bioinformatics_utils

Here are some useful small basic scripts for bioinformatics, mainly for work with DNA/RNA or protein sequences.

get_sequence_length.py

Given a fasta/q file, returns a table with the readnames (1st column) and their corresponding length (2nd column).

Prerequisite :

Biopython needs to be installed

Options :

-l <min_read_length> will set a minimum threshold on the length

Example command line

~/scripts/get_sequence_length.py -l 0 \
  -f ~/raw_data/references/S_aureus/S_aureus_G07I_assembly.fna \
  -t fasta

create_fasta_from_seqname_speed_up.py

Given a fasta/q file and a file containing a selection of sequence names to select, the scritp will search for these sequences in the fasta/q file and put them in a new file.

If no output filename is given (optional), the new file will be in the same directory as the original fasta/q file, with the additional suffix '_selection'.

Options

-n <names_file> : path to the text file containing the names of the sequences to select, one name per line. -f <input_fastx> : path to the fasta/q file containing the sequences to fetch (among other). -t <file_type> : specify the type of fastx input file (fasta or fastq) -o <output_file> : path to the output file name (optional).

Prerequisites

This scripts uses a big amount of ram if the input fasta/q is big. Biopython needs to be installed

Example command line

/home/aline/scripts/create_fasta_from_seqname_speed_up.py \
  -n /mnt/metagenomic/hmmsearch/2010_ppk_in_ref_and_bins/list_of_sequences_to_keep.csv \
  -f /mnt/metagenomic/hmmsearch/2010_ppk_in_ref_and_bins/output_protein_seq_TIGR03705.faa \
  -t fasta