SVG/PNG export (#3)

* Click options for helper scripts

* Patched output from SVG/PNG export; added default options

README.md

@@ -70,11 +70,15 @@ The following options are available:
   "options": {
     "fontSize": 9, // font size for labels and amino acids (if available)
     "fontFamily": "Helvetica",
-    "labelFontColor": "#222222",
-    "labelBackgroundColor": "#e9e9e9",
+    "labelFontColor": "#333333",
+    "labelBackgroundPlusStrandColor": "#ffffff",
+    "labelBackgroundMinusStrandColor": "#ffffff",
+    "labelStrokePlusStrandColor": "#999999",
+    "labelStrokeMinusStrandColor": "#999999",
     "plusStrandColor": "#bdbfff", // color of coding parts of the exon on the plus strand
     "minusStrandColor": "#fabec2", // color of coding parts of the exon on the negative strand
     "utrColor": "#C0EAAF", // color of untranslated regions of the exons
+    "backgroundColor": "#ffffff", // color of track background
     "transcriptHeight": 12, // height of the transcripts
     "transcriptSpacing": 2, // space in between the transcripts
     "name": "Gene transcripts",
@@ -103,7 +107,7 @@ Whenever there is a statement such as the following, assuming `higlass-transcrip
 import { TranscriptsTrack } from 'higlass-transcripts';
 ```
 
-Then TranscriptsTrack would automatically be imported from the `./es` directory (set via package.json's `"module"` value). 
+Then `TranscriptsTrack` would automatically be imported from the `./es` directory (set via package.json's `"module"` value). 
 
 ## Support
 

scripts/aggregate_transcripts.py

@@ -10,20 +10,7 @@
 import math
 import collections as col
 import json
-
-filepath = "extracted_transcripts_20200814.txt"
-#filepath = "gene_table_v2_transcripts_names_new.txt"
-output_file = "transcripts_20200814.beddb"
-#output_file = "transcripts_20200723_3.beddb"
-importance_column = 5
-has_header = False
-chromosome = None
-max_transcripts_per_tile = 5
-tile_size = 1024
-delimiter = '\t'
-chromsizes_filename = 'hg38_full.txt'
-offset = 0
-
+import click
 
 def load_chromsizes(chromsizes_filename, assembly=None):
     """
@@ -473,17 +460,38 @@ def line_to_np_array(line):
     conn.commit()
     return True
 
+@click.command(context_settings=dict(
+    allow_extra_args=False,
+))
+@click.help_option('--help', '-h')
+@click.option('-i', '--input-filename', required=True, type=str)
+@click.option('-c', '--chromsizes-filename', required=True, type=str)
+@click.option('-o', '--output-filename', required=True, type=str)
+def main(**kwargs):
+    filepath = kwargs["input_filename"]
+    #filepath = "gene_table_v2_transcripts_names_new.txt"
+    output_file = kwargs["output_filename"]
+    #output_file = "transcripts_20200723_3.beddb"
+    importance_column = 5
+    has_header = False
+    chromosome = None
+    max_transcripts_per_tile = 5
+    tile_size = 1024
+    delimiter = '\t'
+    chromsizes_filename = kwargs["chromsizes_filename"]
+    offset = 0
+    aggregate_bedfile(
+        filepath,
+        output_file,
+        importance_column,
+        has_header,
+        chromosome,
+        max_transcripts_per_tile,
+        tile_size,
+        delimiter,
+        chromsizes_filename,
+        offset,
+    )
 
-
-aggregate_bedfile(
-    filepath,
-    output_file,
-    importance_column,
-    has_header,
-    chromosome,
-    max_transcripts_per_tile,
-    tile_size,
-    delimiter,
-    chromsizes_filename,
-    offset,
-)
+if __name__ == '__main__':
+    main()

scripts/commands.txt

@@ -1,11 +1,15 @@
 # Extract transcripts data from GTF file
 
-python extract_transcript_data.py
+python extract_transcript_data.py --input-filename annotations.gtf --chromsizes-filename chromSizes.txt --output-filename transcripts.txt
 
-# Aggregate with clods
+# Aggregate with aggregate_transcripts.py
 
-clodius aggregate bedfile --max-per-tile 20 --importance-column 5 --chromsizes-filename chromInfo_hg38.txt --output-file transcripts_20200722.db --delimiter $'\t' gene_table_v2_transcripts_names_new.txt
+python aggregate_transcripts.py --input-filename transcripts.txt --chromsizes-filename chromSizes.txt --output-filename transcripts.beddb
+
+# Aggregate with clodius
+
+clodius aggregate bedfile --max-per-tile 20 --importance-column 5 --chromsizes-filename chromSizes.txt --output-file transcripts.beddb --delimiter $'\t' transcripts.txt
 
 # Ingest to server
 
-python manage.py ingest_tileset --filename data/transcripts_20200722.db --filetype beddb --datatype gene-annotation --uid transcripts_20200722
+python manage.py ingest_tileset --filename transcripts.beddb --filetype beddb --datatype gene-annotation --uid transcripts_abcd1234