toniwestbrook/paladin-plugins

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc

Thanks for taking an interest in my projects! Listed below are my scientific applications developed for work and a variety of hardware and retrocomputing projects I work on in my spare time.

✨ I'm currently working on Cloudburst Connection, an RPG adventure game where you run your own dial-up Bulletin Board System (BBS). Add new features, keep your users happy, and explore other boards as a deeper story unfolds. Check here to follow its development!

UNH and Bioinformatics Projects

Project	Description
RepeatFS	File system providing scientific reproducibility through provenance and automation
PALADIN	Protein sequence alignment tool designed for the accurate functional characterization of metagenomes
PALADIN_Plugins	Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), automation, etc
Mitobin	Taxonomic classification and read binning of mitochondrial DNA
ImageJ_Plugins	A collection of plugins for ImageJ/FIJI

Personal and Synthetic Dreams Projects

Project	Description
Shredz64	Guitar Hero style game for the Commodore 64
NetPaint	100% text-only drawing program, compatible with any terminal emulator that supports the mouse, such as PuTTY, Konsole, iTerm2, and many others
Whirlwind	Nintendo Entertainment System (NES) compatible FPGA core
IntLog	Monitor and log BIOS and DOS interrupts for debugging 16-bit DOS programs

paladin-plugins's Issues

Traceback issues

Hi!
I am trying the general pathways analysis with my data and I get a callback() error that I am having a hard time interpreting.
I prepared the reference:
$paladin prepare -r1

And then map read data to the uniprot reference:

$paladin align -t 4 -o paladin1 uniprot_sprot.fasta.gz 4_CAAGCT_S38_L007_R1_001.fastq.gz

I get paladin1.sam and paladin1_uniprot.tsv as output files

I was curious about using the plugin to esimate pathways
and I tried running:

$/data/cornejo/projects/programs/paladin-plugins/paladin-plugins.py @@pathways -i paladin1_uniprot.tsv -q 20 -s Firmicutes -p ec00521

and

$paladin-plugins.py @@pathways -i paladin1_uniprot.tsv -q 20 -l 2

I am having the issue that I get a callback() error. See below. But I am not sure about how to interpret it..

Populating taxonomic lineage data...
Traceback (most recent call last):
File "/data/cornejo/projects/programs/paladin-plugins/paladin-plugins.py", line 118, in
core.main.exec_pipeline(pipeline)
File "/data/cornejo/projects/programs/paladin-plugins/core/main.py", line 350, in exec_pipeline
dependency.callback_init()
File "/data/cornejo/projects/programs/paladin-plugins/plugins/taxonomy.py", line 78, in taxonomy_init
populate_database()
File "/data/cornejo/projects/programs/paladin-plugins/plugins/taxonomy.py", line 146, in populate_database
DataStore.get_entry("taxonomy").insert_rows("lineage", [(fields[1], fields[8])])
File "/data/cornejo/projects/programs/paladin-plugins/core/datastore.py", line 75, in insert_rows
cursor.executemany("INSERT INTO {0} VALUES ({1})".format(name, param_tokens), data)
sqlite3.OperationalError: disk I/O error

metabolic pathway participation

Hi

How do you compute metabolic pathway participation? What's the manner? Can I convert the outputted values in a kind of measure comparable across the pathways and samples?

For example, pathway abundance measured in RPK o CPM (RPKM), as humann2 does: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-2-pathway-abundance-file

@@uniprot with Uniref

I had the following trouble running @@uniprot for a sam file obtained from an alignment with a Uniref50 db:

paladin-plugins.py @@uniprot -i 1G.sam -c Organism "protein names" go comments ec "database(KEGG)" @@Write report.txt
Gathering SAM data...
Fetching entries 0:5000 of 87309...
Fetching entries 5000:10000 of 87309...
Fetching entries 10000:15000 of 87309...
Fetching entries 15000:20000 of 87309...
Fetching entries 20000:25000 of 87309...
Fetching entries 25000:30000 of 87309...
Fetching entries 30000:35000 of 87309...
Fetching entries 35000:40000 of 87309...
Fetching entries 40000:45000 of 87309...
Fetching entries 45000:50000 of 87309...
Fetching entries 50000:55000 of 87309...
Fetching entries 55000:60000 of 87309...
Fetching entries 60000:65000 of 87309...
Fetching entries 65000:70000 of 87309...
Fetching entries 70000:75000 of 87309...
Fetching entries 75000:80000 of 87309...
Fetching entries 80000:85000 of 87309...
Fetching entries 85000:87309 of 87309...
{'': ['']}
Traceback (most recent call last):
File "/usr/bin/paladin-plugins.py", line 118, in
core.main.exec_pipeline(pipeline)
File "/opt/paladin-plugins/core/main.py", line 357, in exec_pipeline
plugin.callback_main(args)
File "/opt/paladin-plugins/plugins/uniprot.py", line 80, in uniprot_main
headers = "Count\tAbundance\tQuality (Average)\tQuality (Max)\tUniProtKB\tID\t{0}".format("\t".join(uniprot_data["Entry name"][2:]))
KeyError: 'Entry name'

Seems that @@uniprot doesn't work with uniref formatted sam file