Module:	rje_apollo
Description:	WebApollo genome search program
Version:	0.6.3
Last Edit:	19/12/19
Webserver:	http://www.slimsuite.unsw.edu.au/servers/apollo.php

Imported modules: rje rje_db rje_exonerate rje_obj rje_html rje_seqlist rje_blast_V2 gablam

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

Function

RJE_APOLLO is a wrapper for GABLAM that peforms a limited number of focused GABLAM functions and adds some additional data cleanup and outputs. It is primarily designed for use as part of the SLiMSuite REST servers as a way to search the WebApollo genome servers of the Edwards Lab. See the REST output and Apollo webserver for more details.

Version 0.2.0 added the option of running exonerate rather than BLAST+, which will probably become the default option on the server.

Commandline

Input/Output Options

seqin=FASFILE : Fasta file of input sequences to search against genome []
genome=FASFILE : Fasta file of genome to search against
qrytype=X : Type of seqin query file (cds/transcript/dna/protein) [cds]
basefile=FILE : Root of output files [apollo]
maxqry=INT : Maximum number of sequences allowed for seqin [0]

GABLAM Search Options

blaste=NUM : E-Value cut-off for BLAST searches (BLAST -e X) [1e-10]
tophits=INT : Sets max number of BLAST hits returned (blastb and blastv) [10]
localmin=INT : Minimum length of local alignment to output to local stats table [30]
localidmin=PERC : Minimum local %identity of local alignment to output to local stats table [75.0]
keepblast=T/F : Whether to keep the blast results files rather than delete them [True]
blasttask=X : Flavour of blast to use (BLAST -task X) (NOTE: blastn default is megablast) [blast+ default]
exonerate=T/F : Whether to use exonerate in place of GABLAM. Can also set blasttask=exonerate [False]
exopt=X : Additional exonerate options []

System Options

webapollo=URL : URL base for Web Apollo genome browser [https://edwapollo.babs.unsw.edu.au/apollo-2.0.8/]
genomeid=X : Genome identifier code for Web Apollo genome browser (with optional .public), or SPEC:ID list []
tracks=LIST : Comma separated list of tracks to display for WebApollo server []
exoneratebin=PATH : Path to exonerate program bin (can be '' if added to environment path) ['']

History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.1.0 - Initial Working Version.
    # 0.1.1 - Modified HTML output.
    # 0.2.0 - Added basic exonerate output.
    # 0.3.0 - Added transcript query type.
    # 0.4.0 - Added MaxQry=INT : Maximum number of sequences allowed for seqin [0]
    # 0.5.0 - Added QryDesc to exonerate GFF output.
    # 0.6.0 - Added cdict parsing to genomeid.
    # 0.6.1 - Debugging genomeID dict and fixed cdict parsing bug.
    # 0.6.2 - Added QryDesc to HTML output.
    # 0.6.3 - Made protein synonym for prot as qrytype.

rje_apollo REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

General REST Outputs

html = Reduced summary table with links to WebApollo genome
seqin = Input search sequence [fasta]
hitsum = One line summary of hits per query [tdt]
local = Local alignments table [tdt]
locgff = Local alignments table in GFF3 format [gff3]
unique = Local alignments table, reduced to non-overlapping query regions [tdt]

Exonerate REST Outputs

alignment = Exonerate alignment [txt]
exgff = Exonerate GFF2 output [gff2]
cigar = Exonerate cigar output [txt]
dnahits = Fasta file of hit sequences [fasta]
prothits = Fasta file of translated hits (CDS or protein only) [fasta]

BLAST+ REST Outputs

gablam = Full GABLAM summary table of each Query-Hit pair [tdt]
blast = Raw BLAST results [txt]
unigff = Local BLAST+ alignments table, reduced to non-overlapping query regions, in GFF3 format [gff]
sam = Local BLAST alignments table in SAM alignment format (blastn only) [sam]
qblast = BLAST results formatted in query assembly -outfmt 4 [txt]
qaln = Query sequence aligned to consensus for each hit from QBLAST [fasta]
qhits = Degapped consensus hits from QBLAST [fasta]

The Apollo server can be found here: http://www.slimsuite.unsw.edu.au/servers/apollo.php. Alternatively, you can run it using the input form, below.

This server allows simple Exonerate or BLAST+ searches of DNA, CDS or protein sequences against one of our WebApollo genomes. Select the genome to search and the WebApollo instance to generate links for. Optionally, tracks to display can be listed under Advanced Options. Private genomes will need a password for access. This password will also be required to access the REST server results.

Note: some genomes may have multiple WebApollo annotations. It is the genome status, not the Apollo status that determines password requirements. If no WebApollo ID is selected, no links table will be generated - other search results will still be returned.

Search Genome: WebApollo ID: Password:

CDS, DNA or protein sequences to search against genome (fasta):
Search method: | Max number of hits returned:

Paste fasta format sequence(s) into text box: >FAXD1_NOTSC (P82807) Venom prothrombin activator notecarin-D1 [Notechis scutatus scutatus] MAPQLLLCLILTFLWSLPEAESNVFLKSKVANRFLQRTKRSNSLFEEIRPGNIERECIEE KCSKEEAREVFEDNEKTETFWNVYVDGDQCSSNPCHYRGTCKDGIGSYTCTCLPNYEGKN CEKVLYQSCRVDNGNCWHFCKRVQSETQCSCAESYRLGVDGHSCVAEGDFSCGRNIKARN KREASLPDFVQSQKATLLKKSDNPSPDIRIVNGMDCKLGECPWQAVLINEKGEVFCGGTI LSPIHVLTAAHCINQTKSVSVIVGEIDISRKETRRLLSVDKIYVHTKFVPPNYYYVHQNF DRVAYDYDIAIIRMKTPIQFSENVVPACLPTADFANEVLMKQDSGIVSGFGRIRFKEPTS NTLKVITVPYVDRHTCMLSSDFRITQNMFCAGYDTLPQDACQGDSGGPHITAYRDTHFIT GIISWGEGCARKGKYGVYTKVSRFIPWIKKIMSLK

Alternative fasta file upload:

Check/set options below, then click:

After running, click on the html tab to see the summary table of hits with WebApollo links.

This server is still in development. Please report any odd/unwanted behaviour.

BLAST+ Search Options

NOTE: if no hits are returned, try reducing the min local alignment %identity.

E-Value cut-off for BLAST searches:
Min local alignment length:
Min local alignment %identity:

Advanced Options

List of tracks to display in Apollo browser:

Other options:

SLiMSuite REST Server

rje_apollo V0.6.3

WebApollo genome search program