feat(IPVC-2276): skip accessions from gff that are not in the tx_info file, log missing acs to file

[sptaylor]

The exonset file, derived from gff files, contains transcript accessions that are not present in the transcript info file/Seqrepo, and this causes downstream issues. We are adding a step to filter out these missing transcripts from the exonsets file.
Demo:

+ sbin/filter_exonset_transcripts.py --tx-info /workdir/loading/gbff.txinfo.gz --exonsets /workdir/loading/gff.exonsets.gz --missing-ids /workdir/loading/filtered_tx_acs.txt
+ tee /workdir/logs/filter_exonset_transcripts.log
+ gzip -c
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_000853.3 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NR_003491.3 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NR_033319.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NR_033320.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NR_033321.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NR_156186.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001284286.1 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001284289.1 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001284288.1 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001002837.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001284287.1 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 WARNING  [__main__] Exon set transcript NM_001350317.2 not found in txinfo file. Filtering out.
2024-04-04 20:42:22 INFO     [__main__] Filtered out exon sets for 12 transcripts: NR_033320.2,NM_001284286.1,NM_001350317.2,NR_033319.2,NR_156186.2,NM_000853.3,NM_001284287.1,NM_001284288.1,NM_001002837.2,NR_003491.3,NM_001284289.1,NR_033321.2

The filtered exonsets are printed to stdout and the missing transcript ids are printed to file.

[sptaylor]

Updated the name to reflect the function takes a list of files

[bsgiles73]

My description in the ticket really made it look like this was an issue with ncbi_parse_genomic_gff.py, but it is not. Sorry for the confusion. But now I have a question. If we have extra transcripts in the GFF files, that are missing from SeqRepo, how many places might break? You definitely found one exonset-to-seqinfo. If the extra transcripts are in the GFF. That means they should be in the intermediate file. Which means they get into the databaes, via the uta load-exonset step? Or are they skipped because the transcripts are missing from the transcript table?

[bsgiles73]

Can we add an output directory to the supported arguments. So we can have this file directed to the directory the user chooses?

[bsgiles73]

LGTM

[bsgiles73]

Nice!