Mercurial > repos > petr-novak > dante
diff configuration.py @ 9:ed4d9ede9cb4 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Wed, 03 Jul 2019 09:21:52 -0400 |
| parents | cc10173bd0c5 |
| children | d0431a839606 |
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--- a/configuration.py Wed Jul 03 08:10:33 2019 -0400 +++ b/configuration.py Wed Jul 03 09:21:52 2019 -0400 @@ -2,118 +2,6 @@ ''' configuration file to set up the paths and constants ''' import os -######## 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__)) TOOL_DATA = os.path.join(MAIN_GIT_DIR, "tool-data") TMP = "tmp" @@ -126,3 +14,10 @@ FILT_DOM_GFF = "domains_filtered.gff" EXTRACT_DOM_STAT = "domains_counts.txt" EXTRACT_OUT_DIR = "extracted_domains" +FASTA_LINE = 60 +SOURCE_PROFREP = "profrep" +SOURCE_DANTE = "dante" +DOMAINS_FEATURE = "protein_domain" +PHASE = "." +HEADER_GFF = "##gff-version 3" +DOMAINS_GFF = "output_domains.gff"