reads.py errors

[sheaster]

Hi There,
I had some issues getting RAT to run (CAT and BAT both worked) using a megahit assembly.
In order to fix it (I think), I used the latest release of CAT v6.0.1 and had to change a few lines assigning dictionary keys.

specifically:
reads_v2.txt

• in get_contig_lengths i had to change the c_id key set in the contig_length_dict from "c.split('\n')[0].strip()" to "c.rstrip().split(' ')[0].lstrip('>')" as it was faulting in make_tax_table
• in make_unclassified_seq_fasta I changed the last line in the part writing unclassified_seq_fasta I changed "outf.write('>{0}{1}\n{2}\n'.format(seq_id, suffix,
  fasta_dict[seq]))" to "outf.write('>{0}{1}\n{2}\n'.format(seq_id, suffix,
  fasta_dict[seq_id]))"

The program now runs without errors on my local install with my files - do those changes have any secondary effects in the program I might not be expecting?

I attached my reads.py file that I'm running now as a txt file
Thanks,
Shea

[yuqing-feng]

Dear Shea,
Thank you for sharing your scirpt. This script does not seem to work for me.

1. In lines 395-396, irrevelant codes exist.
2. After deleting these lines, I rerun the software: CAT_pack reads -1 R_1.fastq -2 R_2.fastq -m cr -d 20231120_CAT_gtdb/db/ -t 20231120_CAT_gtdb/tax/ -o new -n 16 -c tests/final_assembly.fasta (assembled using Megahit).
   reads.py", line 953, in make_tax_table
   taxon_dict[taxon]['n_nucleotides']+=contig_length_dict[contig]
   KeyError: 'k141_3004_length_4231_cov_30.2848'