Mercurial > repos > petr-novak > profrep

diff configuration.py @ 0:a5f1638b73be draft

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author petr-novak
date Wed, 26 Jun 2019 08:01:42 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/configuration.py	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,128 @@
+#!/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"