IPVC-2344: Update SeqRepo load to discover local fasta files

[bsgiles73]

This PR adds logic to the sbin/uta-extract script to discover fasta files rather then have them hardcoded. Those files will be copied into a single working directory.

During testing of this work I found an issue with our Docker image. It did not have tabix installed and thus could not add sequences to SeqRepo. So the dockerfile was updated to include it.

To test I ran the following...

sgiles-MD6M:uta shane.giles$ docker compose run uta-extract
WARN[0000] The "UTA_ETL_SKIP_GENE_LOAD" variable is not set. Defaulting to a blank string.
/opt/repos/uta/sbin/ncbi-parse-gbff:33: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
2024-04-24 17:57:08 INFO     [__main__] opened /ncbi-dir/refseq/H_sapiens/mRNA_Prot/human.test.rna.gbff.gz
/usr/local/lib/python3.10/dist-packages/Bio/GenBank/Scanner.py:1217: BiopythonParserWarning: Premature end of file in sequence data
  warnings.warn(
2024-04-24 17:59:19 INFO     [__main__] 642 genes in /ncbi-dir/refseq/H_sapiens/mRNA_Prot/human.test.rna.gbff.gz (Counter({'NM': 1384, 'NR': 380}))
2024-04-24 17:59:19 INFO     [__main__] 642 genes in 1 files (Counter({'NM': 1384, 'NR': 380}))
/opt/repos/uta/sbin/ncbi_parse_genomic_gff.py:33: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
2024-04-24 17:59:20 INFO     [__main__] read 1776 transcript alignments from file(s): /ncbi-dir/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_000853.3 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NR_003491.3 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NR_033319.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NR_033320.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NR_033321.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NR_156186.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001284286.1 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001284289.1 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001284288.1 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001002837.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001284287.1 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 WARNING  [__main__] Exon set transcript NM_001350317.2 not found in txinfo file. Filtering out.
2024-04-24 17:59:21 INFO     [__main__] Filtered out exon sets for 12 transcript(s): NM_001350317.2,NR_003491.3,NM_001002837.2,NM_000853.3,NR_033320.2,NM_001284289.1,NR_033319.2,NM_001284287.1,NR_033321.2,NM_001284288.1,NR_156186.2,NM_001284286.1

Verified the fasta files were copied to the working directory

sgiles-MD6M:uta shane.giles$ cd output/artifacts/
sgiles-MD6M:artifacts shane.giles$ ll
total 29224
-rw-r--r--  1 shane.giles  staff  11122313 Apr 24 11:59 GCF_000001405.25_GRCh37.p13_genomic.fna.gz
-rw-r--r--  1 shane.giles  staff    307826 Apr 24 11:59 GCF_000001405.25_GRCh37.p13_protein.faa.gz
-rw-r--r--  1 shane.giles  staff   1330779 Apr 24 11:59 GCF_000001405.25_GRCh37.p13_rna.fna.gz
-rw-r--r--  1 shane.giles  staff     19252 Apr 24 11:57 assocacs.gz
-rw-r--r--  1 shane.giles  staff     60177 Apr 24 11:59 exonsets.gz
-rw-r--r--  1 shane.giles  staff       174 Apr 24 11:59 filtered_tx_acs.txt
-rw-r--r--  1 shane.giles  staff     33216 Apr 24 11:57 geneinfo.gz
-rw-r--r--  1 shane.giles  staff    301989 Apr 24 11:59 human.test.protein.faa.gz
-rw-r--r--  1 shane.giles  staff   1623010 Apr 24 11:59 human.test.rna.fna.gz
drwxr-xr-x  7 shane.giles  staff       224 Apr 17 16:35 splign-manual
-rw-r--r--  1 shane.giles  staff     79638 Apr 24 11:59 txinfo.gz
-rw-r--r--  1 shane.giles  staff     60481 Apr 24 11:59 unfiltered_exonsets.gz

Then I was able to successfully run seqrepo-load

sgiles-MD6M:uta shane.giles$ docker compose run seqrepo-load
WARN[0000] The "UTA_ETL_SKIP_GENE_LOAD" variable is not set. Defaulting to a blank string.
human.test.protein.faa.gz: 100%|██████████| 5/5 [00:20<00:00,  4.17s/file]