SLiMSuite REST Server


Links
REST Home
EdwardsLab Homepage
EdwardsLab Blog
SLiMSuite Blog
SLiMSuite
Webservers
REST Pages
REST Status
REST Help
REST Tools
REST Alias Data
REST API
REST News
REST Sitemap

rje_misc V0.59.2

Miscellenous script storage module

Module: rje_misc
Description: Miscellenous script storage module
Version: 0.59.2
Last Edit: 15/04/19

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_seq rje_seqlist rje_sequence rje_uniprot rje_xml rje_zen rje_blast_V1


See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is for "one-off" scripts for odd-jobs that often need to be run multiple times and then forgotten forever:

- aicpaper = Conversion of AIC PATIS tables for Jan 2014 AIC paper. - crisp = Analysis of Crisp et al paper data - testing = SWC boot camp testing - holger = reformat fasta - yunan = combine and normalised Yunan data - sageshape = reshape the SuperSAGE data for ANOVA and FDR analysis - 3did = generate 3DID benchmarking datasets - sfstick = Stick together SF files - dtfas = Reformat DT_Sequence data - laavanya = Prepares PTPRD PPI datasets for SLiMFinder - elm_presto_qsub = Makes a list of python command for qsub job - elm_presto_compile = Compiles all the PRESTO results from ELM conservation analyses into a single file - ppi_go_datafarm = Copies PPI and GO datasets into the current MotifAln folder - minimotif = Reformats mini_motif.txt into standard motif RegExps - wag = reconstruct a PAM1 matrix from the Goldman WAG matrix - hprd_elm_copy = Copies HPRD ELM datasets for SLiMDisc analysis - hprd_elm_comp = Extracts rows of *.compare.tdt files where the HPRD dataset matches its ELM - neduvamotif = Reformats raw motif file from Neduva & Russell work - disordertest = Tests the two disorder prediction servers and compares - ygob = Makes orthologue alignments from YGOB files - ygob2 = Makes orthologue alignments from YGOB files following the original ygob! - ensloci = Counts EnsEMBL loci - go_cc = Extracts a list of GO cellular component IDs into a file corresponding to SLiMDisc input - elm_gcut = Cuts down the ELM GABLAM results as they *should* have been output! - ensgo = Makes GO Datasets from EnsEMBL Loci data and BioMart download (& ensgo2) - elmdup = Identifies "duplicate" proteins from different species using orthaln.fas files - elmaln = Sorts ELM alignments - elmFT = Makes a Table of SwissProt Annotations from mapping.tdt and UniProt - termX = Reformats all fasta files in the directory to be UC for X aa at each end of the sequence and LC for rest - 143ppi = Make a table of 14-3-3 interacting proteins from HPRD - allslim = runs slimfinder on all datasets (*.dat & *.fas) in directory - slimtest = Makes a bunch of random datasets to run SLiMFinder on - slimtestsum = Makes a summary table of random datasets run with SLiMFinder - sfvst = SLiMBuild vs. TEIRESIAS time test w/o ambiguity - ensdat = EnsDat cleanup following rje_ensembl boo-boo - slimcons = Custom assembly of EnsDatHuman SLiMFinder runs and CompariMotif results for data analysis in R - locustdb = Temp analysis of Locust EST database - phomo = PhosphoMotif Reformatter - flyseq = Extract sequences from Flybase chado_xml - arath2go = Convert EMBL_ARATH sequence to GO using Arabidopsis download - intenrich = Reformat enriched integrin proteomics results for Pingu - sftargz = TarGZ cleanup of SLiMFinder results - taxadbsum = E hux Taxa DB summary cleanup - bencog = Makes Ben COG links - humsf09 = Human SF09 cleanup - biol3050 = BIOL3050 clone vs ENST cDNA matchup - jrjspf = Reformatting an SPF file for Joe Jenkins - disjson = Parsing of disorder JSON file - pop00freq - snakencbi = Reformatting the fasta and GFF files for snake genomes - starlingncbi = Reformatting the fasta and GFF files for starling genome

Commandline

job=X : Identifier for the job to be performed [None]
infile=FILE : Name of input file for relevant task [None]
batch=GLIST : List of files to process for relevant task []

History Module Version History

    # 0.1 - Initial Compilation with elm_presto_compile job.
    # 0.2 - Added ppi_go_datafarm job
    # 0.3 - minimotif = Reformats mini_motif.txt into standard motif RegExps
    # 0.4 - Added elm_presto_qsub
    # 0.5 - wag = reconstruct a PAM1 matrix from the Goldman WAG matrix
    # 0.6 - hprd_elm_copy = Copies HPRD ELM datasets for SLiMDisc analysis
    # 0.7 - hprd_elm_comp = Extracts rows of *.compare.tdt files where the HPRD dataset matches its ELM
    # 0.8 - neduvamotif = Reformats raw motif file from Neduva & Russell work
    # 0.9 - disordertest = Tests the two disorder prediction servers and compares
    # 0.10 - ygob = Makes orthologue alignments from YGOB files
    # 0.11 - ensloci = Counts EnsEMBL loci
    # 0.12 - go_cc = Extracts a list of GO cellular component IDs into a file corresponding to SLiMDisc input
    # 0.13 - elm_gcut = Cuts down the ELM GABLAM results as they *should* have been output!
    # 0.14 - ensgo = Makes GO Datasets from EnsEMBL Loci data and BioMart download
    # 0.15 - elmdup = Identifies "duplicate" proteins from different species using orthaln.fas files
    # 0.16 - elmaln = Sorts ELM alignments
    # 0.17 - elmFT = Makes a Table of SwissProt Annotations from mapping.tdt and UniProt
    # 0.18 - termX = Reformats all fasta files in the directory to be UC for X aa at each end of the sequence and LC for rest
    # 0.19 - allslim = runs slimfinder on all datasets (*.dat & *.fas) in directory
    # 0.20 - slimtest = Makes a bunch of random datasets to run SLiMFinder on
    # 0.21 - slimtestsum = Makes a summary table of random datasets run with SLiMFinder
    # 0.22 - sfvst = SLiMBuild vs. TEIRESIAS time test w/o ambiguity
    # 0.23 - mailer = E-Mail test
    # 0.24 - ensdat = EnsDat cleanup following rje_ensembl boo-boo
    # 0.25 - slimcons = Custom assembly of EnsDatHuman SLiMFinder runs and CompariMotif results for data analysis in R
    # 0.26 - locustdb = Temp analysis of Locust EST database
    # 0.27 - phomo = PhosphoMotif Finder reformatting
    # 0.28 - flyseq = Extract sequences from Flybase chado_xml
    # 0.29 - arath2go = Convert EMBL_ARATH sequence to GO using Arabidopsis download
    # 0.30 - intenrich = Reformat enriched integrin proteomics results for Pingu
    # 0.31 - laavanya = Prepares PTPRD PPI datasets for SLiMFinder
    # 0.32 - sftargz = TarGZ cleanup of SLiMFinder results
    # 0.33 - taxadbsum = E hux Taxa DB summary cleanup
    # 0.34 - bencog = Makes Ben COG links
    # 0.35 - sftidy = SLiMFinder grand results tidy up.
    # 0.36 - prpsi = Make SI table for PRP project
    # 0.37 - humsf09 = Human SF09 cleanup
    # 0.38 - biol3050 = BIOL3050 clone vs ENST cDNA matchup
    # 0.39 - biol2018 = BIOL2018 domain identification.
    # 0.40 - dtfas = Reformat DT_Sequence data
    # 0.41 - sfstick = Stick together SF files
    # 0.42 - 3did = generate 3DID benchmarking datasets
    # 0.43 - sageshape = reshape the SuperSAGE data for ANOVA and FDR analysis
    # 0.44 - yunan = combine and normalised Yunan data
    # 0.45 - kroc = Kieren ROC analysis
    # 0.46 - holger = reformat fasta
    # 0.47 - testing = SWC boot camp misc testing code
    # 0.48 - aicpaper = Conversion of AIC PATIS tables for Jan 2014 AIC paper.
    # 0.49.0 - jrjspf = Reformatting an SPF file for Joe Jenkins
    # 0.50.0 - crisp = Analysis of Crisp et al paper data
    # 0.51.0 - dcfmsi = Generation of HTML table code for Manefield DCMF data
    # 0.52.0 - mbgsnp = Compilation of MBG SNP Tables
    # 0.53.0 - mbgSNPFreq = Generation of SNP Frequency Changes from SNP Table.
    # 0.54.0 - disjson = Parsing of disorder JSON file
    # 0.55.0 - diphap = Parsing of pseudodiploid fasta file and annotating with diploid or haploid status
    # 0.56.0 - ancNorm = Conversion of raw anchor scores to normalised scores.
    # 0.57.0 - occjoin = Table join for occbench complementary analysis.
    # 0.58.0 - pop00freq = Regenerate SNP frequencies. Modified mbgSNPFreq to handle pop00freq output.
    # 0.59.0 - snakencbi = Reformatting the fasta and GFF files for snake genomes + starlingncbi
    # 0.59.1 - Updated DCMF SI
    # 0.59.2 - Updated DCMF SI -> dcmfSIJGINCBI()

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.