rivm-bioinformatics/ampligone

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

ampligone's Issues

Exit cleanly when no primer-sequence coordinates are found

Currently AmpliGone exits with a load of error messages when a set of primers are given from which the coordinates could not be found on the given reference.

This should exit cleanly

Mixed-case primer input is not supported

Currently AmpliGone is unable to process an input-primer fasta file with sequences both in lowercase as wel as uppercase. Currently only uppercase is supported as this is only supported by the ambiguity-mapping.

AmpliGone should be able to handle both uppercase as well as lowercase input primers.

Give an option to exit cleanly when empty input is given

Currently, AmpliGone is unable to exit cleanly when an empty input file is given.

There should be two changes:
a) AmpliGone should exit cleanly if an empty input fastq is given.
b) There needs to be an extra flag to create empty outputs (for workflows/pipelines) if an empty input is given

Support for multiple sequences in the input reference FASTA file

Dear,

I have encountered an issue when I use AmpliGone for Influenza A datasets.
The input FASTA file contains 8 separate segments which results in the following error when I run AmpliGone (v1.2.1):
File "/usr/local/bin/lmod/AmpliGone/1.2.1/venv/lib/python3.9/site-packages/AmpliGone/AmpliGone.py", line 260, in main primer_df = TP_PrimerLists.result() File "/usr/lib/python3.9/concurrent/futures/_base.py", line 446, in result return self.__get_result() File "/usr/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result raise self._exception File "/usr/lib/python3.9/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, **self.kwargs) File "/usr/local/bin/lmod/AmpliGone/1.2.1/venv/lib/python3.9/site-packages/AmpliGone/fasta2bed.py", line 69, in MakeCoordinateLists return pd.DataFrame( File "/usr/local/bin/lmod/AmpliGone/1.2.1/venv/lib/python3.9/site-packages/pandas/core/frame.py", line 774, in __init__ data = list(data) File "/usr/local/bin/lmod/AmpliGone/1.2.1/venv/lib/python3.9/site-packages/AmpliGone/fasta2bed.py", line 94, in CoordListGen ref_file = SeqIO.read(referencefile, "fasta") File "/usr/local/bin/lmod/AmpliGone/1.2.1/venv/lib/python3.9/site-packages/Bio/SeqIO/__init__.py", line 659, in read raise ValueError("More than one record found in handle") ValueError: More than one record found in handle

The command that I used:
ampligone --reference influenza_a-H3N2.fasta --primers primers.influenza_A.fasta --input sequences.fastq --output sequences_clipped.fastq --threads 4 --amplicon-type fragmented --error-rate 0.1

Would be it possible to resolve this issue?
I have obtained great results for SARS-CoV-2 with this tool.

Best regards,
Bert

Exit gracefully when encountering empty input files

Currently AmpliGone is unable to deal with empty input files and will therefore crash.

We currently expect the input file to actually contain data. However, this cannot be completely guaranteed in automated processes such as pipelines.

AmpliGone should therefore exit gracefully when encountering an empty input file and write an empty output file if necessary.