pegi3s/utilities repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠List of utilities

This Docker image contains different utilities and scripts that may be useful in different scenarios. You can list the utilities by running: docker run --rm pegi3s/utilities help.

These utilities are alphabetically listed bellow along with comprehensive explanations. To show the help of a specific utility, run docker run --rm pegi3s/utilities <utility_name> --help.

The list of utilities is presented below, please refer to this manual⁠ for detailed instructions and examples.

• backup_file: creates a backup file of the file passed as parameter. By default, it adds the extension ".bak" (or ".bak1", ".bak2", and so on, if a file with any of the previous extensions exist).
• batch_fasta_remove_line_breaks: removes the line breaks of sequences in one or more FASTA files.
• batch_fasta_remove_stop_codons: modifies the sequences in one or more FASTA files to remove the stop codons (TAA, TAG and TGA) at the end of sequences. Note that if the input files have line breaks separating the sequences, they should be removed using the fasta_remove_line_breaks script. Otherwise, stop codons will be removed from each sequence line.
• check_multiple_3: verifies if all sequences in a FASTA file are multiple of 3. If so, the exit code is 0. Otherwise, the exit code is 1. Note that the exit code can be captured with $?. Note that if the input file have line breaks separating the sequences, they should be removed using the fasta_remove_line_breaks script. Otherwise, the script may produce unpredictable result.
• create_batches: creates batches for all lines of a given text file. One file per batch is created in the output directory, each one containing a batch of lines of the specified size from the input file.
• create_batches_for_directory: script creates batches for all files and directories under the specified directory. One file per batch is created in the output directory, each one containing a batch of files or directories of the specified size from the input file.
• deinterleave_fastq: deinterleaves a FASTQ file of paired reads into two FASTQ files. Optionally, the output files can be compressed using GZip.
• dockerhub_count_pulls: lists the number of pulls of each image for a given Docker Hub user.
• dockerhub_list_images_with_tags: lists all the images and tags for a given Docker Hub user.
• dockerhub_list_repo_with_tags: lists the tags for a given Docker Hub repository (user/image).
• fasta_extract_accession_numbers: extracts the accession numbers present in the headers of a given FASTA file. The output is a tab-delimited file with the FASTA headers (first column) and the accession found (second column). In case multiple accessions are present, only the first one is reported.
• fasta_pipe_delimited_extractor: extract sequences from FASTA files, according to the information in a given field, separated by pipes.
• fasta_put_headers_back: replaces the sequence headers using the provided mapping file (with input headers in the first column and new headers in the second).
• fasta_remove_line_breaks: removes the line breaks of sequences in a FASTA file.
• fasta_remove_sequences_with_in_frame_stops_or_n: removes the sequences containing N's or in-frame STOP codons (TAA, TAG and TGA) and writes the output into a new file.
• fasta_remove_stop_codons: modifies the sequences in a FASTA file to remove the stop codons (TAA, TAG and TGA) at the end of sequences. Note that if the input file have line breaks separating the sequences, they should be removed using the fasta_remove_line_breaks script. Otherwise, stop codons will be removed from each sequence line.
• fasta_rename_headers_with_taxonomy_info: renames the headers of a FASTA file with the taxonomic information associated to the accession numbers found in them.
• fasta_replace_and_save_headers: replaces the sequence headers by correlative numbers starting at 1 with a specified prefix. Also, a headers map is created so that original sequence headers can be restored using the fasta_put_headers_back script.
• fasta_reverse_complement: reverses the sequences in a FASTA file and converts them into their complement counterparts. Also, a prefix can be added to the header of each sequence. Note that if the input file have line breaks separating the sequences, they should be removed using the fasta_remove_line_breaks script. The scripts fasta_complement and fasta_reverse perform these two tasks separately.
• fasta_sort_by_header: sorts the sequences in a FASTA file according to their full sequence headers. Note that if the input file have line breaks separating the sequences, they should be removed using the fasta_remove_line_breaks script.
• fastq_to_fasta: converts a FASTQ file into a FASTA file.
• get_phylo_taxa: extracts a group of sequences from a file by providing the name of the sequences that flank the group of interest in a phylogenetic tree.
• get_taxonomy: receives a list of accession numbers (either through an input file or the standard input), identifies the species associated to each one of them and gets the requested taxonomic information.
• hdock_to_PDBePISA_conversion: converts a PDB file generated by hdock to a PDB formatted file suitable for PDBePISA (see the pegi3s/hdock_builder and the pegi3s/pisa_server Docker images).
• pdb2fasta: extracts sequences in FASTA format from PDB files. Input may be a single file or a directory with PDB files.
• pisa_xml_extract: extracts information regarding the number of interface residues and the interface area from XML files generated using PDBePISA⁠.
• tm_align_hit_extract: extracts the hit region of sequence 2 from a TM-align output file generated with the pegi3s/tmtools Docker image (1.0.1 or above; it may work with other outputs as well). Input may be a single file or a directory with files.
• rmlastline: removes the last line of one or more files. Note that this command modifies the files passed as parameters.

⁠Changelog

The latest tag contains always the most recent version.

⁠[0.23.0] - 04/03/2026

• Add the tm_align_hit_extract and pdb2fasta utilities.

⁠[0.22.2-docker29.0.1] - 13/01/2026

• Updates base image to pegi3s/docker:29.0.1 to make it compatible with current Docker clients.

⁠[0.22.0] - 14/09/2022

• Add the create_batches and create_batches_for_directory utilities.

⁠[0.21.2] - 09/09/2022

• Fixes the fasta_put_headers_back utility to deal with new special characters () and ().

⁠[0.21.1] - 18/03/2022

• Fixes the hdock_to_PDBePISA_conversion utility.

⁠[0.21.0] - 17/02/2022

• Add the hdock_to_PDBePISA_conversion utility.

⁠[0.20.0] - 29/12/2021

• Add the fasta_sort_by_header utility.

⁠[0.19.1] - 22/12/2021

• Show utilities version to the help script.

⁠[0.19.0] - 18/11/2021

• Rename pipe_delimited_extractor to fasta_pipe_delimited_extractor and adds parameter checking.

⁠[0.18.1] - 04/11/2021

• Unify input parameter checking across all scripts.

⁠[0.18.0] - 04/11/2021

• Add the get_phylo_taxa utility.

⁠[0.17.2] - 13/09/2021

• Modify the fasta_extract_accession_numbers utility to print unique sequence headers.

⁠[0.17.1] - 13/09/2021

• Allow saving the temporary working directory with intermediate files in the fasta_rename_headers_with_taxonomy_info utility.

⁠[0.17.0] - 06/09/2021

• Add the rs (--replace-spaces flag) to the fasta_rename_headers_with_taxonomy_info utility.

⁠[0.16.0] - 22/07/2021

• Add the fasta_extract_accession_numbers, get_taxonomy, and fasta_rename_headers_with_taxonomy_info utilities.
• Fix the fasta_put_headers_back utility to deal with special characters.

⁠[0.15.0] - 21/07/2021

• Fix the fasta_remove_line_breaks utility to work properly with large FASTA files.
• Change the batch_fasta_remove_line_breaks utility to invoke the fasta_remove_line_breaks utility for each input file.

⁠[0.14.0] - 07/01/2021

• Add the pipe_delimited_extractor utility.

⁠[0.13.0] - 25/11/2020

• Add the dockerhub_list_repo_with_tags, fasta_replace_and_save_headers, fasta_put_headers_back, fasta_complement, fasta_reverse, fasta_reverse_complement utilities.
• Modify the fasta_remove_line_breaks to add a newline at the end of the output files.

⁠[0.12.0] - 24/11/2020

• Add the pisa_xml_extract utility.

⁠[0.11.0] - 31/10/2020

• Allow changing the tags of the Docker images used in the fasta_remove_sequences_with_in_frame_stops_or_n utility.

⁠[0.10.0] - 30/10/2020

• Add the dockerhub_list_images_with_tags utility.
• Rename count_dockerhub_pulls to dockerhub_count_pulls.

⁠[0.9.0] - 15/09/2020

• Add the check_multiple_3 utility.

⁠[0.8.0] - 27/01/2020

• Add the backup_file utility.

⁠[0.7.0] - 24/01/2020

• Add the fasta_remove_sequences_with_in_frame_stops_or_n utility.

⁠[0.6.0] - 23/01/2020

• Add the fasta_remove_stop_codons and batch_fasta_remove_stop_codons utilities.

⁠[0.5.0] - 23/01/2020

• Add the batch_fasta_remove_line_breaks utility.

⁠[0.4.0] - 08/01/2020

• Add the fasta_remove_line_breaks utility.

⁠[0.3.0] - 06/11/2019

• Add the count_dockerhub_pulls utility.

⁠[0.2.0] - 11/05/2018

• Add the fastq_to_fasta utility.
• Add --help parameter to all utilities in order to show the usage instructions.

⁠[0.1.0] - 09/05/2018

• Initial utilities image containing the rmlastline and deinterleave_fastq utilities.