Mercurial > repos > petr-novak > profrep

#!/usr/bin/env python3
import os
''' configuration file to set up the paths and constants '''

######## PROFREP #######################################################
## Constansts
N_segment = 50
MAX_FILES_SUBPROFILES = 1000
MAX_PIC_NUM = 50
IMAGE_RES = 300
FASTA_LINE = 60
SEQ_LEN_VIZ = 200000
FORBIDDEN_CHARS = "\\/"
HTML_STR = '''
	<!DOCTYPE html>
	<html>
	<body>
		<h2>PROFREP OUTPUT</h2>
		<h4> Sequences processed: </h4>
		{}
		<h4> Total length: </h4>
		<pre> {} bp </pre>
		<h4> Database: </h4>
		<pre> {} </pre>
		<hr>
		<h3> Repetitive profile(s)</h3> </br>
		{} <br/>
		<h4>References: </h4>
		{}
		</h6>
	</body>
	</html>
	'''

## IO
DOMAINS_GFF = "output_domains.gff"
N_GFF = "N_regions.gff"
REPEATS_GFF = "output_repeats.gff"
HTML = "output.html"
LOG_FILE = "log.txt"
PROFREP_DATA = "tool_data/profrep"
PROFREP_TBL = "prepared_datasets.txt"
PROFREP_OUTPUT_DIR = "profrep_output_dir"
## JBrowse and Tracks Conf
jbrowse_data_dir = "data"
JSON_CONF_R = """{"hooks" : {"modify": "function( track, f, fdiv ) {fdiv.style.backgroundColor = '#278ECF'}"}}"""
JSON_CONF_N = """{"hooks" : {"modify": "function( track, f, fdiv ) {fdiv.style.background = '#474747'}"}}"""
COLORS_HEX = ["#7F7F7F", "#00FF00", "#0000FF", "#FF0000", "#01FFFE", "#FFA6FE",
              "#FFDB66", "#006401", "#010067", "#95003A", "#007DB5", "#FF00F6",
              "#774D00", "#90FB92", "#0076FF", "#D5FF00", "#FF937E", "#6A826C",
              "#FF029D", "#FE8900", "#7A4782", "#7E2DD2", "#85A900", "#FF0056",
              "#A42400", "#00AE7E", "#683D3B", "#BDC6FF", "#263400", "#BDD393",
              "#00B917", "#9E008E", "#001544", "#C28C9F", "#FF74A3", "#01D0FF",
              "#004754", "#E56FFE", "#788231", "#0E4CA1", "#91D0CB", "#BE9970",
              "#968AE8", "#BB8800", "#43002C", "#DEFF74", "#00FFC6", "#FFE502",
              "#620E00", "#008F9C", "#98FF52", "#7544B1", "#B500FF", "#00FF78",
              "#FF6E41", "#005F39", "#6B6882", "#5FAD4E", "#A75740", "#A5FFD2",
              "#FFB167", "#009BFF", "#E85EBE"]
COLORS_RGB = ["127,127,127", "0,255,0", "0,0,255", "255,0,0", "1,255,254",
              "255,166,254", "255,219,102", "0,100,1", "1,0,103", "149,0,58",
              "0,125,181", "255,0,246", "119,77,0", "144,251,146", "0,118,255",
              "213,255,0", "255,147,126", "106,130,108", "255,2,157",
              "254,137,0", "122,71,130", "126,45,210", "133,169,0", "255,0,86",
              "164,36,0", "0,174,126", "104,61,59", "189,198,255", "38,52,0",
              "189,211,147", "0,185,23", "158,0,142", "0,21,68", "194,140,159",
              "255,116,163", "1,208,255", "0,71,84", "229,111,254",
              "120,130,49", "14,76,161", "145,208,203", "190,153,112",
              "150,138,232", "187,136,0", "67,0,44", "222,255,116",
              "0,255,198", "255,229,2", "98,14,0", "0,143,156", "152,255,82",
              "117,68,177", "181,0,255", "0,255,120", "255,110,65", "0,95,57",
              "107,104,130", "95,173,78", "167,87,64", "165,255,210",
              "255,177,103", "0,155,255", "232,94,190"]
TRACK_LIST = '''
	\t,{}\n
	\t"storeClass" : "JBrowse/Store/SeqFeature/BigWig",
	\t"urlTemplate" : "{}",
	\t"type" : "JBrowse/View/Track/Wiggle/XYPlot",
	\t"label" : "{}",
	\t"key" : "{}",
	\t"style": {}
	\t\t"pos_color": "{}"
	\t {},
	\t"scale" : "log"
	\t{}\n
	'''

## GFF tracks
HEADER_GFF = "##gff-version 3"
SOURCE_PROFREP = "profrep"
SOURCE_DANTE = "dante"
PHASE = "."
DOMAINS_FEATURE = "protein_domain"
REPEATS_FEATURE = "repeat"
N_NAME = "N"
N_FEATURE = "N_region"
HEADER_WIG = "variableStep\tchrom="
GFF_EMPTY = "."

######### BIG WIG ######################################################
CHROM_SIZES_FILE = "chrom_sizes.txt"

######### EXTRACT_DATA_DOR_PROFREP #####################################
HITSORT_CLS = "seqclust/clustering/hitsort.cls"
READS_ALL = "seqclust/sequences/sequences.fasta"
ANNOTATION = "PROFREP_CLASSIFICATION_TEMPLATE.csv"

######### PROFREP_DB_REDUCING ##########################################
MEM_LIM = 1500  # MB
CLS_REDUCED = "hitsort_reduced.cls"
READS_ALL_REDUCED = "reads_all_reduced"

######### PROFREP_REFINING #############################################
WITH_DOMAINS = "mobile_element"
QUALITY_DIFF_TO_REMOVE = 0.05  # 5% tolerance of PID

######### DANTE ##############################################
MAIN_GIT_DIR = os.path.dirname(os.path.realpath(__file__))
DOMAINS_DATA = os.path.join(MAIN_GIT_DIR, "domains_data")
TMP = "tmp"
SC_MATRIX = os.path.join(DOMAINS_DATA, "blosum80.txt")
AMBIGUOUS_TAG = "Ambiguous_domain"
## IO
CLASS_FILE = "ALL.classification-new"
LAST_DB_FILE = "ALL_protein-domains_05.fasta"
DOM_PROT_SEQ = "dom_prot_seq.fa"
FILT_DOM_GFF = "domains_filtered.gff"
EXTRACT_DOM_STAT = "domains_counts.txt"
EXTRACT_OUT_DIR = "extracted_domains"
author	petr-novak
date	Wed, 26 Jun 2019 10:23:50 -0400
parents	a5f1638b73be
children