ValueError: Your XML file did not start with <?xml... but instead '\n'

[BioJNO]

Hi Leighton,

I've encountered the above error when running find_differential_primers.py

It seems that one of my input sequences did not return any primers from eprimer3 giving an empty table as output:

EPRIMER3 RESULTS FOR Ppcol17

                  Start  Len   Tm     GC%   Sequence

This is not an issue until the script tries to parse the blast_XML output from this sequence which is empty save for newline characters. Removing the offending sequence from my analysis allows the full script to run without error. Would it be possible to run this so that failure to generate primers for one sequence in the config file returned a warning instead of an exit?

Command line:

`PRODIGAL=$(which prodigal)
EPRIMER3=$(which eprimer3)
BLAST=$(which blastn)

export BLASTDB=/mnt/scratch/local/blast/ncbi/

find_differential_primers.py -i diff_primer_config.txt -o diagnostic_primers -v --prodigal ${PRODIGAL} --eprimer3 ${EPRIMER3} --blast_exe ${BLAST} --blastdb nt --keep_logs --cpus 8 --noprodigal --nocds`

Log file:
differential_primers.sh.out.txt

[widdowquinn]

At the moment, the quickest way to get past this is to remove that sequence from the config file (as you've done).

I'm in the middle of a major rewrite, and one of the goals is to make the whole pipeline a bit more robust to these issues, including giving a warning, as you suggest.