per line) in a parallel fashion using multiprocessing, and subprocess calling wget

  usage: parallel_download list_of_files.txt

• fasta_split: Splits fasta sequences in shorter sequences, using a negative binomial distribution usage: python fasta_split.py -m 800 input_sequences.fa

• compare_fasta_seqs: Compare two or more sequences in a fasta file usage: compare_fasta_seqs multifasta.fa

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To add the tools to your command prompt

• Option 1 : use aliases in your ~/.bash_profile or ~/.bashrc file to add each tool one by one (replace /path/to/DNA_tools/ with the location of the tool)

example :

echo "alias revcom=python /path/to/DNA_tools/reverse_complement.py" >> ~/.bashrc
source ~/.bashrc

• Option 2 : Add all the DNA tools at once to your $PATH environment variable (replace /path/to/ with the location of the DNA_tools directory)

example :

echo "export PATH=$PATH:/path/to/DNA_tools/" >> ~/.bashrc
source ~/.bashrc