diff README.md @ 0:a5f1638b73be draft

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+# REPEATS ANNOTATION TOOLS FOR ASSEMBLIES  #
+
+
+## 1. PROFREP ##
+*- **PROF**iles of **REP**eats -* 
+
+The ProfRep main tool engages outputs of RepeatExplorer for repeats annotation in DNA sequences (typically assemblies but not necessarily). Moreover, it provides repetitive profiles of the sequence, pointing out quantitative representation of individual repeats along the sequence as well as the overall repetitiveness.
+
+### DEPENDENCIES ###
+
+* python 3.4 or higher with packages:
+	* numpy
+	* matplotlib
+	* biopython
+* [BLAST 2.2.28+](https://www.ncbi.nlm.nih.gov/books/NBK279690/) or higher
+* [wigToBigWig](http://hgdownload.cse.ucsc.edu/admin/exe/)
+* [cd-hit](http://weizhongli-lab.org/cd-hit/)
+* [JBrowse](http://jbrowse.org/install/) - **Only bin needed, does not have to be installed under a web server**
+  
+* ProfRep Modules:
+	* gff.py
+	* visualization.py
+	* configuration.py 
+	* protein_domains.py
+	* domains_filtering.py
+	
+* Profrep databases
+
+There are precompiled profrep annotation dataset for limited number of species. List of species can be find in file [prepared_datasets.txt](tool_data/prepared_datasets). Databases include large files and must be downloaded from our website:
+
+    cd tool_data
+    wget http://repeatexplorer.org/repeatexplorer/wp-content/uploads/profrep.tar.gz
+    tar xzvf profrep.tar.gz
+        
+    
+#### INPUTS ####
+
+* **DNA sequence(s) to annotate** [multiFASTA]
+
+* **Species specific dataset** available from RepeatExplorer archive consisting of:
+
+	* NGS reads sequences [multiFASTA]
+		* In RE archive: *seqclust -> sequences -> sequences.fasta*
+	* CLS file of clusters and belonging reads [multiFASTA] 
+		* in RE archive: *seqclust -> clustering -> hitsort.cls*
+	* Classification table [TSV, CSV] 
+		* in RE archive: *PROFREP_CLASSIFICATION_TEMPLATE.csv* (automatic classification)
+
+
+#### OUTPUTS ####
+	
+* **HTML summary report,JBrowse Data Directory** showing basic information and repetitive profile graphs as well as protein domains (optional) for individual sequences (up to 50). This output also serves as an data directory for [JBrowse](https://jbrowse.org/) genome browser. You can create a standalone JBrowse instance for further detailed visualization of the output tracks using Galaxy-integrated tool. This output can also be downloaded as an archive containing all relevant data for visualization via locally installed JBrowse server (see more about visualization in OUTPUT VISUALIZATION below)
+* **Ns GFF** - reports unspecified (N) bases regions in the sequence
+* **Repeats GFF** - reports repetitive regions of a certain length (defaultly **80**) and above hits/copy numbers threshold (defaultly **3**)
+* **Domains GFF** - reports protein domains, classification of domain, chain orientation and alignment sequences
+* Log file
+
+
+### Running ProfRep ###
+
+	usage: profrep.py [-h] -q QUERY -rdb READS -a ANN_TBL -c CLS [-id DB_ID]
+                  [-bs BIT_SCORE] [-m MAX_ALIGNMENTS] [-e E_VALUE]
+                  [-df DUST_FILTER] [-ws WORD_SIZE] [-t TASK] [-n NEW_DB]
+                  [-w WINDOW] [-o OVERLAP] [-pd PROTEIN_DOMAINS]
+                  [-pdb PROTEIN_DATABASE] [-cs CLASSIFICATION] [-wd WIN_DOM]
+                  [-od OVERLAP_DOM] [-thsc THRESHOLD_SCORE]
+                  [-thl {float range 0.0..1.0}] [-thi {float range 0.0..1.0}]
+                  [-ths {float range 0.0..1.0}] [-ir INTERRUPTIONS]
+                  [-mlen MAX_LEN_PROPORTION] [-lg LOG_FILE] [-ouf OUTPUT_GFF]
+                  [-oug DOMAIN_GFF] [-oun N_GFF] [-hf HTML_FILE]
+                  [-hp HTML_PATH] [-cn COPY_NUMBERS] [-gs GENOME_SIZE]
+                  [-thr THRESHOLD_REPEAT] [-thsg THRESHOLD_SEGMENT]
+                  [-jb JBROWSE_BIN]
+                  
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+
+	required arguments:
+	  -q QUERY, --query QUERY
+							input DNA sequence in (multi)fasta format (default:
+							None)
+	  -rdb READS, --reads READS
+							blast database of all sequencing reads (default: None)
+	  -a ANN_TBL, --ann_tbl ANN_TBL
+							clusters annotation table, tab-separated number of
+							cluster and its classification (default: None)
+	  -c CLS, --cls CLS     cls file containing reads assigned to clusters
+							(hitsort.cls) (default: None)
+
+	alternative required arguments - prepared datasets:
+	  -id DB_ID, --db_id DB_ID
+							annotation dataset ID (first column of datasets table)
+							(default: None)
+
+	optional arguments - BLAST Search:
+	  -bs BIT_SCORE, --bit_score BIT_SCORE
+							bitscore threshold (default: 50)
+	  -m MAX_ALIGNMENTS, --max_alignments MAX_ALIGNMENTS
+							blast filtering option: maximal number of alignments
+							in the output (default: 10000000)
+	  -e E_VALUE, --e_value E_VALUE
+							blast setting option: e-value (default: 0.1)
+	  -df DUST_FILTER, --dust_filter DUST_FILTER
+							dust filters low-complexity regions during BLAST
+							search (default: '20 64 1')
+	  -ws WORD_SIZE, --word_size WORD_SIZE
+							blast search option: initial word size for alignment
+							(default: 11)
+	  -t TASK, --task TASK  type of blast to be triggered (default: blastn)
+	  -n NEW_DB, --new_db NEW_DB
+							create a new blast database, USE THIS OPTION IF YOU
+							RUN PROFREP WITH NEW DATABASE FOR THE FIRST TIME
+							(default: True)
+
+	optional arguments - Parallel Processing:
+	  -w WINDOW, --window WINDOW
+							sliding window size for parallel processing (default:
+							5000)
+	  -o OVERLAP, --overlap OVERLAP
+							overlap for parallely processed regions, set greater
+							than a read size (default: 150)
+
+	optional arguments - Protein Domains:
+	  -pd PROTEIN_DOMAINS, --protein_domains PROTEIN_DOMAINS
+							use module for protein domains (default: False)
+	  -pdb PROTEIN_DATABASE, --protein_database PROTEIN_DATABASE
+							protein domains database (default: None)
+	  -cs CLASSIFICATION, --classification CLASSIFICATION
+							protein domains classification file (default: None)
+	  -wd WIN_DOM, --win_dom WIN_DOM
+							protein domains module: sliding window to process
+							large input sequences sequentially (default: 10000000)
+	  -od OVERLAP_DOM, --overlap_dom OVERLAP_DOM
+							protein domains module: overlap of sequences in two
+							consecutive windows (default: 10000)
+	  -thsc THRESHOLD_SCORE, --threshold_score THRESHOLD_SCORE
+							protein domains module: percentage of the best score
+							within the cluster to significant domains (default:
+							80)
+	  -thl {float range 0.0..1.0}, --th_length {float range 0.0..1.0}
+							proportion of alignment length threshold (default:
+							0.8)
+	  -thi {float range 0.0..1.0}, --th_identity {float range 0.0..1.0}
+							proportion of alignment identity threshold (default:
+							0.35)
+	  -ths {float range 0.0..1.0}, --th_similarity {float range 0.0..1.0}
+							threshold for alignment proportional similarity
+							(default: 0.45)
+	  -ir INTERRUPTIONS, --interruptions INTERRUPTIONS
+							interruptions (frameshifts + stop codons) tolerance
+							threshold per 100 AA (default: 3)
+	  -mlen MAX_LEN_PROPORTION, --max_len_proportion MAX_LEN_PROPORTION
+							maximal proportion of alignment length to the original
+							length of protein domain from database (default: 1.2)
+
+	optional arguments - Output Paths:
+	  -lg LOG_FILE, --log_file LOG_FILE
+							path to log file (default: log.txt)
+	  -ouf OUTPUT_GFF, --output_gff OUTPUT_GFF
+							path to output gff of repetitive regions (default:
+							output_repeats.gff)
+	  -oug DOMAIN_GFF, --domain_gff DOMAIN_GFF
+							path to output gff of protein domains (default:
+							output_domains.gff)
+	  -oun N_GFF, --n_gff N_GFF
+							path to output gff of N regions (default:
+							N_regions.gff)
+	  -hf HTML_FILE, --html_file HTML_FILE
+							path to output html file (default: output.html)
+	  -hp HTML_PATH, --html_path HTML_PATH
+							path to html extra files (default: profrep_output_dir)
+
+	optional arguments - Copy Numbers/Hits :
+	  -cn COPY_NUMBERS, --copy_numbers COPY_NUMBERS
+							convert hits to copy numbers (default: False)
+	  -gs GENOME_SIZE, --genome_size GENOME_SIZE
+							genome size is required when converting hits to copy
+							numbers and you use custom data (default: None)
+	  -thr THRESHOLD_REPEAT, --threshold_repeat THRESHOLD_REPEAT
+							threshold for hits/copy numbers per position to be
+							considered repetitive (default: 3)
+	  -thsg THRESHOLD_SEGMENT, --threshold_segment THRESHOLD_SEGMENT
+							threshold for the length of repetitive segment to be
+							reported (default: 80)
+
+	optional arguments - Enviroment Variables:
+	  -jb JBROWSE_BIN, --jbrowse_bin JBROWSE_BIN
+							path to JBrowse bin directory (default: None)
+
+							
+#### HOW TO RUN EXAMPLE ####
+
+		./protein.py --query PATH_TO_DNA_SEQ --reads PATH_TO_READS --ann_tbl PATH_TO_CLUSTERS_CLASSIFICATION  --cls PATH_TO_hitsort.cls 
+		
+	 When running for the first time with a new reads database use:
+		
+		--new_db True
+
+							
+### ProfRep Data Preparation ###
+
+In case of using custom input datasets these tools can be used for easy obtaining the correct files and to prepare the reduced datasets to speed up the main ProfRep analysis:
+
+* Extract Data For ProfRep (extract_data_for_profrep.py)
+* ProfRep DB Reducing (profrep_db_reducing.py)
+
+### ProfRep Supplementary Tools ###
+
+These additional tools can be used for further work with the ProfRep outputs: 
+
+* ProfRep Refiner (profrep_refining.py) 
+* ProfRep Masker (profrep_masking.py)
+* GFF Region Selector (gff_selection.py)
+
+### FOR MORE INFO ABOUT PREPARATION AND SUPPLEMENTARY TOOLS PLEASE READ PROFREP WIKI ###
+
+## 2. DANTE ##
+*- **D**omain based **AN**notation of **T**ransposable **E**lements -* 
+
+
+* Protein Domains Finder [protein_domains.py]
+	* Script performs scanning of given DNA sequence(s) in (multi)fasta format in order to discover protein domains using our protein domains database.
+	* Domains searching is accomplished engaging LASTAL alignment tool.
+	* Domains are subsequently annotated and classified - in case certain domain has multiple annotations assigned, classifation is derived from the common classification level of all of them. 	
+			
+* Proteins Domains Filter [domains_filtering.py]
+	* filters GFF3 output from previous step to obtain certain kind of domain and/or allows to adjust quality filtering  
+
+        
+### DEPENDENCIES ###
+
+* python3.4 or higher with packages:	
+	* numpy
+	* biopython
+* [lastal](http://last.cbrc.jp/doc/last.html) 744 or higher
+* ProfRep/DANTE modules:
+	* configuration.py 
+
+
+### Protein Domains Finder ###
+
+This tool provides **preliminary** output of all domains types which are not filtered for quality.
+
+#### INPUTS ####
+
+* DNA sequence [multiFasta]
+		
+#### OUTPUTS ####
+		
+* **All protein domains GFF3** - individual domains are reported per line as regions (start-end) on the original DNA sequence including the seq ID and strand orientation. The last "Attributes" column contains several comma-separated information related to the domain annotation, alignment and its quality. This file can undergo further filtering using Protein Domain Filter tool.		
+
+#### USAGE ####
+		usage: protein_domains.py [-h] -q QUERY -pdb PROTEIN_DATABASE -cs
+								  CLASSIFICATION [-oug DOMAIN_GFF] [-nld NEW_LDB]
+								  [-dir OUTPUT_DIR] [-thsc THRESHOLD_SCORE]
+								  [-wd WIN_DOM] [-od OVERLAP_DOM]
+								  
+		optional arguments:
+		  -h, --help            show this help message and exit
+		  -oug DOMAIN_GFF, --domain_gff DOMAIN_GFF
+								output domains gff format (default: None)
+		  -nld NEW_LDB, --new_ldb NEW_LDB
+								create indexed database files for lastal in case of
+								working with new protein db (default: False)
+		  -dir OUTPUT_DIR, --output_dir OUTPUT_DIR
+								specify if you want to change the output directory
+								(default: None)
+		  -thsc THRESHOLD_SCORE, --threshold_score THRESHOLD_SCORE
+								percentage of the best score in the cluster to be
+								tolerated when assigning annotations per base
+								(default: 80)
+		  -wd WIN_DOM, --win_dom WIN_DOM
+								window to process large input sequences sequentially
+								(default: 10000000)
+		  -od OVERLAP_DOM, --overlap_dom OVERLAP_DOM
+								overlap of sequences in two consecutive windows
+								(default: 10000)
+
+		required named arguments:
+		  -q QUERY, --query QUERY
+								input DNA sequence to search for protein domains in a
+								fasta format. Multifasta format allowed. (default:
+								None)
+		  -pdb PROTEIN_DATABASE, --protein_database PROTEIN_DATABASE
+								protein domains database file (default: None)
+		  -cs CLASSIFICATION, --classification CLASSIFICATION
+								protein domains classification file (default: None)
+
+
+		
+#### HOW TO RUN EXAMPLE ####
+		./protein_domains.py -q PATH_TO_INPUT_SEQ -pdb PATH_TO_PROTEIN_DB -cs PATH_TO_CLASSIFICATION_FILE
+		
+	 When running for the first time with a new database use -nld option allowing lastal to create indexed database files:
+
+         -nld True
+
+	use other arguments if you wish to rename your outputs or they will be created automatically with standard names 
+	
+### Protein Domains Filter ###
+		
+The script performs Protein Domains Finder output filtering for quality and/or extracting specific type of protein domain or mobile elements of origin. For the filtered domains it reports their translated protein sequence of original DNA.
+
+WHEN NO PARAMETERS GIVEN, IT PERFORMS QUALITY FILTERING USING THE DEFAULT PARAMETRES (optimized for Viridiplantae species)
+
+#### INPUTS ####
+* GFF3 file produced by protein_domains.py OR already filtered GFF3
+	
+#### Filtering options ####
+* QUALITY: 
+	- Min relative length of alignemnt to the protein domain from DB (without gaps)
+	- Identity 
+	- Similarity (scoring matrix: BLOSUM80)
+	- Interruption in the reading frame (frameshifts + stop codons) per every starting 100 AA
+	- Max alignment proportion to the original length of database domain sequence
+* DOMAIN TYPE: 'Name' attribute in GFF - see choices bellow
+Records for ambiguous domain type (e.g. INT/RH) are filtered out automatically
+
+* MOBILE ELEMENT TYPE:
+arbitrary substring of the element classification ('Final_Classification' attribute in GFF)
+		
+#### OUTPUTS ####
+* filtered GFF3 file
+* fasta file of translated protein sequences for the aligned domains that match the filtering criteria 
+	! as it is taken from the best hit alignment reported by LAST, it does not neccessary cover the whole region reported as domain in GFF
+	
+#### USAGE ####		
+		usage: domains_filtering.py [-h] -dg DOM_GFF [-ouf DOMAINS_FILTERED]
+                            [-dps DOMAINS_PROT_SEQ]
+                            [-thl {float range 0.0..1.0}]
+                            [-thi {float range 0.0..1.0}]
+                            [-ths {float range 0.0..1.0}] [-ir INTERRUPTIONS]
+                            [-mlen MAX_LEN_PROPORTION]
+                            [-sd {All,GAG,INT,PROT,RH,RT,aRH,CHDCR,CHDII,TPase,YR,HEL1,HEL2,ENDO}]
+                            [-el ELEMENT_TYPE] [-dir OUTPUT_DIR]
+
+
+
+		optional arguments:
+		  -h, --help            show this help message and exit
+		  -ouf DOMAINS_FILTERED, --domains_filtered DOMAINS_FILTERED
+								output filtered domains gff file (default: None)
+		  -dps DOMAINS_PROT_SEQ, --domains_prot_seq DOMAINS_PROT_SEQ
+								output file containg domains protein sequences
+								(default: None)
+		  -thl {float range 0.0..1.0}, --th_length {float range 0.0..1.0}
+								proportion of alignment length threshold (default:
+								0.8)
+		  -thi {float range 0.0..1.0}, --th_identity {float range 0.0..1.0}
+								proportion of alignment identity threshold (default:
+								0.35)
+		  -ths {float range 0.0..1.0}, --th_similarity {float range 0.0..1.0}
+								threshold for alignment proportional similarity
+								(default: 0.45)
+		  -ir INTERRUPTIONS, --interruptions INTERRUPTIONS
+								interruptions (frameshifts + stop codons) tolerance
+								threshold per 100 AA (default: 3)
+		  -mlen MAX_LEN_PROPORTION, --max_len_proportion MAX_LEN_PROPORTION
+								maximal proportion of alignment length to the original
+								length of protein domain from database (default: 1.2)
+		  -sd {All,GAG,INT,PROT,RH,RT,aRH,CHDCR,CHDII,TPase,YR,HEL1,HEL2,ENDO}, --selected_dom {All,GAG,INT,PROT,RH,RT,aRH,CHDCR,CHDII,TPase,YR,HEL1,HEL2,ENDO}
+								filter output domains based on the domain type
+								(default: All)
+		  -el ELEMENT_TYPE, --element_type ELEMENT_TYPE
+								filter output domains by typing substring from
+								classification (default: )
+		  -dir OUTPUT_DIR, --output_dir OUTPUT_DIR
+								specify if you want to change the output directory
+								(default: None)
+
+		required named arguments:
+		  -dg DOM_GFF, --dom_gff DOM_GFF
+								basic unfiltered gff file of all domains (default:
+								None)
+
+
+
+#### HOW TO RUN EXAMPLE ####
+e.g. getting quality filtered integrase(INT) domains of all gypsy transposable elements:
+	
+	./domains_filtering.py -dom_gff PATH_TO_INPUT_GFF -pdb PATH_TO_PROTEIN_DB -cs PATH_TO_CLASSIFICATION_FILE --selected_dom INT --element_type Ty3/gypsy 
+
+
+### Extract Domains Nucleotide Sequences ###
+
+This tool extracts nucleotide sequences of protein domains from reference DNA based on DANTE's output. It can be used e.g. for deriving phylogenetic relations of individual mobile elements classes within a species. 
+
+#### INPUTS ####
+
+* original DNA sequence in multifasta format to extract the domains from 
+* GFF3 file of protein domains (**DANTE's output** - preferably filtered for quality and specific domain type)
+* Domains database classification table (to check the classification level)
+
+#### OUTPUTS ####
+
+* fasta files of domains nucleotide sequences for individual transposons lineages
+* txt file of domains counts extracted for individual lineages
+
+**- For GALAXY usage all concatenated in a single fasta file**
+
+#### USAGE ####	
+		usage: extract_domains_seqs.py [-h] -i INPUT_DNA -d DOMAINS_GFF -cs
+			CLASSIFICATION [-out OUT_DIR] [-ex EXTENDED]
+
+		optional arguments:
+		  -h, --help            show this help message and exit
+		  -i INPUT_DNA, --input_dna INPUT_DNA
+								path to input DNA sequence
+		  -d DOMAINS_GFF, --domains_gff DOMAINS_GFF
+								GFF file of protein domains
+		  -cs CLASSIFICATION, --classification CLASSIFICATION
+								protein domains classification file
+		  -out OUT_DIR, --out_dir OUT_DIR
+								output directory
+		  -ex EXTENDED, --extended EXTENDED
+								extend the domains edges if not the whole datatabase
+								sequence was aligned
+
+#### HOW TO RUN EXAMPLE ####
+	./extract_domains_seqs.py --domains_gff PATH_PROTEIN_DOMAINS_GFF --input_dna PATH_TO_INPUT_DNA  --classification PROTEIN_DOMAINS_DB_CLASS_TBL --extended True
+
+### GALAXY implementation ###
+
+#### Dependencies ####
+
+* python3.4 or higher with packages:	
+	* numpy
+	* matplotlib
+	* biopython
+* [BLAST 2.2.28+](https://www.ncbi.nlm.nih.gov/books/NBK279671/) or higher
+* [LAST](http://last.cbrc.jp/doc/last.html) 744 or higher:
+	* [download](http://last.cbrc.jp/)
+	* [install](http://last.cbrc.jp/doc/last.html)
+* [wigToBigWig](http://hgdownload.cse.ucsc.edu/admin/exe/)
+* [cd-hit](http://weizhongli-lab.org/cd-hit/)
+* [JBrowse](http://jbrowse.org/install/) - **Only bin needed, does not have to be installed under a web server**
+
+#### Source ######
+
+https://[e-mail]/nina_h/profrep.git
+
+branch "cerit" --> only Pisum Sativum Terno in preparad annotation datasets
+
+branch "develop"/"master" --> extended internal database of species (not published, or for internal purposes)
+
+#### Configuration #####
+
+Add tools
+
+	<section name="Assembly annotation" id="annotation">
+		<label id="profrep_prepare" text="ProfRep Data Preparation" />
+			<tool file="profrep/extract_data_for_profrep.xml" />
+			<tool file="profrep/db_reducing.xml" />
+		<label id="profrep_main" text="Profrep" />
+			<tool file="profrep/profrep.xml" />
+		<label id="profrep_supplementary" text="Profrep Supplementary" />
+			<tool file="profrep/profrep_refine.xml" />
+			<tool file="profrep/profrep_masking.xml" />
+			<tool file="profrep/gff_select_region.xml" />
+		<label id="domains" text="DANTE" />
+			<tool file="profrep/protein_domains.xml" />
+			<tool file="profrep/domains_filtering.xml" />
+			<tool file="profrep/extract_domains_seqs.xml" />
+  </section>
+
+	
+to 
+
+	$__root_dir__/config/tool_conf.xml
+	
+------------------------------------------------------------------------
+
+Place PROFREP_DB files to
+
+	$__tool_data_path__/profrep
+
+*REMARK* PROFREP_DB files contain prepared annotation data for species in the roll-up menu:
+	
+	* sequences.fasta - including BLAST database files which was created by:
+		 makeblastdb -in >sequences.fasta -dbtype nucl
+	* hitosort.cls file
+	* classification table table
+
+Place DANTE_DB files to
+
+	$__tool_data_path__/protein_domains
+	
+*REMARK* DANTE_DB files contain protein domains database files:
+	* protein domains database including LASTAL database files which was created by:
+		lastdb -p -cR01 >database_name< >database_name<
+		(lastal database files are actually enough, original datatabse table does not have to be present)
+	* classification table
+	
+------------------------------------------------------------------------	
+	
+Create
+	
+	$__root_dir__/database/dependencies/profrep/1.0.0/env.sh
+	
+containing:
+	
+	export JBROWSE_BIN=PATH_TO_JBROWSE_DIR/bin
+
+------------------------------------------------------------------------	
+	
+Link the following files into galaxy tool-data dir
+
+	ln -s $__tool_directory__/profrep/domains_data/select_domain.txt $__tool_data_path__
+	ln -s $__tool_directory__/profrep/profrep_data/prepared_datasets.txt $__tool_data_path__
+	
+	
+
+
+
+
+
+
+