# HG changeset patch
# User iuc
# Date 1568753697 14400
# Node ID 014a21767ac42f6ca726de9190ab85def518acbe
# Parent ae9994cf526fb685498ebe68f1893b2a17b45592
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
diff -r ae9994cf526f -r 014a21767ac4 README.rst
--- a/README.rst Thu Oct 04 06:05:31 2018 -0400
+++ b/README.rst Tue Sep 17 16:54:57 2019 -0400
@@ -23,10 +23,7 @@
- [x] Complex colouring rules
- - [ ] Heatmaps
-
- - [ ] Bugs here.
-
+ - [x] Heatmaps
- [x] Tiles
- [x] Scatter Plots
- [x] Line Plots
@@ -34,10 +31,6 @@
- [x] Links
- [x] Axes
- [x] Backgrounds
-- [ ] Highlights
-
- - [ ] Wedge
-
+- [x] Highlights
- [x] Test cases
-- [ ] Grids?
-- [ ] Fine grained Z-depth control
+- [x] Fine grained Z-depth control
diff -r ae9994cf526f -r 014a21767ac4 alignments-to-links.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/alignments-to-links.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,30 @@
+import itertools
+import sys
+
+from Bio import AlignIO
+
+
+format_mapping = {
+ "xmfa": "mauve",
+ "maf": "maf",
+ "nex": "nexus",
+ # 'phylip': 'phylip-relaxed',
+ "stockholm": "stockholm",
+}
+
+for aln in AlignIO.parse(sys.argv[1], format_mapping.get(sys.argv[2], "maf")):
+
+ for (a, b) in itertools.combinations(aln, 2):
+ a_s = a.annotations["start"]
+ b_s = b.annotations["start"]
+
+ if "size" in a.annotations:
+ a_l = a.annotations["size"]
+ b_l = b.annotations["size"]
+ a_e = a_l + a_s
+ b_e = b_l + b_s
+ else:
+ a_e = a.annotations["end"]
+ b_e = b.annotations["end"]
+
+ sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (a.id, a_s, a_e, b.id, b_s, b_e))
diff -r ae9994cf526f -r 014a21767ac4 alignments-to-links.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/alignments-to-links.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,28 @@
+
+
+ reformats alignment files to prepare for Circos
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
+
+
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diff -r ae9994cf526f -r 014a21767ac4 binlinks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/binlinks.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,66 @@
+
+
+ reduce links to a density plot
+
+ macros.xml
+
+
+ '$outfile'
+
+ ]]>
+
+
+
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+ `__
+
+ The purpose of this script is to generate data for histogram and highlight tracks that stores the number, size and consensus position of links. All chromosomes in the input link file are divided into bins (controlled by -bin_size), and link statistics are calculated on a bin-by-bin basis.
+ ]]>
+
+
diff -r ae9994cf526f -r 014a21767ac4 bundlelinks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bundlelinks.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,61 @@
+
+
+ reduce numbers of links in datasets before plotting
+
+ macros.xml
+
+
+ '$outfile'
+
+ ]]>
+
+
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+
+
+ `__
+
+ The purpose of the bundlelinks tool is to reduce the number of links in a dataset by merging (or bundling) adjacent links together. By merging links, you can distill a visually complex representation into one which effectively summarizes the link structure of your data. A bundle is encoded as a new link with a single start and end position, which are formed by the boundaries of the merged links. Bundles are best shown using the ribbon feature.
+
+
+
+
+ ]]>
+
+
diff -r ae9994cf526f -r 014a21767ac4 circgraph.xml
--- a/circgraph.xml Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,409 +0,0 @@
-
-
- creates circos plots from standard bioinformatics datatypes.
-
- macros.xml
- macros_conffiles.xml
-
-
- circos --version
- circos/conf/karyotype.txt &&
-#else
- cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
-#end if
-
-mv '$circos_conf' circos/conf/circos.conf &&
-mv '$ticks_conf' circos/conf/ticks.conf &&
-mv '$ideogram_conf' circos/conf/ideogram.conf &&
-mv '$data_conf' circos/conf/2d.conf &&
-mv '$links_conf' circos/conf/links.conf &&
-mv '$test_case_conf' circos/conf/galaxy_test_case.xml &&
-
-## 2D Data Plots
-#for $hi, $data in enumerate($sec_tdd.data):
- #if str($data.plot_format.plot_format_select) == 'tile':
- python '$__tool_directory__/unified-tiles.py'
- '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
- > circos/data/data-${hi}.txt &&
- #else:
- python $__tool_directory__/unified-histogram.py
- $data.plot_format.plot_format_select
- #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
- #for $fi, $file in enumerate($data.plot_format.data_source):
- '${file}' '${file.ext}'
- #end for
- #else:
- '${data.plot_format.data_source}' '${data.plot_format.data_source.ext}'
- #end if
- > circos/data/data-${hi}.txt &&
- #end if
-#end for
-
-## Link Tracks
-#for $hi, $data in enumerate($sec_links.data):
- cp '${data.data_source}' circos/data/links-${hi}.txt &&
-#end for
-
-tar cvfz circos.tar.gz circos &&
-
-circos -conf circos/conf/circos.conf
- ]]>
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diff -r ae9994cf526f -r 014a21767ac4 circos.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/circos.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,530 @@
+
+
+ visualizes data in a circular layout
+
+ macros.xml
+ macros_conffiles.xml
+ macros_tests.xml
+
+
+ circos --version
+ circos/conf/karyotype.txt &&
+#else if $reference_genome.ref.ref_source == 'karyotype':
+ cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
+#else if str($reference_genome.ref.ref_source) == 'history':
+ ## Process the karyotype.txt file
+ python
+ '$__tool_directory__/fasta-to-karyotype.py'
+ genomeref.fa
+ '${ideogram.color}'
+
+ > circos/conf/karyotype.txt &&
+#end if
+
+touch circos/conf/karyotype-colors.conf &&
+#if $ideogram.bands.bands:
+ #if $ideogram.bands.convert_bands:
+ python '$__tool_directory__/process-cytogenetic-bands.py'
+ '${ideogram.bands.bands}'
+ >> circos/conf/karyotype.txt
+ 2> circos/conf/karyotype-colors.conf &&
+ #else
+ cat '${ideogram.bands.bands}'
+ >> circos/conf/karyotype.txt &&
+ #end if
+#end if
+
+#if $plot_options.colour_profile:
+ #if str($plot_options.colour_profile) == 'cg':
+ cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf &&
+ #end if
+#end if
+
+mv '$circos_conf' circos/conf/circos.conf &&
+mv '$ticks_conf' circos/conf/ticks.conf &&
+mv '$ideogram_conf' circos/conf/ideogram.conf &&
+mv '$data_conf' circos/conf/data.conf &&
+mv '$highlight_conf' circos/conf/highlight.conf &&
+mv '$links_conf' circos/conf/links.conf &&
+mv '$test_case_conf' circos/conf/galaxy_test_case.json &&
+
+## Highlights
+#for $hi, $data in enumerate($sec_highlight.data):
+cp '${data.data_source}' circos/data/highlight-${hi}.txt &&
+#end for
+
+## 2D Data Plots
+#for $hi, $data in enumerate($sec_tdd.data):
+ cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt &&
+#end for
+
+## Link Tracks
+#for $hi, $data in enumerate($sec_links.data):
+ cp '${data.data_source}' circos/data/links-${hi}.txt &&
+#end for
+
+#if $outputs.tar == "yes"
+ tar cvfz circos.tar.gz circos >/dev/null
+#else
+ echo ''
+#end if
+
+#if $outputs.svg == "yes" or $outputs.png == "yes":
+ && circos -conf circos/conf/circos.conf -noparanoid
+#end if
+ ]]>
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diff -r ae9994cf526f -r 014a21767ac4 colours/cg.conf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/colours/cg.conf Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,166 @@
+# RGB color definition. Colors are refered to within configuration files
+# by their name. In order to use a color, you must define it here.
+#
+# e.g. if you really must use 'bisque', then add
+#
+# bisque = 255,228,196
+#
+# Many useful colors are already defined. In general, given a HUE, these
+# colors are defined
+#
+# vlHUE (very light HUE, e.g. vlred)
+# lHUE (light HUE, e.g. red)
+# HUE (e.g. red)
+# dHUE (dark HUE, e.g. dred)
+#
+# In addition to hues, two other color groups are defined.
+#
+# - cytogenetic band colors (e.g. gposNNN, acen, stalk, etc.) which
+# correspond to colors on ideogram bands
+# - UCSC chromosome color palette (e.g. chrNN, chrUn, chrNA)
+
+optblue = 55,133,221
+optgreen = 55,221,125
+optyellow = 221,215,55
+optorange = 221,164,55
+optred = 221,55,55
+optviolet = 145,55,221
+optpurple = 219,55,221
+
+white = 255,255,255
+vvvvlgrey = 250,250,250
+vvvlgrey = 240,240,240
+vvlgrey = 230,230,230
+vlgrey = 220,220,220
+lgrey = 210,210,210
+grey = 200,200,200
+dgrey = 170,170,170
+vdgrey = 140,140,140
+vvdgrey = 100,100,100
+vvvdgrey = 70,70,70
+vvvvdgrey = 40,40,40
+black = 0,0,0
+
+vlred = 255,193,200
+lred = 255,122,137
+red = 247,42,66
+dred = 205,51,69
+
+vlgreen = 204,255,218
+lgreen = 128,255,164
+green = 51,204,94
+dgreen = 38,153,71
+
+vlblue = 128,176,255
+lblue = 64,137,255
+blue = 54,116,217
+dblue = 38,82,153
+
+vlpurple= 242,128,255
+lpurple = 236,64,255
+purple = 189,51,204
+dpurple = 118,32,128
+
+vlyellow = 255,253,202
+lyellow = 255,252,150
+yellow = 255,255,0
+dyellow = 191,186,48
+
+lime = 186,255,0
+
+vlorange = 255,228,193
+lorange = 255,187,110
+orange = 255,136,0
+dorange = 221,143,55
+
+pink = 255,105,180
+
+# CGI colors
+# bluegray
+cgi1 = 58,111,143
+# orange
+cgi2 = 240,142,79
+# mediumgray
+cgi3 = 92,112,124
+# green
+cgi4 = 71,170,66
+# mustard
+cgi5 = 193,202,92
+# dullred
+cgi6 = 217,83,30
+# lightgray
+cgi7 = 174,185,191
+# darkturquoiseblue
+cgi8 = 0,138,176
+# purpleblue
+cgi9 = 87,96,172
+
+# functional colors
+frameshift = 217,83,30
+disrupt = 217,83,30
+nonsense = 217,83,30
+misstart = 217,83,30
+nonstop = 87,96,172
+missense = 87,96,172
+insert = 87,96,172
+delete = 87,96,172
+
+# karyotype colors
+
+gpos100 = 0,0,0
+gpos = 0,0,0
+gpos75 = 130,130,130
+gpos66 = 160,160,160
+gpos50 = 200,200,200
+gpos33 = 210,210,210
+gpos25 = 200,200,200
+gvar = 220,220,220
+gneg = 255,255,255
+acen = 217,47,39
+stalk = 100,127,164
+
+# others
+
+select = 135,177,255
+
+# new york times cmyk-safe
+
+# roygbiv - normal
+nyt_blue = 104,152,178
+nyt_green = 137,129,96
+nyt_yellow = 241,221,117
+nyt_orange = 230,146,57
+nyt_red = 217,47,39
+
+# chromosome color map (UCSC)
+
+chr1 = 153,102,0
+chr2 = 102,102,0
+chr3 = 153,153,30
+chr4 = 204,0,0
+chr5 = 255,0,0
+chr6 = 255,0,204
+chr7 = 255,204,204
+chr8 = 255,153,0
+chr9 = 255,204,0
+chr10 = 255,255,0
+chr11 = 204,255,0
+chr12 = 0,255,0
+chr13 = 53,128,0
+chr14 = 0,0,204
+chr15 = 102,153,255
+chr16 = 153,204,255
+chr17 = 0,255,255
+chr18 = 204,255,255
+chr19 = 153,0,204
+chr20 = 204,51,255
+chr21 = 204,153,255
+chr22 = 102,102,102
+chr23 = 153,153,153
+chrX = 153,153,153
+chr24 = 204,204,204
+chrY = 204,204,204
+chrM = 204,204,153
+chr0 = 204,204,153
+chrUn = 121,204,61
+chrNA = 255,255,255
diff -r ae9994cf526f -r 014a21767ac4 fasta-to-karyotype.py
--- a/fasta-to-karyotype.py Thu Oct 04 06:05:31 2018 -0400
+++ b/fasta-to-karyotype.py Tue Sep 17 16:54:57 2019 -0400
@@ -3,46 +3,14 @@
from Bio import SeqIO
-
-for idx, seq in enumerate(SeqIO.parse(sys.argv[1], 'fasta')):
- sys.stdout.write("chr - {seq_id} {idx} 0 {length} set3-12-qual-{color}\n".format(
- seq_id=seq.id, idx=idx, length=len(seq), color=((idx + 1) % 12)
- ))
-
-if len(sys.argv) > 2:
- # band hs1 p36.32 p36.32 2200000 5100000 gpos25
- # band hs1 p36.31 p36.31 5100000 6900000 gneg
- # band hs1 p36.23 p36.23 6900000 8800000 gpos25
- COLS = ('chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand',
- 'thickStart', 'thickEnd', 'itemRgb')
- with open(sys.argv[2], 'r') as handle:
- for line in handle:
- lineData = dict(zip(COLS, line.split()))
- sys.stdout.write("band {chrom} {name} {name} {chromStart} {chromEnd} {color}\n".format(
- # Can access name because requiring >bed3
- name=lineData['name'],
- chrom=lineData['chrom'],
- chromStart=lineData['chromStart'],
- chromEnd=lineData['chromEnd'],
- # ????
- color=lineData.get('itemRgb', 'gpos50'),
- ))
- # band
- # ID
- # parentChr
- # parentChr
- # START
- # END COLOR
-
-# chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
-# chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
-# chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
-# name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
-# score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
-# strand - Defines the strand - either '+' or '-'.
-# thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
-# thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
-# itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
-# blockCount - The number of blocks (exons) in the BED line.
-# blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
-# blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
+# Process fasta data, extracting only headers
+for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")):
+ sys.stdout.write(
+ "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format(
+ seq_id=seq.id,
+ idx=idx,
+ length=len(seq),
+ color=((idx + 1) % 12),
+ theme=sys.argv[2],
+ )
+ )
diff -r ae9994cf526f -r 014a21767ac4 gc_skew.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gc_skew.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,22 @@
+import sys
+
+import pyBigWig
+from Bio import SeqIO
+from Bio import SeqUtils
+
+
+span = int(sys.argv[2])
+bw = pyBigWig.open(sys.argv[3], "w")
+
+# Prepare header separately because ugh
+data = []
+for rec in SeqIO.parse(sys.argv[1], "fasta"):
+ data.append((rec.id, len(rec)))
+bw.addHeader(data)
+
+for rec in SeqIO.parse(sys.argv[1], "fasta"):
+ gc = SeqUtils.GC_skew(rec.seq, span)
+
+ bw.addEntries(rec.id, 0, values=list(gc), span=span, step=span)
+
+bw.close()
diff -r ae9994cf526f -r 014a21767ac4 gc_skew.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gc_skew.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,63 @@
+
+
+ calculates skew over genomic sequences
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 genome-lengths-to-karyotype.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genome-lengths-to-karyotype.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+import csv
+import sys
+
+
+idx = 0
+with open(sys.argv[1], "r") as csvfile:
+ spamreader = csv.reader(csvfile, delimiter="\t", quotechar='"')
+ for row in spamreader:
+ if len(row) < 2:
+ continue
+
+ seq_id = row[0]
+ length = row[1]
+
+ sys.stdout.write(
+ "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format(
+ seq_id=seq_id,
+ idx=idx,
+ length=length,
+ color=((idx + 1) % 12),
+ theme=sys.argv[2],
+ )
+ )
+ idx += 1
diff -r ae9994cf526f -r 014a21767ac4 macros.xml
--- a/macros.xml Thu Oct 04 06:05:31 2018 -0400
+++ b/macros.xml Tue Sep 17 16:54:57 2019 -0400
@@ -1,21 +1,69 @@
- 0.9-RC2
+ 0.69.8
+
+ @CIRCOS_VERSION@+galaxy1
+
- circos
+ circos
python
bcbiogff
biopython
+ pybigwig
+ circos-tools
+
+
+#def circosColor($value)
+ #set $value = str($value)
+ #set $r = int($value[1:3], 16)
+ #set $g = int($value[3:5], 16)
+ #set $b = int($value[5:], 16)
+$r, $g, $b
+#end def
+#def circosColorAlpha($value, $alpha)
+ #set $value = str($value)
+ #set $r = int($value[1:3], 16)
+ #set $g = int($value[3:5], 16)
+ #set $b = int($value[5:], 16)
+ #set $a = float($alpha)
+$r, $g, $b, $a
+#end def
+#def chromosomesToOrder($value)
+ #set $q = ','.join([x if ':' not in x else x[x:x.index(':')] for x in str($value).split(';')])
+ $q
+#end def
+
+
10.1101/gr.092759.109
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+ token_value="#000000"
+ token_help=""
+ >
+
+
+
+
+
+
+
+
Qualitative: Accent
-
+
@@ -98,11 +140,26 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
@@ -114,8 +171,8 @@
@@ -130,8 +187,9 @@
+
-
+
@@ -139,20 +197,38 @@
-
-
+
+
+
+
+
+
-
-
+
+
+ help="Set to the name of the qualifier in the file you wish to compare against" />
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -165,7 +241,7 @@
-
+
@@ -174,7 +250,7 @@
-
+
@@ -203,7 +279,8 @@
-
+
+
@@ -256,6 +333,9 @@
+
+
+
@@ -276,7 +356,7 @@
-
+
@@ -339,7 +419,7 @@
-
+
diff -r ae9994cf526f -r 014a21767ac4 macros_conffiles.xml
--- a/macros_conffiles.xml Thu Oct 04 06:05:31 2018 -0400
+++ b/macros_conffiles.xml Tue Sep 17 16:54:57 2019 -0400
@@ -2,55 +2,123 @@
>
<>
+
+
+<>
+
+#for $hi, $data in enumerate($sec_tdd.data):
+ #set plot_type = str($data.plot_format.plot_format_select)
+ #if str($plot_type) == 'tile':
+ color-tile-$hi = $circosColor($data.plot_format.format_specific.fill_color)
+ #end if
+#end for
+
+
karyotype = karyotype.txt
+#if str($ideogram.units) == 'bases':
+chromosomes_units = 1
+#else if str($ideogram.units) == 'kb':
+chromosomes_units = 1000
+#else if str($ideogram.units) == 'mb':
+chromosomes_units = 1000000
+#else:
+chromosomes_units = 1000000000
+#end if
+
+#if $ideogram.limit_chromosomes:
+chromosomes = $ideogram.limit_chromosomes
+chromosomes_order = $chromosomesToOrder($ideogram.limit_chromosomes)
+chromosomes_display_default = no
+#end if
+
+#if $ideogram.chromosomes_reverse:
+chromosomes_reverse = $ideogram.chromosomes_reverse
+#end if
- <>
+ # Transcluded from etc/image.generic.conf
+ dir = .
+ file = circos.png
+#if $outputs.png:
+ png = yes
+#end if
+#if $outputs.svg:
+ svg = yes
+#end if
+ # by default angle = 0 is at 3 o'clock position
+ angle_offset = -90
+ auto_alpha_colors = yes
+ auto_alpha_steps = 5
+#if str($plot_options.background.background_select) == 'transparent':
+ background = transparent
+#else
+ background = $circosColor($plot_options.background.background_color)
+#end if
+ radius* = ${plot_options.radius}p
<>
<>
-
- <>
-
-
- <>
-
+<>
+<>
+<>
]]>
radius = ${ticks.radius}r
- color = $circosColor($ticks.color)
+ color = black
+ skip_first_label = ${ticks.skip_first_label}
+ skip_last_label = ${ticks.skip_last_label}
thickness = 2p
- multiplier = ${ticks.multiplier}
+
+ # Multiplier controls how 'u' behaves when used in numbers.
+ #if str($ideogram.units) == 'bases':
+ multiplier = 1
+ #else if str($ideogram.units) == 'kb':
+ multiplier = 1e-3
+ #else if str($ideogram.units) == 'mb':
+ multiplier = 1e-6
+ #else if str($ideogram.units) == 'gb':
+ multiplier = 1e-9
+ #end if
#for $tick_group in $ticks.tick_group:
spacing = ${tick_group.spacing}
size = ${tick_group.size}p
- show_label = ${tick_group.show_tick_labels}
- label_size = ${tick_group.label_size}p
- label_offset = ${tick_group.label_offset}p
- format = ${tick_group.format} kb
- ## TODO: figure out automated tick labels
- ##if ${ticks.multiplier} * ${tick_group.spacing}
+ show_label = ${tick_group.ticks.show_tick_labels}
+ color = $circosColor($tick_group.color)
+
+ #if str($tick_group.ticks.show_tick_labels) == 'yes':
+ label_size = ${tick_group.ticks.label_size}p
+ label_offset = ${tick_group.ticks.label_offset}p
+ #if $tick_group.ticks.format_ext:
+ #if str($ideogram.units) == 'bases':
+ format = ${tick_group.ticks.format}
+ #else if str($ideogram.units) == 'kb':
+ format = ${tick_group.ticks.format} Kb
+ #else if str($ideogram.units) == 'mb':
+ format = ${tick_group.ticks.format} Mb
+ #else if str($ideogram.units) == 'gb':
+ format = ${tick_group.ticks.format} Gb
+ #end if
+ #else
+ format = ${tick_group.ticks.format}
+ #end if
+ #end if
#end for
@@ -59,9 +127,8 @@
-
## spacing between ideograms
default = ${ideogram.spacing}r
@@ -71,67 +138,35 @@
radius = ${ideogram.radius}r
thickness = ${ideogram.thickness}p
fill = yes
-
show_label = ${ideogram.ideogram_labels.show_label}
- label_radius = dims(ideogram,radius) + 0.075r
- label_size = 24
+ label_radius = dims(ideogram,radius) + ${ideogram.ideogram_labels.radius_offset}r
+ label_size = ${ideogram.ideogram_labels.size}
label_parallel = ${ideogram.ideogram_labels.parallel}
+ #if $ideogram.bands.bands:
show_bands = yes
- fill_bands = yes
- band_transparency = 4
-
+ #else
+ show_bands = no
+ #end if
+ fill_bands = ${ideogram.bands.fill_bands}
+ #if int($ideogram.bands.band_transparency) > 0:
+ band_transparency = ${ideogram.bands.band_transparency}
+ #end if
+ band_stroke_color = $circosColor($ideogram.bands.band_stroke_color)
+ band_stroke_thickness = ${ideogram.bands.band_stroke_thickness}
]]>
-
-
- #set plot_type = str($data.plot_format.plot_format_select)
- #def circosColor($value)
- #set $value = str($value)
- #set $r = int($value[1:3], 16)
- #set $g = int($value[3:5], 16)
- #set $b = int($value[5:], 16)
- $r, $g, $b
- #end def
-
- type = ${plot_type}
- file = data/data-${hi}.txt
-
- r1 = ${data.r1}r
- r0 = ${data.r0}r
- orientation = ${data.orientation}
-
-#if str($plot_type) == 'histogram':
- extend_bin = ${data.plot_format.format_specific.extend_bins}
- fill_color = ${data.plot_format.format_specific.fill_color}
-#else if str($plot_type) == 'heatmap':
- color = $circosColor($data.plot_format.format_specific.fill_color)
- scale_log_base = ${data.plot_format.format_specific.scale_log_base}
-#else if str($plot_type) == 'line':
- color = $circosColor($data.plot_format.format_specific.color)
- thickness = ${data.plot_format.format_specific.thickness}
-#else if str($plot_type) == 'scatter':
- glyph = ${data.plot_format.format_specific.glyph}
- glyph_size = ${data.plot_format.format_specific.glyph_size}
- color = $circosColor($data.plot_format.format_specific.color)
- stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
- stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
-#else if str($plot_type) == 'tile':
- color = ${data.plot_format.format_specific.color}
- stroke_color = $circosColor($data.plot_format.format_specific.color)
- stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
- layers = ${data.plot_format.format_specific.layers}
- thickness = ${data.plot_format.format_specific.thickness}
- padding = ${data.plot_format.format_specific.padding}
-
- layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
- #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
- layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
- #end if
-#end if
+
+
+#for $hi, $data in enumerate($sec_highlight.data):
+
+ file = data/highlight-${hi}.txt # ${data.data_source.element_identifier}
+ r1 = ${data.r1}r
+ r0 = ${data.r0}r
+ fill_color = $circosColor($data.fill_color)
#for $rule in $data.sec_rule.rules:
@@ -143,19 +178,177 @@
#set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
condition = $on_str
#elif str($condition.application.application_select) == "pos":
- #if float($condition.application.pos_gt) != 0:
+ #if $condition.application.pos_gt:
condition = var(start) > $condition.application.pos_gt
#end if
- #if float($condition.application.pos_lt) != 0:
+ #if $condition.application.pos_lt:
+ #if $condition.application.pos_lt_sub == 'yes':
+ condition = var(end) < chrlen(var(chr)) - $condition.application.pos_lt
+ #else
+ condition = var(end) < $condition.application.pos_lt
+ #end if
+ #end if
+ #elif str($condition.application.application_select) == "value":
+ #if $condition.application.pos_gt:
+ condition = var(value) > $condition.application.pos_gt
+ #end if
+
+ #if $condition.application.pos_lt:
+ condition = var(value) < $condition.application.pos_lt
+ #end if
+ #elif str($condition.application.application_select) == "var":
+ condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
+ #elif str($condition.application.application_select) == "random":
+ condition = rand() < ${condition.application.value}
+ #end if
+ #end for
+
+ #for $action in $rule.actions:
+ #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
+ #set x_fill_color = $action.action.action_value
+ #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
+ #set x_min = $x_fill_color_count if $action.action.invert else 1
+ #set x_max = 1 if $action.action.invert else $x_fill_color_count
+ #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
+
+ $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
+ #else
+ $action.action.action_select = $circosColor($action.action.action_value)
+ #end if
+ #end for
+ $rule.continue_flow
+
+ #end for
+
+
+#end for
+
+ ]]>
+
+
+
+
+
+@UTILS@
+
+#for $hi, $data in enumerate($sec_tdd.data):
+
+ #set plot_type = str($data.plot_format.plot_format_select)
+ file = data/data-${hi}.txt # ${data.plot_format.data_source.element_identifier}
+ r1 = ${data.r1}r
+ r0 = ${data.r0}r
+ orientation = ${data.orientation}
+ #if str($data.minmax.minmax_select) == 'yes':
+ min = ${$data.minmax.min_value}
+ max = ${$data.minmax.max_value}
+ #end if
+
+#if str($plot_type) in ('histogram', 'histogram-stacked'):
+ type = histogram
+ extend_bin = ${data.plot_format.format_specific.extend_bins}
+ #if str($plot_type) == 'histogram':
+ fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
+ #else:
+ fill_color = $data.plot_format.format_specific.fill_color
+ #end if
+ fill_under = ${data.plot_format.format_specific.fill_under}
+ color = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
+ thickness = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'heatmap':
+ type = ${plot_type}
+ color = ${data.plot_format.format_specific.fill_color}
+ scale_log_base = ${data.plot_format.format_specific.scale_log_base}
+#else if str($plot_type) == 'line':
+ type = ${plot_type}
+ color = $circosColor($data.plot_format.format_specific.stroke_color)
+ thickness = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'scatter':
+ type = ${plot_type}
+ glyph = ${data.plot_format.format_specific.glyph}
+ glyph_size = ${data.plot_format.format_specific.glyph_size}
+ # So this option is ignored, and we have added an always-on rule in the
+ # first place to override the colour. This is because this color option will
+ # only accept named colours, while you can override the colour in a rule
+ # block with an RGB colour.
+ #
+ # Additionally it is named "color" in a scatter track whilst in the rule
+ # you must override it with "fill_color"
+ color = $circosColor($data.plot_format.format_specific.fill_color)
+ stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
+ stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'tile':
+ type = ${plot_type}
+ color = color-tile-$hi
+ stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
+ stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
+ layers = ${data.plot_format.format_specific.layers}
+ thickness = ${data.plot_format.format_specific.thickness}
+ padding = ${data.plot_format.format_specific.padding}
+ margin = ${data.plot_format.format_specific.margin}u
+ layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
+ #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
+ layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
+ #end if
+#else if str($plot_type) == 'text':
+ type = ${plot_type}
+ #if $data.plot_format.format_specific.link.show_link == "yes":
+ show_links = yes
+ link_dims = ${data.plot_format.format_specific.link.link_dims}
+ link_thickness = ${data.plot_format.format_specific.link.link_thickness}p
+ link_color = ${data.plot_format.format_specific.link.link_color}
+ #else
+ show_links = no
+ #end if
+
+ #if $data.plot_format.format_specific.snuggle.label_snuggle == "yes":
+ label_snuggle = ${data.plot_format.format_specific.snuggle.label_snuggle}
+ max_snuggle_distance = ${data.plot_format.format_specific.snuggle.max_snuggle_distance}r
+ snuggle_sampling = ${data.plot_format.format_specific.snuggle.snuggle_sampling}
+ snuggle_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_tolerance}r
+ snuggle_link_overlap_test = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_test}
+ snuggle_link_overlap_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_tolerance}p
+ snuggle_refine = ${data.plot_format.format_specific.snuggle.snuggle_refine}
+ #end if
+
+ label_size = ${data.plot_format.format_specific.label_size}p
+ label_font = condensed
+ padding = 0p
+ rpadding = 0p
+#end if
+
+
+ #if str($plot_type) == 'scatter':
+
+ # Workaround for above commented colour bug.
+ condition = 1
+ fill_color = $circosColor($data.plot_format.format_specific.fill_color)
+ flow = continue
+
+ #end if
+ #for $rule in $data.sec_rule.rules:
+
+ #for $condition in $rule.conditions
+ #if str($condition.application.application_select) == "1":
+ condition = 1
+ #elif str($condition.application.application_select) == "on":
+ #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
+ condition = $on_str
+ #elif str($condition.application.application_select) == "pos":
+ #if $condition.application.pos_gt:
+ condition = var(start) > $condition.application.pos_gt
+ #end if
+
+ #if $condition.application.pos_lt:
condition = var(start) < $condition.application.pos_lt
#end if
#elif str($condition.application.application_select) == "value":
- #if float($condition.application.pos_gt) != 0:
+ #if $condition.application.pos_gt:
condition = var(value) > $condition.application.pos_gt
#end if
- #if float($condition.application.pos_lt) != 0:
+ #if $condition.application.pos_lt:
condition = var(value) < $condition.application.pos_lt
#end if
#elif str($condition.application.application_select) == "var":
@@ -169,9 +362,19 @@
#set x_fill_color_count = int(str($x_fill_color).split('-')[1])
#set x_min = $x_fill_color_count if $action.action.invert else 1
#set x_max = 1 if $action.action.invert else $x_fill_color_count
- #set color_action = "fill_color" if str($plot_type) == 'histogram' else "color"
+ #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
$color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
+ #elif str($action.action.action_select) in ('fill_color', 'stroke_color'):
+ #if str($plot_type) in ('tile', ):
+ color = $circosColor($action.action.action_value)
+ #else:
+ #if str($action.action.action_select) == "stroke_color" and str($plot_type) == "histogram":
+ color = $circosColor($action.action.action_value)
+ #else
+ $action.action.action_select = $circosColor($action.action.action_value)
+ #end if
+ #end if
#else
$action.action.action_select = ${action.action.action_value}
#end if
@@ -203,44 +406,39 @@
#end for
+
]]>
#for $hi, $data in enumerate($sec_links.data):
- #def circosColor($value)
- #set $value = str($value)
- #set $r = int($value[1:3], 16)
- #set $g = int($value[3:5], 16)
- #set $b = int($value[5:], 16)
- $r, $g, $b
- #end def
-
- file = data/links-${hi}.txt
-
- radius = ${data.radius}r
- ribbon = ${data.linktype.ribbon}
- #if $data.linktype.ribbon == 'yes'
- ${data.linktype.twist}
- #end if
- color = $circosColor($data.color)
+ file = data/links-${hi}.txt
+ radius = ${data.radius}r
+ ribbon = ${data.linktype.ribbon}
+ #if $data.linktype.ribbon == 'yes'
+ ${data.linktype.twist}
+ #if $data.linktype.pattern != 'solid':
+ pattern = ${data.linktype.pattern}
+ #end if
+ #end if
+ color = $circosColorAlpha($data.color, $data.color_alpha)
bezier_radius = ${data.bezier_radius}r
thickness = ${data.thickness}
crest = ${data.advanced.crest}
bezier_radius_purity = ${data.advanced.bezier_radius_purity}
-
- #if $data.advanced.perturbation.perturb == 'yes'
- perturb = yes
- perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
- perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
- perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
- #end if
-
- #if $data.advanced.zdepth
- z = ${data.advanced.zdepth}
- #end if
+ #if $data.advanced.perturbation.perturb == 'yes'
+ perturb = yes
+ perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
+ perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
+ perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
+ #end if
+ #if $data.advanced.zdepth
+ z = ${data.advanced.zdepth}
+ #end if
#for $rule in $data.sec_link_rule.rules:
@@ -251,6 +449,8 @@
condition = var($cond)
#elif $cond == 'always'
condition = 1
+ #elif $cond == 'random'
+ condition = rand() < ${condition.application.value}
#else
#set op = $condition.application.comparison.compare
#set val = $condition.application.comparison.compval
@@ -258,6 +458,8 @@
#if $op == 'between' or $op == 'fromto'
#set val2 = $condition.application.comparison.compval2
#set c=''.join([str($op),"(",str($val),",",str($val2),")"])
+ #elif $op == 'on'
+ #set c='(var(chr1) eq "%s" or var(chr2) eq "%s")' % (str($val), str($val))
#else
#set c=''.join([str($op),"(",str($val),")"])
#end if
@@ -280,7 +482,7 @@
#set actiontype = $action.action.action_select
#if $actiontype == 'color':
#if $action.action.dynamic.dynamic_select == "static":
- #set actionval = $circosColor($action.action.dynamic.action_value)
+ #set actionval = $circosColorAlpha($action.action.dynamic.action_value, $action.action.dynamic.action_value_alpha)
$actiontype = $actionval
#else
#set x_fill_color = $action.action.dynamic.action_value
@@ -312,113 +514,11 @@
#end for
+
]]>
-
-
-
-
-
-
-
-
-
-
- #if $reference_genome.reference_genome_source != 'karyotype':
- #if $reference_genome.bands:
-
- #end if
- #end if
-
-
-
-
-
- #for $idx, $tick_group in enumerate($ticks.tick_group):
-
-
-
-
-
-
- #end for
-
- #for $idx, $data_group in enumerate($sec_tdd.data):
-
-
-
-
-
- #if str($data_group.plot_format.plot_format_select) == 'histogram':
- #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
-
-
-
- #else if str($data_group.plot_format.plot_format_select) == 'heatmap':
- #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
-
-
-
- #else if str($data_group.plot_format.plot_format_select) == 'line':
-
-
-
- #else if str($data_group.plot_format.plot_format_select) == 'scatter':
-
-
-
-
-
-
-
-
- #else if str($data_group.plot_format.plot_format_select) == 'tile':
-
-
-
-
-
-
-
-
- #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
-
- #end if
- #end if
- ## Next line intentionally blank
-
- #end for
-
-
-
-
-
- ]]>
+
diff -r ae9994cf526f -r 014a21767ac4 macros_tests.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_tests.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,91 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 process-cytogenetic-bands.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/process-cytogenetic-bands.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+import sys
+
+# band hs1 p36.32 p36.32 2200000 5100000 gpos25
+# band hs1 p36.31 p36.31 5100000 6900000 gneg
+# band hs1 p36.23 p36.23 6900000 8800000 gpos25
+COLS = (
+ "chrom",
+ "chromStart",
+ "chromEnd",
+ "name",
+ "score",
+ "strand",
+ "thickStart",
+ "thickEnd",
+ "itemRgb",
+)
+
+colormap = {}
+# Process optional cytogenetic bands
+# band
+# ID
+# parentChr
+# parentChr
+# START
+# END COLOR
+with open(sys.argv[1], "r") as handle:
+ for line in handle:
+ if line.startswith("#"):
+ continue
+
+ lineData = dict(zip(COLS, line.split()))
+ color = lineData.get("itemRgb", "gpos50")
+
+ if color not in colormap:
+ # Color MUST be an RGB triplet
+ if color.count(",") != 2:
+ continue
+ tmp = color.replace(",", "")
+ # Try interpreting it, without `,`s as an integer. If it fails this
+ # test there are non-numerical values and they might try and send
+ # us an `eval()` or a colour name. We do not currently support
+ # colour names just in case.
+ try:
+ int(tmp)
+ except ValueError:
+ # Does not look like an int
+ continue
+
+ colormap[color] = "gx-karyotype-%s" % len(colormap.keys())
+
+ sys.stderr.write(
+ "{colorName} = {color}\n".format(colorName=colormap[color], color=color)
+ )
+
+ sys.stdout.write(
+ "band {chrom} {name} {name} {chromStart} {chromEnd} {color}\n".format(
+ # Can access name because requiring >bed3
+ name=lineData["name"],
+ chrom=lineData["chrom"],
+ chromStart=lineData["chromStart"],
+ chromEnd=lineData["chromEnd"],
+ # 255,0,0 is a valid colour specifier
+ color=colormap[color],
+ )
+ )
+
+
+# chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
+# chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
+# chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
+# name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
+# score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
+# strand - Defines the strand - either '+' or '-'.
+# thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
+# thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
+# itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
+# blockCount - The number of blocks (exons) in the BED line.
+# blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+# blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
diff -r ae9994cf526f -r 014a21767ac4 resample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/resample.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,51 @@
+
+
+ reduce numbers of points in a dataset before plotting
+
+ macros.xml
+
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `__
+
+ This script is designed to convert very high-resolution data tracks to
+ low-resolution equivalents which are easier to interpret and faster to
+ draw.
+
+ ]]>
+
+
diff -r ae9994cf526f -r 014a21767ac4 scatter-from-wiggle.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scatter-from-wiggle.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+import logging
+import sys
+
+import pyBigWig
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger()
+
+if __name__ == "__main__":
+ bw = pyBigWig.open(sys.argv[1])
+ for chrom in sorted(bw.chroms().keys()):
+ for (start, end, value) in bw.intervals(chrom):
+ sys.stdout.write("%s\t%s\t%s\t%s\n" % (chrom, start, end, value))
diff -r ae9994cf526f -r 014a21767ac4 scatter-from-wiggle.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scatter-from-wiggle.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,30 @@
+
+
+ reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 tableviewer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tableviewer.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,641 @@
+
+
+ easily creates circos plots from tabular data
+
+ macros.xml
+
+
+ tmp &&
+
+make-conf -dir circos/data < tmp &&
+
+tar cvfz circos.tar.gz circos &&
+cd circos &&
+circos -conf etc/circos.conf &&
+mv circos.png ../ &&
+mv circos.svg ../
+ ]]>
+
+ blocks to define the percentile values and associated
+# color/stroke_color characteristics for ribbons. Percentile value defined
+# in the block (e.g. ) is the max percentile value for
+# cells associated with this block.
+# - color_remap=yes, color_autoremap=yes
+# Uses colors associated with each percentile window of size
+# percentile_sampling for each cell
+
+
+color_source = row
+percentile_source = larger
+color_transparency = 1
+color_remap = no
+color_autoremap = no
+
+
+color = dgrey
+transparency = 5
+
+
+
+transparency = 5
+
+
+
+transparency = 4
+
+
+
+transparency = 3
+
+
+
+transparency = 2
+stroke_color = black
+stroke_thickness = 1p
+
+
+
+transparency = 1
+stroke_color = black
+stroke_thickness = 3p
+
+
+
+
+
+color = vdgrey
+#stroke_color = black
+#stroke_thickness = 1p
+
+
+# If you are using color_autoremap=yes above, then
+# define the percentile sampling window and
+# the start/end HSV color values. Percentile window
+# colors are interpolated between this HSV pair.
+#
+# HSV = (hue saturation value)
+# hue=(0..360) saturation=(0..1) value=(0..1)
+
+percentile_sampling = 5
+
+# count - percentile based on counts
+# value - percentile based on value
+
+percentile_method = count
+
+# use all values or only unique values when
+# calculating percentiles
+percentile_unique_only = yes
+
+# use a function, f(X), to remap cell values when calculating percentiles
+# for the purpose of color mapping. This allows you to apply a remapping to how
+# colors are calculated, without actually changing the values. The remap
+# applies only if percentile_method=value
+
+# percentile_remap = sqrt(X)
+
+# Which cell value set to use for percentile color mapping
+# raw - original values
+# filtered - values that pass min/max filters
+# scaled - filtered values that have been scaled if use_scaling is set
+percentile_data_domain = raw
+
+
+h0 = 0
+s0 = 1
+v0 = 1
+h1 = 300
+s1 = 1
+v1 = 1
+
+
+# You can control the color and stroke of ribbons for each
+# quartile (q1, q2, q3, q4). Any values defined here will
+# overwrite colors determined by remapping.
+#
+# For example, if you have a lot of cells and wish to attenuate
+# the visibility of ribbons associated with small values, you can
+# set cell_q1_color=vvlgrey,cell_q1_nostroke=yes to fade the
+# ribbons into the background.
+
+#cell_q1_color = vvlgrey
+#cell_q2_color = vlgrey
+#cell_q3_color = lgrey
+#cell_q4_color = red
+#cell_q1_nostroke = yes
+#cell_q2_nostroke = yes
+#cell_q3_nostroke = yes
+#cell_q4_nostroke = yes
+
+# cell value multiplier, required when all data is small (e.g. <1), in which
+# case set the multiplier to something like 1000 because Circos
+# works only with integer scales
+
+data_mult = 1
+
+################################################################
+# Segment labels can be optionally set to a size that is
+# proportional to the size of the segment. Set min/max size
+# values here. If this line is commented out, then the label
+# size is determined by the circos.conf file used to draw the image
+
+#segment_label_size_range = 60,60
+
+# progression controls how fast the label size changes from
+# min to max (larger value of progression means values close to max
+# are achieved for smaller segments)
+
+segment_label_size_progression = 4
+
+segment_label_uppercase = no
+
+################################################################
+# Segment colors can be specified in the data file (in this
+# case use row_color_col and col_color_row), otherwise colors
+# are interpolated within an HSV range. Color interpolation can be
+# done in two ways: based on segment index (interpolation steps through
+# colors uniformly for each segment) and total size (interpolation
+# steps through colors in proportion to segment size).
+
+
+interpolate_type = size # size or count
+h0 = 0
+s0 = 0.8
+v0 = 0.9
+h1 = 300
+s1 = 0.8
+v1 = 0.9
+
+
+################################################################
+# Shorten the labels of segments. Specify whether to do this
+# with shorten_text=yes|no parameter and provide regular
+# expressions in string_replace which define the text to
+# replace.
+
+shorten_text = no
+
+
+chromosome = chr
+
+
+# exit on any error
+strict_sanity = yes
+
+################################################################
+# if the segment_prefix is set, then rows and columns will be
+# renamed to internal fields segment_prefix + DIGIT
+
+#segment_prefix = id
+color_prefix = color
+
+# field delimiter regular expression
+# if this is not defined, any whitespace will be considered a delimiter
+field_delim = \s
+
+# collapse adjacent delimiters?
+field_delim_collapse = yes
+
+# remove any leading space in the input file
+# by default, this is on - if you set this to "no", make sure that you don't have any leading spaces in your table!
+strip_leading_space = yes
+
+# remove quotes and thousand separators - concatenate characters to remove
+#
+# e.g. to remove characters a b c set remove_cell_rx=abc
+# e.g. to remove characters " ' , set remove_cell_rx="',
+remove_cell_rx = "',
+
+]]>
+ > directive.
+#
+# Some elements of the output image are toggled off by default
+# (e.g. row and column highlights, anchor links to segment labels,
+# tick marks).
+
+
+<>
+<>
+
+
+
+
+ default = 0.010r
+
+
+ thickness = 25p
+ stroke_thickness = 2
+ stroke_color = vdgrey
+ fill = yes
+ fill_color = $circosColor($labels.segment.color)
+
+ # fractional radius position of chromosome ideogram within image
+ radius = 0.70r
+ show_label = $labels.segment.show
+ label_font = $labels.segment.font
+ label_radius = dims(image,radius) - 50p
+ label_size = $labels.segment.size
+ label_parallel = $labels.segment.parallel
+
+ show_bands = no
+
+
+show_ticks = yes
+show_tick_labels = $labels.ticks.show
+
+
+ skip_first_label = no
+ skip_last_label = no
+ radius = dims(ideogram,radius_outer)
+ size = 12p
+ label_font = $labels.ticks.font
+ label_size = $labels.ticks.size
+ label_offset = 5p
+ format = %d
+ color = $circosColor($labels.ticks.color)
+ thickness = 2p
+
+
+ spacing_type = relative
+ rspacing = 0.1
+ show_label = yes
+ label_relative = yes
+ label_size = 20p
+ suffix = %
+ rmultiplier = 100
+ offset = 100p
+
+
+
+ spacing_type = relative
+ rspacing = 0.02
+ show_label = no
+ offset = 100p
+
+
+
+ spacing = 10u
+ show_label = yes
+
+
+
+ spacing = 1u
+ show_label = no
+
+
+
+karyotype = data/karyotype.txt
+
+
+ <>
+
+
+chromosomes_units = 10
+chromosomes_display_default = yes
+chromosomes_order_by_karyotype = yes
+
+
+ stroke_color = vdgrey
+ stroke_thickness = 1
+
+
+ show = yes
+ file = data/row.txt
+ r0 = 1r+300p
+ r1 = 1r+310p
+
+
+
+ show = yes
+ file = data/col.txt
+ r1 = 1r+330p
+ r0 = 1r+320p
+
+
+
+ show = yes
+ file = data/all.txt
+ r1 = 1r+280p
+ r0 = 1r+260p
+
+
+
+ file = data/cap.col.txt
+ r1 = 0.999r-10p
+ r0 = 0.999r-30p
+
+
+
+ file = data/cap.row.txt
+ r1 = 0.999r
+ r0 = 0.999r-20p
+
+
+
+
+
+ ribbon = yes
+ flat = yes
+ file = data/cells.txt
+ bezier_radius = 0.0r
+ radius = 0.999r-30p
+ thickness = 1
+ color = grey
+ stroke_color = dgrey
+ stroke_thickness = 1
+
+
+
+ condition = 1
+ radius1 = 0.999r-20p
+
+
+
+
+
+<>
+<>
+ ]]>
+
+
+
+
+
+
+
+
+
+ outputs['png']
+
+
+ outputs['svg']
+
+
+ outputs['tar']
+
+
+
+
+
+
+
+
+ `__ has a lot of useful information.
+
+You should provide a table that looks like:
+
+::
+
+ labels A B C
+ A 10 15 20
+ D 15 20 25
+ E 20 30 50
+
+The header column and row are strictly required.
+ ]]>
+
+
diff -r ae9994cf526f -r 014a21767ac4 test-data/0/out.png
Binary file test-data/0/out.png has changed
diff -r ae9994cf526f -r 014a21767ac4 test-data/0/out.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/0/out.svg Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,21 @@
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/0-0.wig
--- a/test-data/1/0-0.wig Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,503 +0,0 @@
-track type=wiggle_0 name="example" description="discontinuous sine wave"
-fixedStep chrom=ctgA start=1 step=100 span=20
-0
--0.506365641109759
--0.873297297213995
--0.999755839901149
--0.850919359639177
--0.467771805322476
-0.0441824483318732
-0.543970523363376
-0.893969648197021
-0.99780327442197
-0.826879540532003
-0.428264391396659
--0.0882786064717262
--0.580513008156313
--0.91289603861164
--0.993901956906654
--0.801224790676895
--0.387920558984219
-0.132202352755937
-0.615921726468774
-0.930039504416137
-0.988059506793465
-0.774005214886395
-0.34681910129778
--0.175867902248536
--0.650127523574896
--0.945366563696042
--0.980287334634812
--0.745273974144339
--0.305040291224202
-0.219189974282818
-0.683063594104854
-0.958847282055722
-0.970600619811948
-0.71508718178021
-0.262665724548229
--0.262083959018097
--0.714665612518583
--0.970455331081526
--0.959018280889002
--0.683503793877429
--0.219778160592474
-0.304466082686301
-0.744871858736274
-0.980168039762288
-0.945562938664219
-0.650585494129627
-0.176461360584952
--0.346253571205695
--0.773623338680308
--0.987966438766777
--0.930260871990585
--0.61639657336978
--0.132799924069858
-0.38736481184216
-0.800863899493182
-0.993835297491596
-0.913141966452114
-0.581003804007494
-0.0888791236810795
--0.427719512602322
--0.826540339206424
--0.997763153807204
--0.894239655996039
--0.544476309619657
--0.044784738601126
-0.467238859047214
-0.850602510646281
-0.999742336443933
-0.873590857634893
-0.50688542994917
-0.000602887030758908
--0.505845668220208
--0.873003419373278
--0.999768979974307
--0.851235899346026
--0.468304581575409
-0.043580142003502
-0.543464539388603
-0.893699315464349
-0.997843032362382
-0.827218441309355
-0.428809114528536
--0.0876780571755001
--0.580022001304441
--0.912649778958282
--0.993968255065378
--0.801585390637186
--0.388476165127704
-0.131604733390055
-0.615446655696971
-0.929817798797622
-0.988152215687393
-0.774386809762636
-0.347384505330554
--0.17527437998892
--0.64966931671649
--0.945169845112828
--0.980406273199548
--0.745675818665582
--0.305614388888252
-0.218601708303567
-0.682623146057239
-0.958675934707531
-0.97074555575544
-0.715508491127093
-0.263247394606515
--0.261502098227572
--0.714243783495441
--0.970309689616982
--0.959188931145217
--0.683943745214962
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--0.345122133665854
--0.772858742833902
--0.987779225450561
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--0.504805171046737
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--0.0864768631955748
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--0.174087144563029
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--0.50428464714101
--0.872119882400963
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--0.911909010016595
--0.994164981763242
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-0.988428187236296
-0.775529905025798
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--0.173493431828281
--0.648293279985113
--0.944577628388612
--0.980760950615372
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--0.307336014550815
-0.216836434486577
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-0.971178246338178
-0.716770858148409
-0.264991829836246
--0.259755946408727
--0.712976739390632
--0.969870649348633
--0.959698789831842
--0.685262107018665
--0.222130104859792
-0.302168143970983
-0.743260691160433
-0.979687298063475
-0.946345000960895
-0.652415009983898
-0.17883455038485
--0.34399019435602
--0.772093023335059
--0.987590576010932
--0.931142960240324
--0.618293718815172
--0.13518972446219
-0.385140417328934
-0.79941742514918
-0.993565047754595
-0.914122357899222
-0.582964873838637
-0.091280867284509
--0.425538444762198
--0.825180530889296
--0.997599044898223
--0.895316435894515
--0.546497473784151
--0.0471937347087195
-0.465105377598017
-0.849332024119238
-0.999684688874618
-0.874761922988011
-0.508962741027838
-0.00301443077113541
--0.503763939941528
--0.871824735950293
--0.999817906332802
--0.852498963013576
--0.470433982491772
-0.0411707604773582
-0.541438629983896
-0.892614737164045
-0.997998437093437
-0.828571036474523
-0.430986446472459
--0.0852755434877088
--0.57805586746054
--0.911661424007995
--0.994229834656976
--0.803024875624353
--0.390697175677724
-0.129213779751557
-0.613544137356508
-0.92892759749641
-0.988519459263516
-0.775910373196683
-0.349644856759043
--0.17289965603339
--0.647834129578325
--0.944379536061519
--0.980878463517946
--0.747280484962623
--0.30790966663318
-0.216247851967423
-0.680858874319544
-0.957987061413159
-0.971321770608431
-0.717191126305919
-0.265573115893276
--0.259173706691886
--0.712553872855609
--0.969723597478254
--0.959868045160799
--0.685701063017834
--0.22271788961521
-0.301593384195272
-0.742857223512596
-0.979566222305013
-0.946539656785734
-0.652871796525078
-0.179427685870145
--0.343424037051613
--0.771709742563807
--0.987495712830468
--0.931362636389977
--0.618767443774911
--0.13578705225865
-0.384583968225014
-0.799055079818084
-0.993496582423937
-0.91436662533687
-0.583454612012034
-0.0918812207856598
--0.424992790627422
--0.824839828674128
--0.997557111133059
--0.895584817555511
--0.547002268691819
--0.0477959413987577
-0.464571584118009
-0.849013630425847
-0.999669368573369
-0.87505389471161
-0.509481606783953
-0.0036173145149015
--0.503243049637554
--0.871529272615042
--0.999829229416663
--0.85281395456664
--0.470965905729547
-0.0405683771373384
-0.540931660176769
-0.892342781239334
-0.998036381447947
-0.828908432665215
-0.431530388323292
--0.0846748370315997
--0.577563808283757
--0.911413506635259
--0.994294326175203
--0.803384017503629
--0.391252073800153
-0.128615923384498
-0.613067949822471
-0.928704202868774
-0.988610371990796
-0.776290559345248
-0.350209627413543
--0.172305817394175
--0.647374743701449
--0.944181100478148
--0.980995619897873
--0.747680972860835
--0.308483206798754
-0.215659190848055
-0.680417187299892
-0.957813972427147
-0.971464941829636
-0.717611133783957
-0.266154305421701
--0.258591372772452
--0.71213074732663
--0.969576193139719
--0.960036951603826
--0.686139769783315
--0.223305593418733
-0.301018514798568
-0.742453485856362
-0.979444790500868
-0.946733968569148
-0.653328345765115
-0.180020756138357
--0.342857754921908
--0.77132618129705
--0.987400490722168
--0.931581974014641
--0.619240943829511
--0.13638433070021
-0.38402737933528
-0.798692444052197
-0.993427755984289
-0.914610560427116
-0.583944138115545
-0.0924815408904855
--0.424446982019324
--0.824498826652114
--0.997514814783015
--0.895852873695781
--0.547506864779039
--0.048398130716271
-0.464037621778865
-0.848694928139091
-0.99965368491949
-0.875345548376914
-0.51000028735736
-0.00422019694387214
--0.502721976418416
--0.871233492502601
-
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/1.gff3
--- a/test-data/1/1.gff3 Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,268 +0,0 @@
-##gff-version 3
-# Note: See http://song.sourceforge.net
-ctgA example contig 1 50001 . . . Name=ctgA
-ctgA example remark 1659 1984 1110 + . Name=f07;Note=This is an example
-ctgA example remark 3014 6130 999 + . Name=f06;Note=This is another example
-ctgA example remark 4715 5968 444 - . Name=f05;Note=Ok! Ok! I get the message.
-ctgA example remark 13280 16394 203 + . Name=f08
-ctgA example remark 15329 15533 1000 + . Name=f10
-ctgA example remark 19157 22915 100 - . Name=f13
-ctgA example remark 22132 24633 320 + . Name=f15
-ctgA example remark 23072 23185 850 + . Name=f14
-ctgA example remark 24562 28338 208 + . Name=f02
-ctgA example remark 36034 38167 100 + . Name=f09
-ctgA example remark 36649 40440 300 - . Name=f03
-ctgA example remark 37242 38653 10 + . Name=f04
-ctgA example remark 44705 47713 400 - . Name=f01
-ctgA example remark 46990 48410 100 - . Name=f11
-ctgA example remark 49758 50000 3040 - . Name=f12
-
-ctgA example SNP 1000 1000 0.987 . . ID=FakeSNP1;Name=FakeSNP;Note=This is a fake SNP that should appear at 1000 with length 1
-
-ctgA example remark 1000 2000 . . . Name=Remark:hga;Alias=hga
-ctgA example protein_coding_primary_transcript 1100 2000 . + . Name=Gene:hga;Alias=hga
-ctgA example polypeptide 1200 1900 . + . Name=Protein:HGA;Alias=hga
-ctgA example protein_coding_primary_transcript 1600 3000 . - . Name=Gene:hgb;Alias=hgb
-ctgA example polypeptide 1800 2900 . - . Name=Protein:HGB;Alias=hgb
-
-ctgA example polypeptide_domain 11911 15561 . + 502 Name=m11;Note=kinase
-ctgA example polypeptide_domain 13801 14007 . - 415 Name=m05;Note=helix loop helix
-ctgA example polypeptide_domain 14731 17239 . - 746 Name=m14;Note=kinase
-ctgA example polypeptide_domain 15396 16159 . + 40 Name=m03;Note=zinc finger
-ctgA example polypeptide_domain 17023 17675 . + 830 Name=m08;Note=7-transmembrane
-ctgA example polypeptide_domain 17667 17690 . + 943 Name=m13;Note=DEAD box
-ctgA example polypeptide_domain 18048 18552 . - 658 Name=m07;Note=7-transmembrane
-ctgA example polypeptide_domain 21748 25612 . + 467 Name=m12;Note=kinase
-ctgA example polypeptide_domain 28332 30033 . - 711 Name=m02;Note=HOX
-ctgA example polypeptide_domain 28342 28447 . - 533 Name=m10;Note=DEAD box
-ctgA example polypeptide_domain 30578 31748 . + 646 Name=m06;Note=SUSHI repeat
-ctgA example polypeptide_domain 33325 35791 . + 479 Name=m04;Note=Ig-like
-ctgA example polypeptide_domain 37497 40559 . - 711 Name=m15;Note=7-transmembrane
-ctgA example polypeptide_domain 46012 48851 . + 533 Name=m09;Note=kinase
-ctgA example polypeptide_domain 48253 48366 . + 646 Name=m01;Note=WD40
-
-ctgA example match 32329 32359 . + 825 Name=seg01
-ctgA example match 26122 26126 . + 185 Name=seg02
-ctgA example match 26497 26869 . + 502 Name=seg02
-ctgA example match 27201 27325 . + 442 Name=seg02
-ctgA example match 27372 27433 . + 970 Name=seg02
-ctgA example match 27565 27565 . + 519 Name=seg02
-ctgA example match 27813 28091 . + 592 Name=seg02
-ctgA example match 28093 28201 . + 475 Name=seg02
-ctgA example match 28329 28377 . + 17 Name=seg02
-ctgA example match 28829 29194 . + 276 Name=seg02
-ctgA example match 29517 29702 . + 492 Name=seg02
-ctgA example match 29713 30061 . + 465 Name=seg02
-ctgA example match 30329 30774 . + 525 Name=seg02
-ctgA example match 30808 31306 . + 619 Name=seg02
-ctgA example match 31516 31729 . + 248 Name=seg02
-ctgA example match 31753 32154 . + 613 Name=seg02
-ctgA example match 32595 32696 . + 701 Name=seg02
-ctgA example match 32892 32901 . + 724 Name=seg02
-ctgA example match 33127 33388 . + 977 Name=seg02
-ctgA example match 33439 33443 . + 502 Name=seg02
-ctgA example match 33759 34209 . + 415 Name=seg02
-ctgA example match 34401 34466 . + 746 Name=seg02
-ctgA example match 6885 7241 . - 40 Name=seg03
-ctgA example match 7410 7737 . - 830 Name=seg03
-ctgA example match 8055 8080 . - 943 Name=seg03
-ctgA example match 8306 8999 . - 658 Name=seg03
-ctgA example match 5233 5302 . - 467 Name=seg04
-ctgA example match 5800 6101 . - 711 Name=seg04
-ctgA example match 6442 6854 . - 533 Name=seg04
-ctgA example match 7106 7211 . - 646 Name=seg04
-ctgA example match 7695 8177 . - 479 Name=seg04
-ctgA example match 8545 8783 . - 568 Name=seg04
-ctgA example match 8869 8935 . - 62 Name=seg04
-ctgA example match 9404 9825 . - 191 Name=seg04
-ctgA example match 26503 26799 . - 645 Name=seg05
-ctgA example match 27172 27185 . - 774 Name=seg05
-ctgA example match 27448 27860 . - 643 Name=seg05
-ctgA example match 27887 28076 . - 361 Name=seg05
-ctgA example match 28225 28316 . - 444 Name=seg05
-ctgA example match 28777 29058 . - 109 Name=seg05
-ctgA example match 29513 29647 . - 67 Name=seg05
-ctgA example match 30108 30216 . - 964 Name=seg05
-ctgA example match 30465 30798 . - 563 Name=seg05
-ctgA example match 31232 31236 . - 313 Name=seg05
-ctgA example match 31421 31817 . - 530 Name=seg05
-ctgA example match 32010 32057 . - 788 Name=seg05
-ctgA example match 32208 32680 . - 441 Name=seg05
-ctgA example match 33053 33325 . - 152 Name=seg05
-ctgA example match 33438 33868 . - 226 Name=seg05
-ctgA example match 34244 34313 . - 838 Name=seg05
-ctgA example match 34605 34983 . - 529 Name=seg05
-ctgA example match 35333 35507 . - 822 Name=seg05
-ctgA example match 35642 35904 . - 107 Name=seg05
-ctgA example match 19249 19559 . + 404 Name=seg06
-ctgA example match 19975 20260 . + 882 Name=seg06
-ctgA example match 20379 20491 . + 16 Name=seg06
-ctgA example match 20533 21005 . + 645 Name=seg06
-ctgA example match 21122 21331 . + 237 Name=seg06
-ctgA example match 21682 22176 . + 36 Name=seg06
-ctgA example match 22374 22570 . + 893 Name=seg06
-ctgA example match 23025 23427 . + 169 Name=seg06
-ctgA example match 44191 44514 . - 295 Name=seg07
-ctgA example match 44552 45043 . - 645 Name=seg07
-ctgA example match 45373 45600 . - 683 Name=seg07
-ctgA example match 45897 46315 . - 580 Name=seg07
-ctgA example match 46491 46890 . - 291 Name=seg07
-ctgA example match 47126 47297 . - 880 Name=seg07
-ctgA example match 47735 47983 . - 587 Name=seg07
-ctgA example match 48447 48709 . - 159 Name=seg07
-ctgA example match 48931 49186 . - 496 Name=seg07
-ctgA example match 49472 49699 . - 921 Name=seg07
-ctgA example match 49957 50000 . - 226 Name=seg07
-ctgA example match 18509 18985 . + 915 Name=seg08
-ctgA example match 18989 19388 . + 791 Name=seg08
-ctgA example match 19496 19962 . + 600 Name=seg08
-ctgA example match 20093 20580 . + 140 Name=seg08
-ctgA example match 20970 21052 . + 460 Name=seg08
-ctgA example match 21270 21277 . + 228 Name=seg08
-ctgA example match 21685 22168 . + 373 Name=seg08
-ctgA example match 22564 22869 . + 570 Name=seg08
-ctgA example match 22958 23298 . + 831 Name=seg08
-ctgA example match 23412 23469 . + 811 Name=seg08
-ctgA example match 23932 23932 . + 22 Name=seg08
-ctgA example match 24328 24787 . + 894 Name=seg08
-ctgA example match 25228 25367 . + 463 Name=seg08
-ctgA example match 36616 37057 . - 736 Name=seg09
-ctgA example match 37208 37227 . - 409 Name=seg09
-ctgA example match 29771 29942 . + 402 Name=seg10
-ctgA example match 30042 30340 . + 513 Name=seg10
-ctgA example match 30810 31307 . + 22 Name=seg10
-ctgA example match 31761 31984 . + 228 Name=seg10
-ctgA example match 32374 32937 . + 752 Name=seg10
-ctgA example match 24228 24510 . + 35 Name=seg11
-ctgA example match 24868 25012 . + 276 Name=seg11
-ctgA example match 25212 25426 . + 709 Name=seg11
-ctgA example match 25794 25874 . + 666 Name=seg11
-ctgA example match 26075 26519 . + 604 Name=seg11
-ctgA example match 26930 26940 . + 31 Name=seg11
-ctgA example match 26975 27063 . + 764 Name=seg11
-ctgA example match 27415 27799 . + 973 Name=seg11
-ctgA example match 27880 27943 . + 823 Name=seg11
-ctgA example match 28225 28346 . + 931 Name=seg11
-ctgA example match 28375 28570 . + 697 Name=seg11
-ctgA example match 28758 29041 . + 241 Name=seg11
-ctgA example match 29101 29302 . + 343 Name=seg11
-ctgA example match 29604 29702 . + 771 Name=seg11
-ctgA example match 29867 29885 . + 147 Name=seg11
-ctgA example match 30241 30246 . + 949 Name=seg11
-ctgA example match 30575 30738 . + 928 Name=seg11
-ctgA example match 12531 12895 . + 693 Name=seg12
-ctgA example match 13122 13449 . + 750 Name=seg12
-ctgA example match 13452 13745 . + 502 Name=seg12
-ctgA example match 13908 13965 . + 177 Name=seg12
-ctgA example match 13998 14488 . + 605 Name=seg12
-ctgA example match 14564 14899 . + 939 Name=seg12
-ctgA example match 15185 15276 . + 249 Name=seg12
-ctgA example match 15639 15736 . + 597 Name=seg12
-ctgA example match 15745 15870 . + 364 Name=seg12
-ctgA example match 49406 49476 . + 706 Name=seg13
-ctgA example match 49762 50000 . + 605 Name=seg13
-ctgA example match 41137 41318 . - 729 Name=seg14
-ctgA example match 41754 41948 . - 21 Name=seg14
-ctgA example match 42057 42474 . - 63 Name=seg14
-ctgA example match 42890 43270 . - 356 Name=seg14
-ctgA example match 43395 43811 . - 70 Name=seg14
-ctgA example match 44065 44556 . - 430 Name=seg14
-ctgA example match 44763 45030 . - 730 Name=seg14
-ctgA example match 45231 45488 . - 531 Name=seg14
-ctgA example match 45790 46022 . - 247 Name=seg14
-ctgA example match 46092 46318 . - 552 Name=seg14
-ctgA example match 46816 46992 . - 547 Name=seg14
-ctgA example match 47449 47829 . - 879 Name=seg14
-ctgA example match 39265 39361 . - 750 Name=seg15
-ctgA example match 39753 40034 . - 875 Name=seg15
-ctgA example match 40515 40954 . - 135 Name=seg15
-ctgA example match 41252 41365 . - 534 Name=seg15
-ctgA example match 41492 41504 . - 653 Name=seg15
-ctgA example match 41941 42377 . - 374 Name=seg15
-ctgA example match 42748 42954 . - 847 Name=seg15
-ctgA example match 43401 43897 . - 15 Name=seg15
-ctgA example match 44043 44113 . - 905 Name=seg15
-ctgA example match 44399 44888 . - 868 Name=seg15
-ctgA example match 45281 45375 . - 462 Name=seg15
-ctgA example match 45711 46041 . - 262 Name=seg15
-ctgA example match 46425 46564 . - 823 Name=seg15
-ctgA example match 46738 47087 . - 7 Name=seg15
-ctgA example match 47329 47595 . - 928 Name=seg15
-ctgA example match 47858 47979 . - 64 Name=seg15
-ctgA example match 48169 48453 . - 305 Name=seg15
-
-# single exon gene - one CDS only
-ctgA bare_predicted CDS 10000 11500 . + 0 Name=Apple1;Note=CDS with no parent
-
-# multi-exon gene - several linked CDSs
-ctgA predicted mRNA 13000 17200 . + 0 ID=cds-Apple2;Name=Apple2;Note=mRNA with CDSs but no UTRs
-ctgA predicted CDS 13500 13800 . + 0 Parent=cds-Apple2
-ctgA predicted CDS 15000 15500 . + 1 Parent=cds-Apple2
-ctgA predicted CDS 16500 17000 . + 2 Parent=cds-Apple2
-
-ctgA exonerate mRNA 17400 23000 . + . ID=rna-Apple3;Name=Apple3;Note=mRNA with both CDSs and UTRs
-ctgA exonerate UTR 17400 17999 . + . Parent=rna-Apple3
-ctgA exonerate CDS 18000 18800 . + 0 Parent=rna-Apple3
-ctgA exonerate CDS 19000 19500 . + 1 Parent=rna-Apple3
-ctgA exonerate CDS 21000 21200 . + 2 Parent=rna-Apple3
-ctgA exonerate UTR 21201 23000 . + . Parent=rna-Apple3
-
-ctgA example gene 1050 9000 . + . ID=EDEN;Name=EDEN;Note=protein kinase
-ctgA example mRNA 1050 9000 . + . ID=EDEN.1;Parent=EDEN;Name=EDEN.1;Note=Eden splice form 1;Index=1
-ctgA example five_prime_UTR 1050 1200 . + . Parent=EDEN.1
-ctgA example CDS 1201 1500 . + 0 Parent=EDEN.1
-ctgA example CDS 3000 3902 . + 0 Parent=EDEN.1
-ctgA example CDS 5000 5500 . + 0 Parent=EDEN.1
-ctgA example CDS 7000 7608 . + 0 Parent=EDEN.1
-ctgA example three_prime_UTR 7609 9000 . + . Parent=EDEN.1
-
-ctgA example mRNA 1050 9000 . + . ID=EDEN.2;Parent=EDEN;Name=EDEN.2;Note=Eden splice form 2;Index=1
-ctgA example five_prime_UTR 1050 1200 . + . Parent=EDEN.2
-ctgA example CDS 1201 1500 . + 0 Parent=EDEN.2
-ctgA example CDS 5000 5500 . + 0 Parent=EDEN.2
-ctgA example CDS 7000 7608 . + 0 Parent=EDEN.2
-ctgA example three_prime_UTR 7609 9000 . + . Parent=EDEN.2
-
-ctgA example mRNA 1300 9000 . + . ID=EDEN.3;Parent=EDEN;Name=EDEN.3;Note=Eden splice form 3;Index=1
-ctgA example five_prime_UTR 1300 1500 . + . Parent=EDEN.3
-ctgA example five_prime_UTR 3000 3300 . + . Parent=EDEN.3
-ctgA example CDS 3301 3902 . + 0 Parent=EDEN.3
-ctgA example CDS 5000 5500 . + 1 Parent=EDEN.3
-ctgA example CDS 7000 7600 . + 1 Parent=EDEN.3
-ctgA example three_prime_UTR 7601 9000 . + . Parent=EDEN.3
-
-ctgA example BAC 1000 20000 . . . ID=b101.2;Name=b101.2;Note=Fingerprinted BAC with end reads
-ctgA example clone_start 1000 1500 . + . Parent=b101.2
-ctgA example clone_end 19500 20000 . - . Parent=b101.2
-
-ctgA est EST_match 1050 3202 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 654
-ctgA est match_part 1050 1500 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
-ctgA est match_part 3000 3202 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
-
-ctgA est EST_match 5410 7503 . - . ID=Match2;Name=agt830.3;Target=agt830.3 1 595
-ctgA est match_part 5410 5500 . - . Parent=Match2;Name=agt830.3;Target=agt830.3 505 595
-ctgA est match_part 7000 7503 . - . Parent=Match2;Name=agt830.3;Target=agt830.3 1 504
-
-ctgA est EST_match 1050 7300 . + . ID=Match3;Name=agt221.5;Target=agt221.5 1 1253
-ctgA est match_part 1050 1500 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 1 451
-ctgA est match_part 5000 5500 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 452 952
-ctgA est match_part 7000 7300 . + . Parent=Match3;Name=agt221.5;Target=agt221.5 953 1253
-
-ctgA est EST_match 7500 8000 . - . ID=Match4;Name=agt221.3;Target=agt221.3 1 501
-
-ctgA est EST_match 1150 7200 . + . ID=Match5;Name=agt767.5;Target=agt767.5 1 1153
-ctgA est match_part 1150 1500 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 1 351
-ctgA est match_part 5000 5500 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 352 852
-ctgA est match_part 7000 7200 . + . Parent=Match5;Name=agt767.5;Target=agt767.5 853 1153
-
-ctgA est EST_match 8000 9000 . - . ID=Match6;Name=agt767.3;Target=agt767.3 1 1001
-
-
-
-ctgB example contig 1 6079 . . . Name=ctgB
-ctgB example remark 1659 1984 . + . Name=f07;Note=This is an example
-ctgB example remark 3014 6130 . + . Name=f06;Note=This is another example
-ctgB example remark 4715 5968 . - . Name=f05;Note=ああ、この機能は、世界中を旅しています！
-##FASTA
->foobar
-ACTGATGATCGCTAGATGCTCGACTAGC
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/2.wig
--- a/test-data/1/2.wig Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,503 +0,0 @@
-track type=wiggle_0 name="example" description="discontinuous sine wave"
-fixedStep chrom=ctgA start=1 step=100 span=20
-0
--0.506365641109759
--0.873297297213995
--0.999755839901149
--0.850919359639177
--0.467771805322476
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-0.543970523363376
-0.893969648197021
-0.99780327442197
-0.826879540532003
-0.428264391396659
--0.0882786064717262
--0.580513008156313
--0.91289603861164
--0.993901956906654
--0.801224790676895
--0.387920558984219
-0.132202352755937
-0.615921726468774
-0.930039504416137
-0.988059506793465
-0.774005214886395
-0.34681910129778
--0.175867902248536
--0.650127523574896
--0.945366563696042
--0.980287334634812
--0.745273974144339
--0.305040291224202
-0.219189974282818
-0.683063594104854
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-0.970600619811948
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-0.262665724548229
--0.262083959018097
--0.714665612518583
--0.970455331081526
--0.959018280889002
--0.683503793877429
--0.219778160592474
-0.304466082686301
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-0.176461360584952
--0.346253571205695
--0.773623338680308
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--0.61639657336978
--0.132799924069858
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--0.427719512602322
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--0.505845668220208
--0.873003419373278
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--0.0876780571755001
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--0.17527437998892
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--0.745675818665582
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--0.261502098227572
--0.714243783495441
--0.970309689616982
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--0.683943745214962
--0.220366267018746
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--0.345687915259853
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--0.133397447114619
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--0.427174478343574
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--0.89450933876326
--0.544981897973607
--0.0453870125923442
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--0.505325511469513
--0.87270922421956
--0.999781756658628
--0.851552129651776
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--0.0870774760106846
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--0.389031630070668
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--0.174680794021833
--0.649210873720956
--0.94497278298608
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--0.746077392153944
--0.306188375469783
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--0.260920142388146
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--0.345122133665854
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--0.42662928881852
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--0.503763939941528
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--0.343424037051613
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--0.424992790627422
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--0.503243049637554
--0.871529272615042
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--0.0846748370315997
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--0.803384017503629
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--0.172305817394175
--0.647374743701449
--0.944181100478148
--0.980995619897873
--0.747680972860835
--0.308483206798754
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--0.258591372772452
--0.71213074732663
--0.969576193139719
--0.960036951603826
--0.686139769783315
--0.223305593418733
-0.301018514798568
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-0.180020756138357
--0.342857754921908
--0.77132618129705
--0.987400490722168
--0.931581974014641
--0.619240943829511
--0.13638433070021
-0.38402737933528
-0.798692444052197
-0.993427755984289
-0.914610560427116
-0.583944138115545
-0.0924815408904855
--0.424446982019324
--0.824498826652114
--0.997514814783015
--0.895852873695781
--0.547506864779039
--0.048398130716271
-0.464037621778865
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-0.99965368491949
-0.875345548376914
-0.51000028735736
-0.00422019694387214
--0.502721976418416
--0.871233492502601
-
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/out.png
Binary file test-data/1/out.png has changed
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/out.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1/out.svg Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,2604 @@
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/output.png
Binary file test-data/1/output.png has changed
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/output.svg
--- a/test-data/1/output.svg Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2784 +0,0 @@
-
-
-
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/sine.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1/sine.tab Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,496 @@
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+ctgA 43500 43600 0.540931660176769
+ctgA 43600 43700 0.892342781239334
+ctgA 43700 43800 0.998036381447947
+ctgA 43800 43900 0.828908432665215
+ctgA 43900 44000 0.431530388323292
+ctgA 44000 44100 -0.0846748370315997
+ctgA 44100 44200 -0.577563808283757
+ctgA 44200 44300 -0.911413506635259
+ctgA 44300 44400 -0.994294326175203
+ctgA 44400 44500 -0.803384017503629
+ctgA 44500 44600 -0.391252073800153
+ctgA 44600 44700 0.128615923384498
+ctgA 44700 44800 0.613067949822471
+ctgA 44800 44900 0.928704202868774
+ctgA 44900 45000 0.988610371990796
+ctgA 45000 45100 0.776290559345248
+ctgA 45100 45200 0.350209627413543
+ctgA 45200 45300 -0.172305817394175
+ctgA 45300 45400 -0.647374743701449
+ctgA 45400 45500 -0.944181100478148
+ctgA 45500 45600 -0.980995619897873
+ctgA 45600 45700 -0.747680972860835
+ctgA 45700 45800 -0.308483206798754
+ctgA 45800 45900 0.215659190848055
+ctgA 45900 46000 0.680417187299892
+ctgA 46000 46100 0.957813972427147
+ctgA 46100 46200 0.971464941829636
+ctgA 46200 46300 0.717611133783957
+ctgA 46300 46400 0.266154305421701
+ctgA 46400 46500 -0.258591372772452
+ctgA 46500 46600 -0.71213074732663
+ctgA 46600 46700 -0.969576193139719
+ctgA 46700 46800 -0.960036951603826
+ctgA 46800 46900 -0.686139769783315
+ctgA 46900 47000 -0.223305593418733
+ctgA 47000 47100 0.301018514798568
+ctgA 47100 47200 0.742453485856362
+ctgA 47200 47300 0.979444790500868
+ctgA 47300 47400 0.946733968569148
+ctgA 47400 47500 0.653328345765115
+ctgA 47500 47600 0.180020756138357
+ctgA 47600 47700 -0.342857754921908
+ctgA 47700 47800 -0.77132618129705
+ctgA 47800 47900 -0.987400490722168
+ctgA 47900 48000 -0.931581974014641
+ctgA 48000 48100 -0.619240943829511
+ctgA 48100 48200 -0.13638433070021
+ctgA 48200 48300 0.38402737933528
+ctgA 48300 48400 0.798692444052197
+ctgA 48400 48500 0.993427755984289
+ctgA 48500 48600 0.914610560427116
+ctgA 48600 48700 0.583944138115545
+ctgA 48700 48800 0.0924815408904855
+ctgA 48800 48900 -0.424446982019324
+ctgA 48900 49000 -0.824498826652114
+ctgA 49000 49100 -0.997514814783015
+ctgA 49100 49200 -0.895852873695781
+ctgA 49200 49300 -0.547506864779039
+ctgA 49300 49400 -0.048398130716271
+ctgA 49400 49500 0.464037621778865
+ctgA 49500 49600 0.848694928139091
+ctgA 49600 49700 0.99965368491949
+ctgA 49700 49800 0.875345548376914
+ctgA 49800 49900 0.51000028735736
diff -r ae9994cf526f -r 014a21767ac4 test-data/1/tiles.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1/tiles.bed Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,201 @@
+ctgA 0 50001 strand=0,name=ctgA,value=0
+ctgA 999 2000 strand=0,name=Remark:hga,value=0
+ctgA 999 1000 strand=0,name=FakeSNP,value=0.987
+ctgA 999 20000 strand=0,name=b101.2,value=0
+ctgA 1049 9000 strand=1,name=EDEN,value=0
+ctgA 1049 3202 strand=1,name=agt830.5,value=0
+ctgA 1049 7300 strand=1,name=agt221.5,value=0
+ctgA 1099 2000 strand=1,name=Gene:hga,value=0
+ctgA 1149 7200 strand=1,name=agt767.5,value=0
+ctgA 1199 1900 strand=1,name=Protein:HGA,value=0
+ctgA 1599 3000 strand=-1,name=Gene:hgb,value=0
+ctgA 1658 1984 strand=1,name=f07,value=1110
+ctgA 1799 2900 strand=-1,name=Protein:HGB,value=0
+ctgA 3013 6130 strand=1,name=f06,value=999
+ctgA 4714 5968 strand=-1,name=f05,value=444
+ctgA 5232 5302 strand=-1,name=seg04,value=0
+ctgA 5409 7503 strand=-1,name=agt830.3,value=0
+ctgA 5799 6101 strand=-1,name=seg04,value=0
+ctgA 6441 6854 strand=-1,name=seg04,value=0
+ctgA 6884 7241 strand=-1,name=seg03,value=0
+ctgA 7105 7211 strand=-1,name=seg04,value=0
+ctgA 7409 7737 strand=-1,name=seg03,value=0
+ctgA 7499 8000 strand=-1,name=agt221.3,value=0
+ctgA 7694 8177 strand=-1,name=seg04,value=0
+ctgA 7999 9000 strand=-1,name=agt767.3,value=0
+ctgA 8054 8080 strand=-1,name=seg03,value=0
+ctgA 8305 8999 strand=-1,name=seg03,value=0
+ctgA 8544 8783 strand=-1,name=seg04,value=0
+ctgA 8868 8935 strand=-1,name=seg04,value=0
+ctgA 9403 9825 strand=-1,name=seg04,value=0
+ctgA 9999 11500 strand=1,name=Apple1,value=0
+ctgA 11910 15561 strand=1,name=m11,value=0
+ctgA 12530 12895 strand=1,name=seg12,value=0
+ctgA 12999 17200 strand=1,name=Apple2,value=0
+ctgA 13121 13449 strand=1,name=seg12,value=0
+ctgA 13279 16394 strand=1,name=f08,value=203
+ctgA 13451 13745 strand=1,name=seg12,value=0
+ctgA 13800 14007 strand=-1,name=m05,value=0
+ctgA 13907 13965 strand=1,name=seg12,value=0
+ctgA 13997 14488 strand=1,name=seg12,value=0
+ctgA 14563 14899 strand=1,name=seg12,value=0
+ctgA 14730 17239 strand=-1,name=m14,value=0
+ctgA 15184 15276 strand=1,name=seg12,value=0
+ctgA 15328 15533 strand=1,name=f10,value=1000
+ctgA 15395 16159 strand=1,name=m03,value=0
+ctgA 15638 15736 strand=1,name=seg12,value=0
+ctgA 15744 15870 strand=1,name=seg12,value=0
+ctgA 17022 17675 strand=1,name=m08,value=0
+ctgA 17399 23000 strand=1,name=Apple3,value=0
+ctgA 17666 17690 strand=1,name=m13,value=0
+ctgA 18047 18552 strand=-1,name=m07,value=0
+ctgA 18508 18985 strand=1,name=seg08,value=0
+ctgA 18988 19388 strand=1,name=seg08,value=0
+ctgA 19156 22915 strand=-1,name=f13,value=100
+ctgA 19248 19559 strand=1,name=seg06,value=0
+ctgA 19495 19962 strand=1,name=seg08,value=0
+ctgA 19974 20260 strand=1,name=seg06,value=0
+ctgA 20092 20580 strand=1,name=seg08,value=0
+ctgA 20378 20491 strand=1,name=seg06,value=0
+ctgA 20532 21005 strand=1,name=seg06,value=0
+ctgA 20969 21052 strand=1,name=seg08,value=0
+ctgA 21121 21331 strand=1,name=seg06,value=0
+ctgA 21269 21277 strand=1,name=seg08,value=0
+ctgA 21681 22176 strand=1,name=seg06,value=0
+ctgA 21684 22168 strand=1,name=seg08,value=0
+ctgA 21747 25612 strand=1,name=m12,value=0
+ctgA 22131 24633 strand=1,name=f15,value=320
+ctgA 22373 22570 strand=1,name=seg06,value=0
+ctgA 22563 22869 strand=1,name=seg08,value=0
+ctgA 22957 23298 strand=1,name=seg08,value=0
+ctgA 23024 23427 strand=1,name=seg06,value=0
+ctgA 23071 23185 strand=1,name=f14,value=850
+ctgA 23411 23469 strand=1,name=seg08,value=0
+ctgA 23931 23932 strand=1,name=seg08,value=0
+ctgA 24227 24510 strand=1,name=seg11,value=0
+ctgA 24327 24787 strand=1,name=seg08,value=0
+ctgA 24561 28338 strand=1,name=f02,value=208
+ctgA 24867 25012 strand=1,name=seg11,value=0
+ctgA 25211 25426 strand=1,name=seg11,value=0
+ctgA 25227 25367 strand=1,name=seg08,value=0
+ctgA 25793 25874 strand=1,name=seg11,value=0
+ctgA 26074 26519 strand=1,name=seg11,value=0
+ctgA 26121 26126 strand=1,name=seg02,value=0
+ctgA 26496 26869 strand=1,name=seg02,value=0
+ctgA 26502 26799 strand=-1,name=seg05,value=0
+ctgA 26929 26940 strand=1,name=seg11,value=0
+ctgA 26974 27063 strand=1,name=seg11,value=0
+ctgA 27171 27185 strand=-1,name=seg05,value=0
+ctgA 27200 27325 strand=1,name=seg02,value=0
+ctgA 27371 27433 strand=1,name=seg02,value=0
+ctgA 27414 27799 strand=1,name=seg11,value=0
+ctgA 27447 27860 strand=-1,name=seg05,value=0
+ctgA 27564 27565 strand=1,name=seg02,value=0
+ctgA 27812 28091 strand=1,name=seg02,value=0
+ctgA 27879 27943 strand=1,name=seg11,value=0
+ctgA 27886 28076 strand=-1,name=seg05,value=0
+ctgA 28092 28201 strand=1,name=seg02,value=0
+ctgA 28224 28316 strand=-1,name=seg05,value=0
+ctgA 28224 28346 strand=1,name=seg11,value=0
+ctgA 28328 28377 strand=1,name=seg02,value=0
+ctgA 28331 30033 strand=-1,name=m02,value=0
+ctgA 28341 28447 strand=-1,name=m10,value=0
+ctgA 28374 28570 strand=1,name=seg11,value=0
+ctgA 28757 29041 strand=1,name=seg11,value=0
+ctgA 28776 29058 strand=-1,name=seg05,value=0
+ctgA 28828 29194 strand=1,name=seg02,value=0
+ctgA 29100 29302 strand=1,name=seg11,value=0
+ctgA 29512 29647 strand=-1,name=seg05,value=0
+ctgA 29516 29702 strand=1,name=seg02,value=0
+ctgA 29603 29702 strand=1,name=seg11,value=0
+ctgA 29712 30061 strand=1,name=seg02,value=0
+ctgA 29770 29942 strand=1,name=seg10,value=0
+ctgA 29866 29885 strand=1,name=seg11,value=0
+ctgA 30041 30340 strand=1,name=seg10,value=0
+ctgA 30107 30216 strand=-1,name=seg05,value=0
+ctgA 30240 30246 strand=1,name=seg11,value=0
+ctgA 30328 30774 strand=1,name=seg02,value=0
+ctgA 30464 30798 strand=-1,name=seg05,value=0
+ctgA 30574 30738 strand=1,name=seg11,value=0
+ctgA 30577 31748 strand=1,name=m06,value=0
+ctgA 30807 31306 strand=1,name=seg02,value=0
+ctgA 30809 31307 strand=1,name=seg10,value=0
+ctgA 31231 31236 strand=-1,name=seg05,value=0
+ctgA 31420 31817 strand=-1,name=seg05,value=0
+ctgA 31515 31729 strand=1,name=seg02,value=0
+ctgA 31752 32154 strand=1,name=seg02,value=0
+ctgA 31760 31984 strand=1,name=seg10,value=0
+ctgA 32009 32057 strand=-1,name=seg05,value=0
+ctgA 32207 32680 strand=-1,name=seg05,value=0
+ctgA 32328 32359 strand=1,name=seg01,value=0
+ctgA 32373 32937 strand=1,name=seg10,value=0
+ctgA 32594 32696 strand=1,name=seg02,value=0
+ctgA 32891 32901 strand=1,name=seg02,value=0
+ctgA 33052 33325 strand=-1,name=seg05,value=0
+ctgA 33126 33388 strand=1,name=seg02,value=0
+ctgA 33324 35791 strand=1,name=m04,value=0
+ctgA 33437 33868 strand=-1,name=seg05,value=0
+ctgA 33438 33443 strand=1,name=seg02,value=0
+ctgA 33758 34209 strand=1,name=seg02,value=0
+ctgA 34243 34313 strand=-1,name=seg05,value=0
+ctgA 34400 34466 strand=1,name=seg02,value=0
+ctgA 34604 34983 strand=-1,name=seg05,value=0
+ctgA 35332 35507 strand=-1,name=seg05,value=0
+ctgA 35641 35904 strand=-1,name=seg05,value=0
+ctgA 36033 38167 strand=1,name=f09,value=100
+ctgA 36615 37057 strand=-1,name=seg09,value=0
+ctgA 36648 40440 strand=-1,name=f03,value=300
+ctgA 37207 37227 strand=-1,name=seg09,value=0
+ctgA 37241 38653 strand=1,name=f04,value=10
+ctgA 37496 40559 strand=-1,name=m15,value=0
+ctgA 39264 39361 strand=-1,name=seg15,value=0
+ctgA 39752 40034 strand=-1,name=seg15,value=0
+ctgA 40514 40954 strand=-1,name=seg15,value=0
+ctgA 41136 41318 strand=-1,name=seg14,value=0
+ctgA 41251 41365 strand=-1,name=seg15,value=0
+ctgA 41491 41504 strand=-1,name=seg15,value=0
+ctgA 41753 41948 strand=-1,name=seg14,value=0
+ctgA 41940 42377 strand=-1,name=seg15,value=0
+ctgA 42056 42474 strand=-1,name=seg14,value=0
+ctgA 42747 42954 strand=-1,name=seg15,value=0
+ctgA 42889 43270 strand=-1,name=seg14,value=0
+ctgA 43394 43811 strand=-1,name=seg14,value=0
+ctgA 43400 43897 strand=-1,name=seg15,value=0
+ctgA 44042 44113 strand=-1,name=seg15,value=0
+ctgA 44064 44556 strand=-1,name=seg14,value=0
+ctgA 44190 44514 strand=-1,name=seg07,value=0
+ctgA 44398 44888 strand=-1,name=seg15,value=0
+ctgA 44551 45043 strand=-1,name=seg07,value=0
+ctgA 44704 47713 strand=-1,name=f01,value=400
+ctgA 44762 45030 strand=-1,name=seg14,value=0
+ctgA 45230 45488 strand=-1,name=seg14,value=0
+ctgA 45280 45375 strand=-1,name=seg15,value=0
+ctgA 45372 45600 strand=-1,name=seg07,value=0
+ctgA 45710 46041 strand=-1,name=seg15,value=0
+ctgA 45789 46022 strand=-1,name=seg14,value=0
+ctgA 45896 46315 strand=-1,name=seg07,value=0
+ctgA 46011 48851 strand=1,name=m09,value=0
+ctgA 46091 46318 strand=-1,name=seg14,value=0
+ctgA 46424 46564 strand=-1,name=seg15,value=0
+ctgA 46490 46890 strand=-1,name=seg07,value=0
+ctgA 46737 47087 strand=-1,name=seg15,value=0
+ctgA 46815 46992 strand=-1,name=seg14,value=0
+ctgA 46989 48410 strand=-1,name=f11,value=100
+ctgA 47125 47297 strand=-1,name=seg07,value=0
+ctgA 47328 47595 strand=-1,name=seg15,value=0
+ctgA 47448 47829 strand=-1,name=seg14,value=0
+ctgA 47734 47983 strand=-1,name=seg07,value=0
+ctgA 47857 47979 strand=-1,name=seg15,value=0
+ctgA 48168 48453 strand=-1,name=seg15,value=0
+ctgA 48252 48366 strand=1,name=m01,value=0
+ctgA 48446 48709 strand=-1,name=seg07,value=0
+ctgA 48930 49186 strand=-1,name=seg07,value=0
+ctgA 49405 49476 strand=1,name=seg13,value=0
+ctgA 49471 49699 strand=-1,name=seg07,value=0
+ctgA 49757 50000 strand=-1,name=f12,value=3040
+ctgA 49761 50000 strand=1,name=seg13,value=0
+ctgA 49956 50000 strand=-1,name=seg07,value=0
+ctgB 0 6079 strand=0,name=ctgB,value=0
+ctgB 1658 1984 strand=1,name=f07,value=0
+ctgB 3013 6130 strand=1,name=f06,value=0
+ctgB 4714 5968 strand=-1,name=f05,value=0
diff -r ae9994cf526f -r 014a21767ac4 test-data/alignments/1.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments/1.maf Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,18 @@
+##maf version=1 scoring=lastz.v1.04.00
+# lastz.v1.04.00 --strand=both --ambiguous=iupac --chain --traceback=160M --format=maf --action:target=multiple
+#
+# hsp_threshold = 3000
+# gapped_threshold = 3000
+# x_drop = 910
+# y_drop = 9400
+# gap_open_penalty = 400
+# gap_extend_penalty = 30
+# A C G T
+# A 91 -114 -31 -123
+# C -114 100 -125 -31
+# G -31 -125 100 -114
+# T -123 -31 -114 91
+a score=8421
+s CP020543.1 76314 796 + 4617024 ATGTTGCTTATGGCATTGATAAAAACTTTCTTTTTGGTTGTGGTGTTTCAATCACGTCAGTTTTGTTACATAACAACGACGTGAGTTTTGTTTTCCACGTTTTTATTGATGATATCCCTGAAGCCGATATCCAGCGTTTAGCCCAATTGGCGAAAAGCTATCGTACCTGTATCCAGATCCATCTGGTAAATTGTGAACGGCTTAAGGCATTACCGACGACCAAAAATTGGTCTATTGCCATGTATTTCCGTTTTGTAATTGCAGATTACTTTATTGA-------TCAACAAGATAAGATCCTTTACCTGGATGCTGATATCGCCTGTCAGGGAAACTTAAAGCCGCTGATAACAATGGATCTTGCCAATAACGTTGCTGCTGTTGTTACTGAACGCGATGCTAACTGGTGGTCGTTACGGGGTCAAAGTCTGCAGTGTAATGAACTTGAAAAGGGTTACTTTAATTCAGGTGTCCTGTTAATTAAT-----ACACTAGCGTGGGCGCAG----GAGTCCGTTTCTGCTAAAGCGATGTCGATGCTTGCTGATAAAACCATCGTTTCCCATTTAACCTATATGGATCAAGATATTCTTAATCTTATCCTGTTAGGGAAAGTTAAATTCATTGATGCTAAATACAATACGCAG---TTTAGTTTAAATTATGAATTAAAAAAATCATTTGTTTGTC------------------------CAATTAATGATGAAACCGTATTAATTCATTATGTCGGCCCGACAAAACCCTGGCATTACTGGGCCAGTTATCCAAGTGCGCAACCATTTATCAAAGCCAAAGAAGCATCGCCCTGGAAAAA
+s CP020543.2 77326 805 + 4617024 ATGTTTCCTACGGTATCGATAAGAATTTTTTGTATGGTGCTGGCGTTTCAATTTCTTCCGTTTTGATTAATAATTCAGATATTAATTTTGTCTTTCATGTTTTCACTGATTATGTGGATGATGATTATTTAAAGTCATTTAATGAAACAGCAAAACAATTTAATACCTCAATTATTGTATATTTAATTGACCCCAAATACTTTGCTGATCTGCCGACGTCACAGTTTTGGTCGTACGCGACATACTTCAGGGTATTGTCTTTTGAATATCTGAGTGAAAGTATTTCCACA-------CTGCTGTATCTGGATGCCGATGTTGTTTGTAAAGGAAGCCTGAAACCTCTCACAGAAATTATATTTAAAGATGAGTTTGCTGCGGTCATTCCTGA---CAATGATAGTACTCAGGCGGCATGTGCAAAACGCCTCAACATTCCCGAAATGAATGGACGTTATTTCAATGCAGGCGTTATCTATGTCAATCTTAAAAAATGGCATGAA-GCAAATTTGACACCGTATTTACTCAAACTTTTACGA--------GGGGAAACTAAATATGGCTCTCTTAAATATTTAGATCAGGATGCGTTGAATATCGC------------ATTTAA---TATGAATAATATCTACCTTGCGAAGGGTTTTGATACTATTTATACCCTGAAAAACGAACTTTATGATCGTAGTCATCGAAAGTATCAGCAAACCATTACCGATAAAACAGTGTTGATTCACTATACAGGGATAACTAAACCATGGCATAGCTGGGCTGGATATCCGTCTGCATCATACTTTAATATCGCGCGTGAACAATCTCCCTGGAAGAA
+s CP020543.3 77326 805 + 4617024 ATGTTTCCTACGGTATCGATAAGAATTTTTTGTATGGTGCTGGCGTTTCAATTTCTTCCGTTTTGATTAATAATTCAGATATTAATTTTGTCTTTCATGTTTTCACTGATTATGTGGATGATGATTATTTAAAGTCATTTAATGAAACAGCAAAACAATTTAATACCTCAATTATTGTATATTTAATTGACCCCAAATACTTTGCTGATCTGCCGACGTCACAGTTTTGGTCGTACGCGACATACTTCAGGGTATTGTCTTTTGAATATCTGAGTGAAAGTATTTCCACA-------CTGCTGTATCTGGATGCCGATGTTGTTTGTAAAGGAAGCCTGAAACCTCTCACAGAAATTATATTTAAAGATGAGTTTGCTGCGGTCATTCCTGA---CAATGATAGTACTCAGGCGGCATGTGCAAAACGCCTCAACATTCCCGAAATGAATGGACGTTATTTCAATGCAGGCGTTATCTATGTCAATCTTAAAAAATGGCATGAA-GCAAATTTGACACCGTATTTACTCAAACTTTTACGA--------GGGGAAACTAAATATGGCTCTCTTAAATATTTAGATCAGGATGCGTTGAATATCGC------------ATTTAA---TATGAATAATATCTACCTTGCGAAGGGTTTTGATACTATTTATACCCTGAAAAACGAACTTTATGATCGTAGTCATCGAAAGTATCAGCAAACCATTACCGATAAAACAGTGTTGATTCACTATACAGGGATAACTAAACCATGGCATAGCTGGGCTGGATATCCGTCTGCATCATACTTTAATATCGCGCGTGAACAATCTCCCTGGAAGAA
diff -r ae9994cf526f -r 014a21767ac4 test-data/alignments/1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments/1.tab Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,3 @@
+CP020543.1 76314 77110 CP020543.2 77326 78131
+CP020543.1 76314 77110 CP020543.3 77326 78131
+CP020543.2 77326 78131 CP020543.3 77326 78131
diff -r ae9994cf526f -r 014a21767ac4 test-data/binlinks/1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/binlinks/1.out Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,36 @@
+chr22 14000000 14999999 326.0000
+chr22 15000000 15999999 2532.0000
+chr22 16000000 16999999 4175.0000
+chr22 17000000 17999999 3303.0000
+chr22 18000000 18999999 2432.0000
+chr22 19000000 19999999 2323.0000
+chr22 20000000 20999999 3353.0000
+chr22 21000000 21999999 4355.0000
+chr22 22000000 22999999 3372.0000
+chr22 23000000 23999999 3445.0000
+chr22 24000000 24999999 2953.0000
+chr22 25000000 25999999 4186.0000
+chr22 26000000 26999999 2234.0000
+chr22 27000000 27999999 1921.0000
+chr22 28000000 28999999 2273.0000
+chr22 29000000 29999999 3312.0000
+chr22 30000000 30999999 3516.0000
+chr22 31000000 31999999 3814.0000
+chr22 32000000 32999999 2528.0000
+chr22 33000000 33999999 4752.0000
+chr22 34000000 34999999 3032.0000
+chr22 35000000 35999999 3696.0000
+chr22 36000000 36999999 3168.0000
+chr22 37000000 37999999 3435.0000
+chr22 38000000 38999999 2384.0000
+chr22 39000000 39999999 3101.0000
+chr22 40000000 40999999 2732.0000
+chr22 41000000 41999999 2534.0000
+chr22 42000000 42999999 3479.0000
+chr22 43000000 43999999 4606.0000
+chr22 44000000 44999999 2126.0000
+chr22 45000000 45999999 4586.0000
+chr22 46000000 46999999 3711.0000
+chr22 47000000 47999999 5564.0000
+chr22 48000000 48999999 4823.0000
+chr22 49000000 49999999 1994.0000
diff -r ae9994cf526f -r 014a21767ac4 test-data/binlinks/1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/binlinks/1.tab Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,54401 @@
+chr22 14430407 14430408 chr22 14430407 14430408
+chr22 14431496 14431497 chr22 14431496 14431497
+chr22 14433658 14433659 chr22 14433658 14433659
+chr22 14433790 14433791 chr22 14433790 14433791
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diff -r ae9994cf526f -r 014a21767ac4 test-data/bundlelinks/1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r ae9994cf526f -r 014a21767ac4 test-data/bundlelinks/1.tab
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diff -r ae9994cf526f -r 014a21767ac4 test-data/gc_skew/1.bw
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diff -r ae9994cf526f -r 014a21767ac4 test-data/resample/1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r ae9994cf526f -r 014a21767ac4 test-data/resample/1.tab
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+CP020543.1 27726 27815 . 0 -
+CP020543.1 27812 27925 . 0 -
+CP020543.1 27948 28106 . 0 -
+CP020543.1 28103 28393 . 0 -
+CP020543.1 28380 28478 . 0 +
+CP020543.1 28584 30272 . 0 +
+CP020543.1 30276 30566 . 0 +
+CP020543.1 30641 31231 . 0 +
+CP020543.1 31231 32733 . 0 +
+CP020543.1 32743 34062 . 0 +
+CP020543.1 34200 35591 . 0 +
+CP020543.1 35636 37402 . 0 -
+CP020543.1 37577 38911 . 0 +
+CP020543.1 38964 39416 . 0 +
+CP020543.1 39437 39628 . 0 -
+CP020543.1 39627 40817 nepI 0 +
+CP020543.1 40858 41151 . 0 -
+CP020543.1 41188 41376 . 0 +
+CP020543.1 41373 42191 . 0 +
+CP020543.1 42195 43118 . 0 -
+CP020543.1 43229 44413 . 0 -
+CP020543.1 44795 44941 . 0 -
+CP020543.1 45437 46819 . 0 +
+CP020543.1 46829 49147 . 0 +
+CP020543.1 49200 50909 . 0 -
+CP020543.1 51030 52421 . 0 -
+CP020543.1 52701 53906 . 0 +
+CP020543.1 54072 56153 . 0 -
+CP020543.1 56159 56848 . 0 -
+CP020543.1 56855 58963 . 0 -
+CP020543.1 58982 59257 . 0 -
+CP020543.1 59312 59935 . 0 -
+CP020543.1 60193 61875 . 0 +
+CP020543.1 61872 62489 . 0 -
+CP020543.1 62781 63605 . 0 -
+CP020543.1 63826 64689 . 0 -
+CP020543.1 64702 64884 . 0 -
+CP020543.1 64816 65532 . 0 +
+CP020543.1 65598 66239 . 0 +
+CP020543.1 66276 66872 . 0 -
+CP020543.1 66979 67434 . 0 -
+CP020543.1 67415 68635 . 0 -
+CP020543.1 68807 69475 . 0 +
+CP020543.1 69692 69928 . 0 +
+CP020543.1 69949 70116 . 0 +
+CP020543.1 70214 71023 . 0 +
+CP020543.1 71062 71541 . 0 -
+CP020543.1 71549 72826 . 0 -
+CP020543.1 73239 74297 . 0 +
+CP020543.1 74294 75418 . 0 +
+CP020543.1 75411 76208 . 0 +
+CP020543.1 76224 77240 . 0 +
+CP020543.1 77257 78252 . 0 +
+CP020543.1 78262 78954 . 0 +
+CP020543.1 78980 80005 . 0 +
+CP020543.1 80090 81073 . 0 +
+CP020543.1 81119 82372 . 0 +
+CP020543.1 82442 83413 . 0 -
+CP020543.1 83417 84463 . 0 -
+CP020543.1 84473 85405 . 0 -
+CP020543.1 85619 86815 . 0 +
+CP020543.1 86825 87850 . 0 +
+CP020543.1 88089 89123 . 0 +
+CP020543.1 89110 90069 . 0 -
+CP020543.1 90073 91356 . 0 -
+CP020543.1 91366 92910 . 0 -
+CP020543.1 92934 93131 . 0 -
+CP020543.1 93155 93586 . 0 +
+CP020543.1 93728 93979 . 0 +
+CP020543.1 94042 94509 . 0 +
diff -r ae9994cf526f -r 014a21767ac4 test-data/text/1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/text/1.out Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,100 @@
+CP020543.1 49 1452 dnaA strand=1,value=0
+CP020543.1 1457 2557 . strand=1,value=0
+CP020543.1 2557 3630 . strand=1,value=0
+CP020543.1 3659 6073 . strand=1,value=0
+CP020543.1 6304 6711 . strand=1,value=0
+CP020543.1 6826 7638 . strand=1,value=0
+CP020543.1 7684 8340 . strand=-1,value=0
+CP020543.1 8618 9307 . strand=1,value=0
+CP020543.1 9304 10182 . strand=1,value=0
+CP020543.1 10166 10783 . strand=1,value=0
+CP020543.1 10780 11928 . strand=1,value=0
+CP020543.1 12048 13340 . strand=1,value=0
+CP020543.1 13337 14401 . strand=-1,value=0
+CP020543.1 14469 15716 . strand=1,value=0
+CP020543.1 15718 16050 . strand=-1,value=0
+CP020543.1 16356 16769 . strand=1,value=0
+CP020543.1 16881 17309 . strand=1,value=0
+CP020543.1 17505 19166 . strand=1,value=0
+CP020543.1 19163 19879 . strand=-1,value=0
+CP020543.1 20175 21791 . strand=1,value=0
+CP020543.1 21791 23113 . strand=1,value=0
+CP020543.1 23110 23184 . strand=-1,value=0
+CP020543.1 23154 23612 . strand=-1,value=0
+CP020543.1 23559 23704 . strand=1,value=0
+CP020543.1 23682 24890 . strand=1,value=0
+CP020543.1 25061 25408 . strand=1,value=0
+CP020543.1 25398 25760 . strand=1,value=0
+CP020543.1 25757 26254 . strand=1,value=0
+CP020543.1 26262 27446 . strand=-1,value=0
+CP020543.1 27486 27668 . strand=-1,value=0
+CP020543.1 27726 27815 . strand=-1,value=0
+CP020543.1 27812 27925 . strand=-1,value=0
+CP020543.1 27948 28106 . strand=-1,value=0
+CP020543.1 28103 28393 . strand=-1,value=0
+CP020543.1 28380 28478 . strand=1,value=0
+CP020543.1 28584 30272 . strand=1,value=0
+CP020543.1 30276 30566 . strand=1,value=0
+CP020543.1 30641 31231 . strand=1,value=0
+CP020543.1 31231 32733 . strand=1,value=0
+CP020543.1 32743 34062 . strand=1,value=0
+CP020543.1 34200 35591 . strand=1,value=0
+CP020543.1 35636 37402 . strand=-1,value=0
+CP020543.1 37577 38911 . strand=1,value=0
+CP020543.1 38964 39416 . strand=1,value=0
+CP020543.1 39437 39628 . strand=-1,value=0
+CP020543.1 39627 40817 nepI strand=1,value=0
+CP020543.1 40858 41151 . strand=-1,value=0
+CP020543.1 41188 41376 . strand=1,value=0
+CP020543.1 41373 42191 . strand=1,value=0
+CP020543.1 42195 43118 . strand=-1,value=0
+CP020543.1 43229 44413 . strand=-1,value=0
+CP020543.1 44795 44941 . strand=-1,value=0
+CP020543.1 45437 46819 . strand=1,value=0
+CP020543.1 46829 49147 . strand=1,value=0
+CP020543.1 49200 50909 . strand=-1,value=0
+CP020543.1 51030 52421 . strand=-1,value=0
+CP020543.1 52701 53906 . strand=1,value=0
+CP020543.1 54072 56153 . strand=-1,value=0
+CP020543.1 56159 56848 . strand=-1,value=0
+CP020543.1 56855 58963 . strand=-1,value=0
+CP020543.1 58982 59257 . strand=-1,value=0
+CP020543.1 59312 59935 . strand=-1,value=0
+CP020543.1 60193 61875 . strand=1,value=0
+CP020543.1 61872 62489 . strand=-1,value=0
+CP020543.1 62781 63605 . strand=-1,value=0
+CP020543.1 63826 64689 . strand=-1,value=0
+CP020543.1 64702 64884 . strand=-1,value=0
+CP020543.1 64816 65532 . strand=1,value=0
+CP020543.1 65598 66239 . strand=1,value=0
+CP020543.1 66276 66872 . strand=-1,value=0
+CP020543.1 66979 67434 . strand=-1,value=0
+CP020543.1 67415 68635 . strand=-1,value=0
+CP020543.1 68807 69475 . strand=1,value=0
+CP020543.1 69692 69928 . strand=1,value=0
+CP020543.1 69949 70116 . strand=1,value=0
+CP020543.1 70214 71023 . strand=1,value=0
+CP020543.1 71062 71541 . strand=-1,value=0
+CP020543.1 71549 72826 . strand=-1,value=0
+CP020543.1 73239 74297 . strand=1,value=0
+CP020543.1 74294 75418 . strand=1,value=0
+CP020543.1 75411 76208 . strand=1,value=0
+CP020543.1 76224 77240 . strand=1,value=0
+CP020543.1 77257 78252 . strand=1,value=0
+CP020543.1 78262 78954 . strand=1,value=0
+CP020543.1 78980 80005 . strand=1,value=0
+CP020543.1 80090 81073 . strand=1,value=0
+CP020543.1 81119 82372 . strand=1,value=0
+CP020543.1 82442 83413 . strand=-1,value=0
+CP020543.1 83417 84463 . strand=-1,value=0
+CP020543.1 84473 85405 . strand=-1,value=0
+CP020543.1 85619 86815 . strand=1,value=0
+CP020543.1 86825 87850 . strand=1,value=0
+CP020543.1 88089 89123 . strand=1,value=0
+CP020543.1 89110 90069 . strand=-1,value=0
+CP020543.1 90073 91356 . strand=-1,value=0
+CP020543.1 91366 92910 . strand=-1,value=0
+CP020543.1 92934 93131 . strand=-1,value=0
+CP020543.1 93155 93586 . strand=1,value=0
+CP020543.1 93728 93979 . strand=1,value=0
+CP020543.1 94042 94509 . strand=1,value=0
diff -r ae9994cf526f -r 014a21767ac4 test-data/text/2.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/text/2.gff3 Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,100 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM584v2
+#!genome-build-accession NCBI_Assembly:GCF_000005845.2
+##sequence-region NC_000913.3 1 4641652
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
+NC_000913.3 RefSeq region 1 4641652 . + . ID=NC_000913.3:1..4641652;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
+NC_000913.3 RefSeq gene 190 255 . + . ID=gene-b0001;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001
+NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds-NP_414542.1;Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3 RefSeq gene 337 2799 . + . ID=gene-b0002;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds-NP_414543.1;Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene-b0003;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003
+NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds-NP_414544.1;Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene-b0004;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004
+NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds-NP_414545.1;Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;gene=thrC;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene-b0005;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005
+NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds-NP_414546.1;Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;protein_id=NP_414546.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 5566 5601 . + . ID=id-12;Note=REP1a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 5637 5670 . - . ID=id-13;Note=REP1b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene-b0006;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006
+NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds-NP_414547.1;Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;protein_id=NP_414547.1;transl_table=11
+NC_000913.3 RefSeq gene 6529 7959 . - . ID=gene-b0007;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene=yaaJ;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007
+NC_000913.3 RefSeq CDS 6529 7959 . - 0 ID=cds-NP_414548.1;Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;gene=yaaJ;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;protein_id=NP_414548.1;transl_table=11
+NC_000913.3 RefSeq gene 8238 9191 . + . ID=gene-b0008;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene=talB;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008
+NC_000913.3 RefSeq CDS 8238 9191 . + 0 ID=cds-NP_414549.1;Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;gene=talB;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;protein_id=NP_414549.1;transl_table=11
+NC_000913.3 RefSeq gene 9306 9893 . + . ID=gene-b0009;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene=mog;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009
+NC_000913.3 RefSeq CDS 9306 9893 . + 0 ID=cds-NP_414550.1;Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;gene=mog;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;protein_id=NP_414550.1;transl_table=11
+NC_000913.3 RefSeq gene 9928 10494 . - . ID=gene-b0010;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene=satP;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010
+NC_000913.3 RefSeq CDS 9928 10494 . - 0 ID=cds-NP_414551.1;Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;gene=satP;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;protein_id=NP_414551.1;transl_table=11
+NC_000913.3 RefSeq gene 10643 11356 . - . ID=gene-b0011;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene=yaaW;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011
+NC_000913.3 RefSeq CDS 10643 11356 . - 0 ID=cds-NP_414552.1;Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;gene=yaaW;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;protein_id=NP_414552.1;transl_table=11
+NC_000913.3 RefSeq gene 10830 11315 . + . ID=gene-b0012;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene=mbiA;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012
+NC_000913.3 RefSeq CDS 10830 11315 . + 0 ID=cds-YP_009518733.1;Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;gene=mbiA;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;protein_id=YP_009518733.1;transl_table=11
+NC_000913.3 RefSeq gene 11382 11786 . - . ID=gene-b0013;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene=yaaI;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013
+NC_000913.3 RefSeq CDS 11382 11786 . - 0 ID=cds-NP_414554.1;Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;gene=yaaI;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;protein_id=NP_414554.1;transl_table=11
+NC_000913.3 RefSeq gene 12163 14079 . + . ID=gene-b0014;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene=dnaK;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014
+NC_000913.3 RefSeq CDS 12163 14079 . + 0 ID=cds-NP_414555.1;Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;gene=dnaK;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;protein_id=NP_414555.1;transl_table=11
+NC_000913.3 RefSeq gene 14168 15298 . + . ID=gene-b0015;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene=dnaJ;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015
+NC_000913.3 RefSeq CDS 14168 15298 . + 0 ID=cds-NP_414556.1;Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;gene=dnaJ;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;protein_id=NP_414556.1;transl_table=11
+NC_000913.3 RefSeq mobile_genetic_element 15387 16731 . + . ID=id-34;gbkey=mobile_element;mobile_element_type=insertion sequence:IS186A
+NC_000913.3 RefSeq gene 15445 16557 . + . ID=gene-b0016;Dbxref=ASAP:ABE-0000058,ECOCYC:G6083,EcoGene:EG60001,GeneID:944754;Name=insL-1;gbkey=Gene;gene=insL-1;gene_biotype=protein_coding;gene_synonym=ECK0016,yi81-1;locus_tag=b0016
+NC_000913.3 RefSeq CDS 15445 16557 . + 0 ID=cds-NP_414557.1;Parent=gene-b0016;Dbxref=UniProtKB/Swiss-Prot:P0CF91,Genbank:NP_414557.1,ASAP:ABE-0000058,ECOCYC:G6083,EcoGene:EG60001,GeneID:944754;Name=NP_414557.1;gbkey=CDS;gene=insL-1;locus_tag=b0016;orig_transcript_id=gnl|b0016|mrna.b0016;product=IS186/IS421 transposase;protein_id=NP_414557.1;transl_table=11
+NC_000913.3 RefSeq gene 16751 16960 . - . ID=gene-b0018;Dbxref=ASAP:ABE-0000064,ECOCYC:EG10373,EcoGene:EG12074,GeneID:944756;Name=mokC;gbkey=Gene;gene=mokC;gene_biotype=protein_coding;gene_synonym=ECK0018,gefL;locus_tag=b0018
+NC_000913.3 RefSeq CDS 16751 16960 . - 0 ID=cds-NP_414559.1;Parent=gene-b0018;Dbxref=UniProtKB/Swiss-Prot:P33236,Genbank:NP_414559.1,ASAP:ABE-0000064,ECOCYC:EG10373,EcoGene:EG12074,GeneID:944756;Name=NP_414559.1;gbkey=CDS;gene=mokC;locus_tag=b0018;orig_transcript_id=gnl|b0018|mrna.b0018;product=regulatory protein MokC;protein_id=NP_414559.1;transl_table=11
+NC_000913.3 RefSeq gene 16751 16903 . - . ID=gene-b4412;Dbxref=ASAP:ABE-0047278,ECOCYC:G0-9563,EcoGene:EG10373,GeneID:2847744;Name=hokC;gbkey=Gene;gene=hokC;gene_biotype=protein_coding;gene_synonym=ECK0017,gef;locus_tag=b4412
+NC_000913.3 RefSeq CDS 16751 16903 . - 0 ID=cds-YP_025292.1;Parent=gene-b4412;Dbxref=UniProtKB/Swiss-Prot:P0ACG4,Genbank:YP_025292.1,ASAP:ABE-0047278,ECOCYC:G0-9563,EcoGene:EG10373,GeneID:2847744;Name=YP_025292.1;gbkey=CDS;gene=hokC;locus_tag=b4412;orig_transcript_id=gnl|b4412|mrna.b4412;product=protein HokC;protein_id=YP_025292.1;transl_table=11
+NC_000913.3 RefSeq gene 16952 17006 . + . ID=gene-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;Name=sokC;gbkey=Gene;gene=sokC;gene_biotype=ncRNA;gene_synonym=ECK0019,sof;locus_tag=b4413
+NC_000913.3 RefSeq ncRNA 16952 17006 . + . ID=rna-b4413;Parent=gene-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;gbkey=ncRNA;gene=sokC;locus_tag=b4413;product=antisense RNA blocking mokC and hokC translation
+NC_000913.3 RefSeq exon 16952 17006 . + . ID=exon-b4413-1;Parent=rna-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;gbkey=ncRNA;gene=sokC;locus_tag=b4413;product=antisense RNA blocking mokC and hokC translation
+NC_000913.3 RefSeq gene 17489 18655 . + . ID=gene-b0019;Dbxref=ASAP:ABE-0000068,ECOCYC:EG10652,EcoGene:EG10652,GeneID:944758;Name=nhaA;gbkey=Gene;gene=nhaA;gene_biotype=protein_coding;gene_synonym=ant,antA,ECK0020,hyc;locus_tag=b0019
+NC_000913.3 RefSeq CDS 17489 18655 . + 0 ID=cds-NP_414560.1;Parent=gene-b0019;Dbxref=UniProtKB/Swiss-Prot:P13738,Genbank:NP_414560.1,ASAP:ABE-0000068,ECOCYC:EG10652,EcoGene:EG10652,GeneID:944758;Name=NP_414560.1;gbkey=CDS;gene=nhaA;locus_tag=b0019;orig_transcript_id=gnl|b0019|mrna.b0019;product=Na(+):H(+) antiporter NhaA;protein_id=NP_414560.1;transl_table=11
+NC_000913.3 RefSeq gene 18715 19620 . + . ID=gene-b0020;Dbxref=ASAP:ABE-0000072,ECOCYC:EG11078,EcoGene:EG11078,GeneID:944757;Name=nhaR;gbkey=Gene;gene=nhaR;gene_biotype=protein_coding;gene_synonym=antO,ECK0021,yaaB;locus_tag=b0020
+NC_000913.3 RefSeq CDS 18715 19620 . + 0 ID=cds-NP_414561.1;Parent=gene-b0020;Dbxref=UniProtKB/Swiss-Prot:P0A9G2,Genbank:NP_414561.1,ASAP:ABE-0000072,ECOCYC:EG11078,EcoGene:EG11078,GeneID:944757;Name=NP_414561.1;gbkey=CDS;gene=nhaR;locus_tag=b0020;orig_transcript_id=gnl|b0020|mrna.b0020;product=DNA-binding transcriptional activator NhaR;protein_id=NP_414561.1;transl_table=11
+NC_000913.3 RefSeq mobile_genetic_element 19796 20563 . - . ID=id-47;gbkey=mobile_element;mobile_element_type=insertion sequence:IS1A
+NC_000913.3 RefSeq gene 19811 20314 . - . ID=gene-b0021;Dbxref=ASAP:ABE-0000075,ECOCYC:G6085,EcoGene:EG60002,GeneID:944743;Name=insB-1;gbkey=Gene;gene=insB-1;gene_biotype=protein_coding;gene_synonym=ECK0022;locus_tag=b0021
+NC_000913.3 RefSeq CDS 19811 20314 . - 0 ID=cds-NP_414562.1;Parent=gene-b0021;Dbxref=UniProtKB/Swiss-Prot:P0CF25,Genbank:NP_414562.1,ASAP:ABE-0000075,ECOCYC:G6085,EcoGene:EG60002,GeneID:944743;Name=NP_414562.1;gbkey=CDS;gene=insB-1;locus_tag=b0021;orig_transcript_id=gnl|b0021|mrna.b0021;product=IS1 protein InsB;protein_id=NP_414562.1;transl_table=11
+NC_000913.3 RefSeq gene 20233 20508 . - . ID=gene-b0022;Dbxref=ASAP:ABE-0000078,ECOCYC:G6086,EcoGene:EG40001,GeneID:948449;Name=insA-1;gbkey=Gene;gene=insA-1;gene_biotype=protein_coding;gene_synonym=ECK0023;locus_tag=b0022
+NC_000913.3 RefSeq CDS 20233 20508 . - 0 ID=cds-NP_414563.1;Parent=gene-b0022;Dbxref=UniProtKB/Swiss-Prot:P0CF07,Genbank:NP_414563.1,ASAP:ABE-0000078,ECOCYC:G6086,EcoGene:EG40001,GeneID:948449;Name=NP_414563.1;gbkey=CDS;gene=insA-1;locus_tag=b0022;orig_transcript_id=gnl|b0022|mrna.b0022;product=IS1 protein InsA;protein_id=NP_414563.1;transl_table=11
+NC_000913.3 RefSeq gene 20815 21078 . - . ID=gene-b0023;Dbxref=ASAP:ABE-0000082,ECOCYC:EG10919,EcoGene:EG10919,GeneID:944759;Name=rpsT;gbkey=Gene;gene=rpsT;gene_biotype=protein_coding;gene_synonym=ECK0024,sup(s20),supS,supS20;locus_tag=b0023
+NC_000913.3 RefSeq CDS 20815 21078 . - 0 ID=cds-NP_414564.1;Parent=gene-b0023;Dbxref=UniProtKB/Swiss-Prot:P0A7U7,Genbank:NP_414564.1,ASAP:ABE-0000082,ECOCYC:EG10919,EcoGene:EG10919,GeneID:944759;Name=NP_414564.1;gbkey=CDS;gene=rpsT;locus_tag=b0023;orig_transcript_id=gnl|b0023|mrna.b0023;product=30S ribosomal subunit protein S20;protein_id=NP_414564.1;transl_table=11
+NC_000913.3 RefSeq gene 21181 21399 . + . ID=gene-b0024;Dbxref=ASAP:ABE-0000089,ECOCYC:G6087,EcoGene:EG14386,GeneID:949128;Name=yaaY;gbkey=Gene;gene=yaaY;gene_biotype=protein_coding;gene_synonym=ECK0025;locus_tag=b0024
+NC_000913.3 RefSeq CDS 21181 21399 . + 0 ID=cds-NP_414565.1;Parent=gene-b0024;Dbxref=UniProtKB/Swiss-Prot:P75620,Genbank:NP_414565.1,ASAP:ABE-0000089,ECOCYC:G6087,EcoGene:EG14386,GeneID:949128;Name=NP_414565.1;gbkey=CDS;gene=yaaY;locus_tag=b0024;orig_transcript_id=gnl|b0024|mrna.b0024;product=DUF2575 domain-containing protein YaaY;protein_id=NP_414565.1;transl_table=11
+NC_000913.3 RefSeq gene 21407 22348 . + . ID=gene-b0025;Dbxref=ASAP:ABE-0000091,ECOCYC:EG11079,EcoGene:EG11079,GeneID:949129;Name=ribF;gbkey=Gene;gene=ribF;gene_biotype=protein_coding;gene_synonym=ECK0026,yaaC;locus_tag=b0025
+NC_000913.3 RefSeq CDS 21407 22348 . + 0 ID=cds-NP_414566.1;Parent=gene-b0025;Dbxref=UniProtKB/Swiss-Prot:P0AG40,Genbank:NP_414566.1,ASAP:ABE-0000091,ECOCYC:EG11079,EcoGene:EG11079,GeneID:949129;Name=NP_414566.1;gbkey=CDS;gene=ribF;locus_tag=b0025;orig_transcript_id=gnl|b0025|mrna.b0025;product=bifunctional riboflavin kinase/FMN adenylyltransferase;protein_id=NP_414566.1;transl_table=11
+NC_000913.3 RefSeq gene 22391 25207 . + . ID=gene-b0026;Dbxref=ASAP:ABE-0000094,ECOCYC:EG10492,EcoGene:EG10492,GeneID:944761;Name=ileS;gbkey=Gene;gene=ileS;gene_biotype=protein_coding;gene_synonym=ECK0027,ilvS;locus_tag=b0026
+NC_000913.3 RefSeq CDS 22391 25207 . + 0 ID=cds-NP_414567.1;Parent=gene-b0026;Dbxref=UniProtKB/Swiss-Prot:P00956,Genbank:NP_414567.1,ASAP:ABE-0000094,ECOCYC:EG10492,EcoGene:EG10492,GeneID:944761;Name=NP_414567.1;gbkey=CDS;gene=ileS;locus_tag=b0026;orig_transcript_id=gnl|b0026|mrna.b0026;product=isoleucine--tRNA ligase;protein_id=NP_414567.1;transl_table=11
+NC_000913.3 RefSeq gene 25207 25701 . + . ID=gene-b0027;Dbxref=ASAP:ABE-0000096,ECOCYC:EG10548,EcoGene:EG10548,GeneID:944800;Name=lspA;gbkey=Gene;gene=lspA;gene_biotype=protein_coding;gene_synonym=ECK0028,lsp;locus_tag=b0027
+NC_000913.3 RefSeq CDS 25207 25701 . + 0 ID=cds-NP_414568.1;Parent=gene-b0027;Dbxref=UniProtKB/Swiss-Prot:P00804,Genbank:NP_414568.1,ASAP:ABE-0000096,ECOCYC:EG10548,EcoGene:EG10548,GeneID:944800;Name=NP_414568.1;gbkey=CDS;gene=lspA;locus_tag=b0027;orig_transcript_id=gnl|b0027|mrna.b0027;product=lipoprotein signal peptidase;protein_id=NP_414568.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 25711 25746 . + . ID=id-62;Note=REP2a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 25763 25796 . - . ID=id-63;Note=REP2b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 25826 26275 . + . ID=gene-b0028;Dbxref=ASAP:ABE-0000101,ECOCYC:EG11080,EcoGene:EG11080,GeneID:944807;Name=fkpB;gbkey=Gene;gene=fkpB;gene_biotype=protein_coding;gene_synonym=ECK0029,slpA,yaaD;locus_tag=b0028
+NC_000913.3 RefSeq CDS 25826 26275 . + 0 ID=cds-NP_414569.1;Parent=gene-b0028;Dbxref=UniProtKB/Swiss-Prot:P0AEM0,Genbank:NP_414569.1,ASAP:ABE-0000101,ECOCYC:EG11080,EcoGene:EG11080,GeneID:944807;Name=NP_414569.1;gbkey=CDS;gene=fkpB;locus_tag=b0028;orig_transcript_id=gnl|b0028|mrna.b0028;product=peptidyl-prolyl cis-trans isomerase FkpB;protein_id=NP_414569.1;transl_table=11
+NC_000913.3 RefSeq gene 26277 27227 . + . ID=gene-b0029;Dbxref=ASAP:ABE-0000103,ECOCYC:EG11081,EcoGene:EG11081,GeneID:944777;Name=ispH;gbkey=Gene;gene=ispH;gene_biotype=protein_coding;gene_synonym=ECK0030,lytB,yaaE;locus_tag=b0029
+NC_000913.3 RefSeq CDS 26277 27227 . + 0 ID=cds-NP_414570.1;Parent=gene-b0029;Dbxref=UniProtKB/Swiss-Prot:P62623,Genbank:NP_414570.1,ASAP:ABE-0000103,ECOCYC:EG11081,EcoGene:EG11081,GeneID:944777;Name=NP_414570.1;gbkey=CDS;gene=ispH;locus_tag=b0029;orig_transcript_id=gnl|b0029|mrna.b0029;product=1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase;protein_id=NP_414570.1;transl_table=11
+NC_000913.3 RefSeq gene 27293 28207 . + . ID=gene-b0030;Dbxref=ASAP:ABE-0000109,ECOCYC:EG11082,EcoGene:EG11082,GeneID:944796;Name=rihC;gbkey=Gene;gene=rihC;gene_biotype=protein_coding;gene_synonym=ECK0031,yaaF;locus_tag=b0030
+NC_000913.3 RefSeq CDS 27293 28207 . + 0 ID=cds-NP_414571.1;Parent=gene-b0030;Dbxref=UniProtKB/Swiss-Prot:P22564,Genbank:NP_414571.1,ASAP:ABE-0000109,ECOCYC:EG11082,EcoGene:EG11082,GeneID:944796;Name=NP_414571.1;gbkey=CDS;gene=rihC;locus_tag=b0030;orig_transcript_id=gnl|b0030|mrna.b0030;product=ribonucleoside hydrolase RihC;protein_id=NP_414571.1;transl_table=11
+NC_000913.3 RefSeq gene 28374 29195 . + . ID=gene-b0031;Dbxref=ASAP:ABE-0000112,ECOCYC:EG10206,EcoGene:EG10206,GeneID:944762;Name=dapB;gbkey=Gene;gene=dapB;gene_biotype=protein_coding;gene_synonym=ECK0032;locus_tag=b0031
+NC_000913.3 RefSeq CDS 28374 29195 . + 0 ID=cds-NP_414572.1;Parent=gene-b0031;Dbxref=UniProtKB/Swiss-Prot:P04036,Genbank:NP_414572.1,ASAP:ABE-0000112,ECOCYC:EG10206,EcoGene:EG10206,GeneID:944762;Name=NP_414572.1;gbkey=CDS;gene=dapB;locus_tag=b0031;orig_transcript_id=gnl|b0031|mrna.b0031;product=4-hydroxy-tetrahydrodipicolinate reductase;protein_id=NP_414572.1;transl_table=11
+NC_000913.3 RefSeq gene 29651 30799 . + . ID=gene-b0032;Dbxref=ASAP:ABE-0000118,ECOCYC:EG10134,EcoGene:EG10134,GeneID:949025;Name=carA;gbkey=Gene;gene=carA;gene_biotype=protein_coding;gene_synonym=arg,cap,ECK0033,pyrA;locus_tag=b0032
+NC_000913.3 RefSeq CDS 29651 30799 . + 0 ID=cds-NP_414573.1;Parent=gene-b0032;Dbxref=UniProtKB/Swiss-Prot:P0A6F1,Genbank:NP_414573.1,ASAP:ABE-0000118,ECOCYC:EG10134,EcoGene:EG10134,GeneID:949025;Name=NP_414573.1;gbkey=CDS;gene=carA;locus_tag=b0032;orig_transcript_id=gnl|b0032|mrna.b0032;product=carbamoyl phosphate synthetase subunit alpha;protein_id=NP_414573.1;transl_table=11
+NC_000913.3 RefSeq gene 30817 34038 . + . ID=gene-b0033;Dbxref=ASAP:ABE-0000121,ECOCYC:EG10135,EcoGene:EG10135,GeneID:944775;Name=carB;gbkey=Gene;gene=carB;gene_biotype=protein_coding;gene_synonym=cap,ECK0034,pyrA;locus_tag=b0033
+NC_000913.3 RefSeq CDS 30817 34038 . + 0 ID=cds-NP_414574.1;Parent=gene-b0033;Dbxref=UniProtKB/Swiss-Prot:P00968,Genbank:NP_414574.1,ASAP:ABE-0000121,ECOCYC:EG10135,EcoGene:EG10135,GeneID:944775;Name=NP_414574.1;gbkey=CDS;gene=carB;locus_tag=b0033;orig_transcript_id=gnl|b0033|mrna.b0033;product=carbamoyl phosphate synthetase subunit beta;protein_id=NP_414574.1;transl_table=11
+NC_000913.3 RefSeq gene 34300 34695 . + . ID=gene-b0034;Dbxref=ASAP:ABE-0000125,ECOCYC:G6088,EcoGene:EG13451,GeneID:944795;Name=caiF;gbkey=Gene;gene=caiF;gene_biotype=protein_coding;gene_synonym=ECK0035;locus_tag=b0034
+NC_000913.3 RefSeq CDS 34300 34695 . + 0 ID=cds-NP_414576.4;Parent=gene-b0034;Dbxref=UniProtKB/Swiss-Prot:P0AE58,Genbank:NP_414576.4,ASAP:ABE-0000125,ECOCYC:G6088,EcoGene:EG13451,GeneID:944795;Name=NP_414576.4;gbkey=CDS;gene=caiF;locus_tag=b0034;orig_transcript_id=gnl|b0034|mrna.b0034;product=DNA-binding transcriptional activator CaiF;protein_id=NP_414576.4;transl_table=11
+NC_000913.3 RefSeq repeat_region 34728 34763 . + . ID=id-78;Note=REP3;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 34781 35371 . - . ID=gene-b0035;Dbxref=ASAP:ABE-0000128,ECOCYC:EG12608,EcoGene:EG12608,GeneID:948999;Name=caiE;gbkey=Gene;gene=caiE;gene_biotype=protein_coding;gene_synonym=ECK0036;locus_tag=b0035
+NC_000913.3 RefSeq CDS 34781 35371 . - 0 ID=cds-NP_414577.2;Parent=gene-b0035;Dbxref=UniProtKB/Swiss-Prot:P39206,Genbank:NP_414577.2,ASAP:ABE-0000128,ECOCYC:EG12608,EcoGene:EG12608,GeneID:948999;Name=NP_414577.2;gbkey=CDS;gene=caiE;locus_tag=b0035;orig_transcript_id=gnl|b0035|mrna.b0035;product=putative transferase CaiE;protein_id=NP_414577.2;transl_table=11
+NC_000913.3 RefSeq gene 35377 36162 . - . ID=gene-b0036;Dbxref=ASAP:ABE-0000130,ECOCYC:EG11557,EcoGene:EG11557,GeneID:948995;Name=caiD;gbkey=Gene;gene=caiD;gene_biotype=protein_coding;gene_synonym=ECK0037,yaaL;locus_tag=b0036
+NC_000913.3 RefSeq CDS 35377 36162 . - 0 ID=cds-NP_414578.2;Parent=gene-b0036;Dbxref=UniProtKB/Swiss-Prot:P31551,Genbank:NP_414578.2,ASAP:ABE-0000130,ECOCYC:EG11557,EcoGene:EG11557,GeneID:948995;Name=NP_414578.2;gbkey=CDS;gene=caiD;locus_tag=b0036;orig_transcript_id=gnl|b0036|mrna.b0036;product=crotonobetainyl-CoA hydratase;protein_id=NP_414578.2;transl_table=11
+NC_000913.3 RefSeq gene 36271 37824 . - . ID=gene-b0037;Dbxref=ASAP:ABE-0000133,ECOCYC:EG11558,EcoGene:EG11558,GeneID:944886;Name=caiC;gbkey=Gene;gene=caiC;gene_biotype=protein_coding;gene_synonym=ECK0038,yaaM;locus_tag=b0037
+NC_000913.3 RefSeq CDS 36271 37824 . - 0 ID=cds-NP_414579.4;Parent=gene-b0037;Dbxref=UniProtKB/Swiss-Prot:P31552,Genbank:NP_414579.4,ASAP:ABE-0000133,ECOCYC:EG11558,EcoGene:EG11558,GeneID:944886;Name=NP_414579.4;gbkey=CDS;gene=caiC;locus_tag=b0037;orig_transcript_id=gnl|b0037|mrna.b0037;product=carnitine-CoA ligase;protein_id=NP_414579.4;transl_table=11
+NC_000913.3 RefSeq gene 37898 39115 . - . ID=gene-b0038;Dbxref=ASAP:ABE-0000136,ECOCYC:EG11559,EcoGene:EG11559,GeneID:948997;Name=caiB;gbkey=Gene;gene=caiB;gene_biotype=protein_coding;gene_synonym=ECK0039,yaaN;locus_tag=b0038
+NC_000913.3 RefSeq CDS 37898 39115 . - 0 ID=cds-NP_414580.1;Parent=gene-b0038;Dbxref=UniProtKB/Swiss-Prot:P31572,Genbank:NP_414580.1,ASAP:ABE-0000136,ECOCYC:EG11559,EcoGene:EG11559,GeneID:948997;Name=NP_414580.1;gbkey=CDS;gene=caiB;locus_tag=b0038;orig_transcript_id=gnl|b0038|mrna.b0038;product=gamma-butyrobetainyl-CoA:carnitine CoA transferase;protein_id=NP_414580.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 39152 39185 . + . ID=id-87;Note=REP4a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 39198 39233 . - . ID=id-88;Note=REP4b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 39244 40386 . - . ID=gene-b0039;Dbxref=ASAP:ABE-0000139,ECOCYC:EG11560,EcoGene:EG11560,GeneID:949064;Name=caiA;gbkey=Gene;gene=caiA;gene_biotype=protein_coding;gene_synonym=ECK0040,yaaO;locus_tag=b0039
+NC_000913.3 RefSeq CDS 39244 40386 . - 0 ID=cds-NP_414581.1;Parent=gene-b0039;Dbxref=UniProtKB/Swiss-Prot:P60584,Genbank:NP_414581.1,ASAP:ABE-0000139,ECOCYC:EG11560,EcoGene:EG11560,GeneID:949064;Name=NP_414581.1;gbkey=CDS;gene=caiA;locus_tag=b0039;orig_transcript_id=gnl|b0039|mrna.b0039;product=crotonobetainyl-CoA reductase;protein_id=NP_414581.1;transl_table=11
+NC_000913.3 RefSeq gene 40417 41931 . - . ID=gene-b0040;Dbxref=ASAP:ABE-0000141,ECOCYC:EG11561,EcoGene:EG11561,GeneID:944765;Name=caiT;gbkey=Gene;gene=caiT;gene_biotype=protein_coding;gene_synonym=ECK0041,yaaP;locus_tag=b0040
+NC_000913.3 RefSeq CDS 40417 41931 . - 0 ID=cds-NP_414582.1;Parent=gene-b0040;Dbxref=UniProtKB/Swiss-Prot:P31553,Genbank:NP_414582.1,ASAP:ABE-0000141,ECOCYC:EG11561,EcoGene:EG11561,GeneID:944765;Name=NP_414582.1;gbkey=CDS;gene=caiT;locus_tag=b0040;orig_transcript_id=gnl|b0040|mrna.b0040;product=L-carnitine:gamma-butyrobetaine antiporter;protein_id=NP_414582.1;transl_table=11
diff -r ae9994cf526f -r 014a21767ac4 test-data/text/2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/text/2.out Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,42 @@
+NC_000913.3 0 4641652 ANONYMOUS strand=1,value=0
+NC_000913.3 189 255 thrL strand=1,value=0
+NC_000913.3 336 2799 thrA strand=1,value=0
+NC_000913.3 2800 3733 thrB strand=1,value=0
+NC_000913.3 3733 5020 thrC strand=1,value=0
+NC_000913.3 5233 5530 yaaX strand=1,value=0
+NC_000913.3 5682 6459 yaaA strand=-1,value=0
+NC_000913.3 6528 7959 yaaJ strand=-1,value=0
+NC_000913.3 8237 9191 talB strand=1,value=0
+NC_000913.3 9305 9893 mog strand=1,value=0
+NC_000913.3 9927 10494 satP strand=-1,value=0
+NC_000913.3 10642 11356 yaaW strand=-1,value=0
+NC_000913.3 10829 11315 mbiA strand=1,value=0
+NC_000913.3 11381 11786 yaaI strand=-1,value=0
+NC_000913.3 12162 14079 dnaK strand=1,value=0
+NC_000913.3 14167 15298 dnaJ strand=1,value=0
+NC_000913.3 15444 16557 insL-1 strand=1,value=0
+NC_000913.3 16750 16960 mokC strand=-1,value=0
+NC_000913.3 16750 16903 hokC strand=-1,value=0
+NC_000913.3 16951 17006 sokC strand=1,value=0
+NC_000913.3 17488 18655 nhaA strand=1,value=0
+NC_000913.3 18714 19620 nhaR strand=1,value=0
+NC_000913.3 19810 20314 insB-1 strand=-1,value=0
+NC_000913.3 20232 20508 insA-1 strand=-1,value=0
+NC_000913.3 20814 21078 rpsT strand=-1,value=0
+NC_000913.3 21180 21399 yaaY strand=1,value=0
+NC_000913.3 21406 22348 ribF strand=1,value=0
+NC_000913.3 22390 25207 ileS strand=1,value=0
+NC_000913.3 25206 25701 lspA strand=1,value=0
+NC_000913.3 25825 26275 fkpB strand=1,value=0
+NC_000913.3 26276 27227 ispH strand=1,value=0
+NC_000913.3 27292 28207 rihC strand=1,value=0
+NC_000913.3 28373 29195 dapB strand=1,value=0
+NC_000913.3 29650 30799 carA strand=1,value=0
+NC_000913.3 30816 34038 carB strand=1,value=0
+NC_000913.3 34299 34695 caiF strand=1,value=0
+NC_000913.3 34780 35371 caiE strand=-1,value=0
+NC_000913.3 35376 36162 caiD strand=-1,value=0
+NC_000913.3 36270 37824 caiC strand=-1,value=0
+NC_000913.3 37897 39115 caiB strand=-1,value=0
+NC_000913.3 39243 40386 caiA strand=-1,value=0
+NC_000913.3 40416 41931 caiT strand=-1,value=0
diff -r ae9994cf526f -r 014a21767ac4 test-data/tiles/1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiles/1.bed Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,100 @@
+CP020543.1 49 1452 dnaA 0 +
+CP020543.1 1457 2557 . 0 +
+CP020543.1 2557 3630 . 0 +
+CP020543.1 3659 6073 . 0 +
+CP020543.1 6304 6711 . 0 +
+CP020543.1 6826 7638 . 0 +
+CP020543.1 7684 8340 . 0 -
+CP020543.1 8618 9307 . 0 +
+CP020543.1 9304 10182 . 0 +
+CP020543.1 10166 10783 . 0 +
+CP020543.1 10780 11928 . 0 +
+CP020543.1 12048 13340 . 0 +
+CP020543.1 13337 14401 . 0 -
+CP020543.1 14469 15716 . 0 +
+CP020543.1 15718 16050 . 0 -
+CP020543.1 16356 16769 . 0 +
+CP020543.1 16881 17309 . 0 +
+CP020543.1 17505 19166 . 0 +
+CP020543.1 19163 19879 . 0 -
+CP020543.1 20175 21791 . 0 +
+CP020543.1 21791 23113 . 0 +
+CP020543.1 23110 23184 . 0 -
+CP020543.1 23154 23612 . 0 -
+CP020543.1 23559 23704 . 0 +
+CP020543.1 23682 24890 . 0 +
+CP020543.1 25061 25408 . 0 +
+CP020543.1 25398 25760 . 0 +
+CP020543.1 25757 26254 . 0 +
+CP020543.1 26262 27446 . 0 -
+CP020543.1 27486 27668 . 0 -
+CP020543.1 27726 27815 . 0 -
+CP020543.1 27812 27925 . 0 -
+CP020543.1 27948 28106 . 0 -
+CP020543.1 28103 28393 . 0 -
+CP020543.1 28380 28478 . 0 +
+CP020543.1 28584 30272 . 0 +
+CP020543.1 30276 30566 . 0 +
+CP020543.1 30641 31231 . 0 +
+CP020543.1 31231 32733 . 0 +
+CP020543.1 32743 34062 . 0 +
+CP020543.1 34200 35591 . 0 +
+CP020543.1 35636 37402 . 0 -
+CP020543.1 37577 38911 . 0 +
+CP020543.1 38964 39416 . 0 +
+CP020543.1 39437 39628 . 0 -
+CP020543.1 39627 40817 nepI 0 +
+CP020543.1 40858 41151 . 0 -
+CP020543.1 41188 41376 . 0 +
+CP020543.1 41373 42191 . 0 +
+CP020543.1 42195 43118 . 0 -
+CP020543.1 43229 44413 . 0 -
+CP020543.1 44795 44941 . 0 -
+CP020543.1 45437 46819 . 0 +
+CP020543.1 46829 49147 . 0 +
+CP020543.1 49200 50909 . 0 -
+CP020543.1 51030 52421 . 0 -
+CP020543.1 52701 53906 . 0 +
+CP020543.1 54072 56153 . 0 -
+CP020543.1 56159 56848 . 0 -
+CP020543.1 56855 58963 . 0 -
+CP020543.1 58982 59257 . 0 -
+CP020543.1 59312 59935 . 0 -
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+CP020543.1 62781 63605 . 0 -
+CP020543.1 63826 64689 . 0 -
+CP020543.1 64702 64884 . 0 -
+CP020543.1 64816 65532 . 0 +
+CP020543.1 65598 66239 . 0 +
+CP020543.1 66276 66872 . 0 -
+CP020543.1 66979 67434 . 0 -
+CP020543.1 67415 68635 . 0 -
+CP020543.1 68807 69475 . 0 +
+CP020543.1 69692 69928 . 0 +
+CP020543.1 69949 70116 . 0 +
+CP020543.1 70214 71023 . 0 +
+CP020543.1 71062 71541 . 0 -
+CP020543.1 71549 72826 . 0 -
+CP020543.1 73239 74297 . 0 +
+CP020543.1 74294 75418 . 0 +
+CP020543.1 75411 76208 . 0 +
+CP020543.1 76224 77240 . 0 +
+CP020543.1 77257 78252 . 0 +
+CP020543.1 78262 78954 . 0 +
+CP020543.1 78980 80005 . 0 +
+CP020543.1 80090 81073 . 0 +
+CP020543.1 81119 82372 . 0 +
+CP020543.1 82442 83413 . 0 -
+CP020543.1 83417 84463 . 0 -
+CP020543.1 84473 85405 . 0 -
+CP020543.1 85619 86815 . 0 +
+CP020543.1 86825 87850 . 0 +
+CP020543.1 88089 89123 . 0 +
+CP020543.1 89110 90069 . 0 -
+CP020543.1 90073 91356 . 0 -
+CP020543.1 91366 92910 . 0 -
+CP020543.1 92934 93131 . 0 -
+CP020543.1 93155 93586 . 0 +
+CP020543.1 93728 93979 . 0 +
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diff -r ae9994cf526f -r 014a21767ac4 test-data/tiles/1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiles/1.out Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,100 @@
+CP020543.1 49 1452 name=dnaA,strand=1,value=0
+CP020543.1 1457 2557 name=.,strand=1,value=0
+CP020543.1 2557 3630 name=.,strand=1,value=0
+CP020543.1 3659 6073 name=.,strand=1,value=0
+CP020543.1 6304 6711 name=.,strand=1,value=0
+CP020543.1 6826 7638 name=.,strand=1,value=0
+CP020543.1 7684 8340 name=.,strand=-1,value=0
+CP020543.1 8618 9307 name=.,strand=1,value=0
+CP020543.1 9304 10182 name=.,strand=1,value=0
+CP020543.1 10166 10783 name=.,strand=1,value=0
+CP020543.1 10780 11928 name=.,strand=1,value=0
+CP020543.1 12048 13340 name=.,strand=1,value=0
+CP020543.1 13337 14401 name=.,strand=-1,value=0
+CP020543.1 14469 15716 name=.,strand=1,value=0
+CP020543.1 15718 16050 name=.,strand=-1,value=0
+CP020543.1 16356 16769 name=.,strand=1,value=0
+CP020543.1 16881 17309 name=.,strand=1,value=0
+CP020543.1 17505 19166 name=.,strand=1,value=0
+CP020543.1 19163 19879 name=.,strand=-1,value=0
+CP020543.1 20175 21791 name=.,strand=1,value=0
+CP020543.1 21791 23113 name=.,strand=1,value=0
+CP020543.1 23110 23184 name=.,strand=-1,value=0
+CP020543.1 23154 23612 name=.,strand=-1,value=0
+CP020543.1 23559 23704 name=.,strand=1,value=0
+CP020543.1 23682 24890 name=.,strand=1,value=0
+CP020543.1 25061 25408 name=.,strand=1,value=0
+CP020543.1 25398 25760 name=.,strand=1,value=0
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+CP020543.1 27812 27925 name=.,strand=-1,value=0
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+CP020543.1 28103 28393 name=.,strand=-1,value=0
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+CP020543.1 34200 35591 name=.,strand=1,value=0
+CP020543.1 35636 37402 name=.,strand=-1,value=0
+CP020543.1 37577 38911 name=.,strand=1,value=0
+CP020543.1 38964 39416 name=.,strand=1,value=0
+CP020543.1 39437 39628 name=.,strand=-1,value=0
+CP020543.1 39627 40817 name=nepI,strand=1,value=0
+CP020543.1 40858 41151 name=.,strand=-1,value=0
+CP020543.1 41188 41376 name=.,strand=1,value=0
+CP020543.1 41373 42191 name=.,strand=1,value=0
+CP020543.1 42195 43118 name=.,strand=-1,value=0
+CP020543.1 43229 44413 name=.,strand=-1,value=0
+CP020543.1 44795 44941 name=.,strand=-1,value=0
+CP020543.1 45437 46819 name=.,strand=1,value=0
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+CP020543.1 49200 50909 name=.,strand=-1,value=0
+CP020543.1 51030 52421 name=.,strand=-1,value=0
+CP020543.1 52701 53906 name=.,strand=1,value=0
+CP020543.1 54072 56153 name=.,strand=-1,value=0
+CP020543.1 56159 56848 name=.,strand=-1,value=0
+CP020543.1 56855 58963 name=.,strand=-1,value=0
+CP020543.1 58982 59257 name=.,strand=-1,value=0
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+CP020543.1 62781 63605 name=.,strand=-1,value=0
+CP020543.1 63826 64689 name=.,strand=-1,value=0
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+CP020543.1 64816 65532 name=.,strand=1,value=0
+CP020543.1 65598 66239 name=.,strand=1,value=0
+CP020543.1 66276 66872 name=.,strand=-1,value=0
+CP020543.1 66979 67434 name=.,strand=-1,value=0
+CP020543.1 67415 68635 name=.,strand=-1,value=0
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+CP020543.1 74294 75418 name=.,strand=1,value=0
+CP020543.1 75411 76208 name=.,strand=1,value=0
+CP020543.1 76224 77240 name=.,strand=1,value=0
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+CP020543.1 78980 80005 name=.,strand=1,value=0
+CP020543.1 80090 81073 name=.,strand=1,value=0
+CP020543.1 81119 82372 name=.,strand=1,value=0
+CP020543.1 82442 83413 name=.,strand=-1,value=0
+CP020543.1 83417 84463 name=.,strand=-1,value=0
+CP020543.1 84473 85405 name=.,strand=-1,value=0
+CP020543.1 85619 86815 name=.,strand=1,value=0
+CP020543.1 86825 87850 name=.,strand=1,value=0
+CP020543.1 88089 89123 name=.,strand=1,value=0
+CP020543.1 89110 90069 name=.,strand=-1,value=0
+CP020543.1 90073 91356 name=.,strand=-1,value=0
+CP020543.1 91366 92910 name=.,strand=-1,value=0
+CP020543.1 92934 93131 name=.,strand=-1,value=0
+CP020543.1 93155 93586 name=.,strand=1,value=0
+CP020543.1 93728 93979 name=.,strand=1,value=0
+CP020543.1 94042 94509 name=.,strand=1,value=0
diff -r ae9994cf526f -r 014a21767ac4 test-data/tiles/2.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiles/2.gff3 Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,100 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM584v2
+#!genome-build-accession NCBI_Assembly:GCF_000005845.2
+##sequence-region NC_000913.3 1 4641652
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
+NC_000913.3 RefSeq region 1 4641652 . + . ID=NC_000913.3:1..4641652;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
+NC_000913.3 RefSeq gene 190 255 . + . ID=gene-b0001;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001
+NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds-NP_414542.1;Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3 RefSeq gene 337 2799 . + . ID=gene-b0002;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds-NP_414543.1;Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene-b0003;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003
+NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds-NP_414544.1;Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene-b0004;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004
+NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds-NP_414545.1;Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;gene=thrC;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene-b0005;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005
+NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds-NP_414546.1;Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;protein_id=NP_414546.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 5566 5601 . + . ID=id-12;Note=REP1a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 5637 5670 . - . ID=id-13;Note=REP1b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene-b0006;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006
+NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds-NP_414547.1;Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;protein_id=NP_414547.1;transl_table=11
+NC_000913.3 RefSeq gene 6529 7959 . - . ID=gene-b0007;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene=yaaJ;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007
+NC_000913.3 RefSeq CDS 6529 7959 . - 0 ID=cds-NP_414548.1;Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;gene=yaaJ;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;protein_id=NP_414548.1;transl_table=11
+NC_000913.3 RefSeq gene 8238 9191 . + . ID=gene-b0008;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene=talB;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008
+NC_000913.3 RefSeq CDS 8238 9191 . + 0 ID=cds-NP_414549.1;Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;gene=talB;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;protein_id=NP_414549.1;transl_table=11
+NC_000913.3 RefSeq gene 9306 9893 . + . ID=gene-b0009;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene=mog;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009
+NC_000913.3 RefSeq CDS 9306 9893 . + 0 ID=cds-NP_414550.1;Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;gene=mog;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;protein_id=NP_414550.1;transl_table=11
+NC_000913.3 RefSeq gene 9928 10494 . - . ID=gene-b0010;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene=satP;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010
+NC_000913.3 RefSeq CDS 9928 10494 . - 0 ID=cds-NP_414551.1;Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;gene=satP;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;protein_id=NP_414551.1;transl_table=11
+NC_000913.3 RefSeq gene 10643 11356 . - . ID=gene-b0011;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene=yaaW;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011
+NC_000913.3 RefSeq CDS 10643 11356 . - 0 ID=cds-NP_414552.1;Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;gene=yaaW;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;protein_id=NP_414552.1;transl_table=11
+NC_000913.3 RefSeq gene 10830 11315 . + . ID=gene-b0012;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene=mbiA;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012
+NC_000913.3 RefSeq CDS 10830 11315 . + 0 ID=cds-YP_009518733.1;Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;gene=mbiA;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;protein_id=YP_009518733.1;transl_table=11
+NC_000913.3 RefSeq gene 11382 11786 . - . ID=gene-b0013;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene=yaaI;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013
+NC_000913.3 RefSeq CDS 11382 11786 . - 0 ID=cds-NP_414554.1;Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;gene=yaaI;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;protein_id=NP_414554.1;transl_table=11
+NC_000913.3 RefSeq gene 12163 14079 . + . ID=gene-b0014;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene=dnaK;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014
+NC_000913.3 RefSeq CDS 12163 14079 . + 0 ID=cds-NP_414555.1;Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;gene=dnaK;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;protein_id=NP_414555.1;transl_table=11
+NC_000913.3 RefSeq gene 14168 15298 . + . ID=gene-b0015;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene=dnaJ;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015
+NC_000913.3 RefSeq CDS 14168 15298 . + 0 ID=cds-NP_414556.1;Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;gene=dnaJ;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;protein_id=NP_414556.1;transl_table=11
+NC_000913.3 RefSeq mobile_genetic_element 15387 16731 . + . ID=id-34;gbkey=mobile_element;mobile_element_type=insertion sequence:IS186A
+NC_000913.3 RefSeq gene 15445 16557 . + . ID=gene-b0016;Dbxref=ASAP:ABE-0000058,ECOCYC:G6083,EcoGene:EG60001,GeneID:944754;Name=insL-1;gbkey=Gene;gene=insL-1;gene_biotype=protein_coding;gene_synonym=ECK0016,yi81-1;locus_tag=b0016
+NC_000913.3 RefSeq CDS 15445 16557 . + 0 ID=cds-NP_414557.1;Parent=gene-b0016;Dbxref=UniProtKB/Swiss-Prot:P0CF91,Genbank:NP_414557.1,ASAP:ABE-0000058,ECOCYC:G6083,EcoGene:EG60001,GeneID:944754;Name=NP_414557.1;gbkey=CDS;gene=insL-1;locus_tag=b0016;orig_transcript_id=gnl|b0016|mrna.b0016;product=IS186/IS421 transposase;protein_id=NP_414557.1;transl_table=11
+NC_000913.3 RefSeq gene 16751 16960 . - . ID=gene-b0018;Dbxref=ASAP:ABE-0000064,ECOCYC:EG10373,EcoGene:EG12074,GeneID:944756;Name=mokC;gbkey=Gene;gene=mokC;gene_biotype=protein_coding;gene_synonym=ECK0018,gefL;locus_tag=b0018
+NC_000913.3 RefSeq CDS 16751 16960 . - 0 ID=cds-NP_414559.1;Parent=gene-b0018;Dbxref=UniProtKB/Swiss-Prot:P33236,Genbank:NP_414559.1,ASAP:ABE-0000064,ECOCYC:EG10373,EcoGene:EG12074,GeneID:944756;Name=NP_414559.1;gbkey=CDS;gene=mokC;locus_tag=b0018;orig_transcript_id=gnl|b0018|mrna.b0018;product=regulatory protein MokC;protein_id=NP_414559.1;transl_table=11
+NC_000913.3 RefSeq gene 16751 16903 . - . ID=gene-b4412;Dbxref=ASAP:ABE-0047278,ECOCYC:G0-9563,EcoGene:EG10373,GeneID:2847744;Name=hokC;gbkey=Gene;gene=hokC;gene_biotype=protein_coding;gene_synonym=ECK0017,gef;locus_tag=b4412
+NC_000913.3 RefSeq CDS 16751 16903 . - 0 ID=cds-YP_025292.1;Parent=gene-b4412;Dbxref=UniProtKB/Swiss-Prot:P0ACG4,Genbank:YP_025292.1,ASAP:ABE-0047278,ECOCYC:G0-9563,EcoGene:EG10373,GeneID:2847744;Name=YP_025292.1;gbkey=CDS;gene=hokC;locus_tag=b4412;orig_transcript_id=gnl|b4412|mrna.b4412;product=protein HokC;protein_id=YP_025292.1;transl_table=11
+NC_000913.3 RefSeq gene 16952 17006 . + . ID=gene-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;Name=sokC;gbkey=Gene;gene=sokC;gene_biotype=ncRNA;gene_synonym=ECK0019,sof;locus_tag=b4413
+NC_000913.3 RefSeq ncRNA 16952 17006 . + . ID=rna-b4413;Parent=gene-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;gbkey=ncRNA;gene=sokC;locus_tag=b4413;product=antisense RNA blocking mokC and hokC translation
+NC_000913.3 RefSeq exon 16952 17006 . + . ID=exon-b4413-1;Parent=rna-b4413;Dbxref=ASAP:ABE-0047238,ECOCYC:G0-9581,EcoGene:EG31128,GeneID:2847745;gbkey=ncRNA;gene=sokC;locus_tag=b4413;product=antisense RNA blocking mokC and hokC translation
+NC_000913.3 RefSeq gene 17489 18655 . + . ID=gene-b0019;Dbxref=ASAP:ABE-0000068,ECOCYC:EG10652,EcoGene:EG10652,GeneID:944758;Name=nhaA;gbkey=Gene;gene=nhaA;gene_biotype=protein_coding;gene_synonym=ant,antA,ECK0020,hyc;locus_tag=b0019
+NC_000913.3 RefSeq CDS 17489 18655 . + 0 ID=cds-NP_414560.1;Parent=gene-b0019;Dbxref=UniProtKB/Swiss-Prot:P13738,Genbank:NP_414560.1,ASAP:ABE-0000068,ECOCYC:EG10652,EcoGene:EG10652,GeneID:944758;Name=NP_414560.1;gbkey=CDS;gene=nhaA;locus_tag=b0019;orig_transcript_id=gnl|b0019|mrna.b0019;product=Na(+):H(+) antiporter NhaA;protein_id=NP_414560.1;transl_table=11
+NC_000913.3 RefSeq gene 18715 19620 . + . ID=gene-b0020;Dbxref=ASAP:ABE-0000072,ECOCYC:EG11078,EcoGene:EG11078,GeneID:944757;Name=nhaR;gbkey=Gene;gene=nhaR;gene_biotype=protein_coding;gene_synonym=antO,ECK0021,yaaB;locus_tag=b0020
+NC_000913.3 RefSeq CDS 18715 19620 . + 0 ID=cds-NP_414561.1;Parent=gene-b0020;Dbxref=UniProtKB/Swiss-Prot:P0A9G2,Genbank:NP_414561.1,ASAP:ABE-0000072,ECOCYC:EG11078,EcoGene:EG11078,GeneID:944757;Name=NP_414561.1;gbkey=CDS;gene=nhaR;locus_tag=b0020;orig_transcript_id=gnl|b0020|mrna.b0020;product=DNA-binding transcriptional activator NhaR;protein_id=NP_414561.1;transl_table=11
+NC_000913.3 RefSeq mobile_genetic_element 19796 20563 . - . ID=id-47;gbkey=mobile_element;mobile_element_type=insertion sequence:IS1A
+NC_000913.3 RefSeq gene 19811 20314 . - . ID=gene-b0021;Dbxref=ASAP:ABE-0000075,ECOCYC:G6085,EcoGene:EG60002,GeneID:944743;Name=insB-1;gbkey=Gene;gene=insB-1;gene_biotype=protein_coding;gene_synonym=ECK0022;locus_tag=b0021
+NC_000913.3 RefSeq CDS 19811 20314 . - 0 ID=cds-NP_414562.1;Parent=gene-b0021;Dbxref=UniProtKB/Swiss-Prot:P0CF25,Genbank:NP_414562.1,ASAP:ABE-0000075,ECOCYC:G6085,EcoGene:EG60002,GeneID:944743;Name=NP_414562.1;gbkey=CDS;gene=insB-1;locus_tag=b0021;orig_transcript_id=gnl|b0021|mrna.b0021;product=IS1 protein InsB;protein_id=NP_414562.1;transl_table=11
+NC_000913.3 RefSeq gene 20233 20508 . - . ID=gene-b0022;Dbxref=ASAP:ABE-0000078,ECOCYC:G6086,EcoGene:EG40001,GeneID:948449;Name=insA-1;gbkey=Gene;gene=insA-1;gene_biotype=protein_coding;gene_synonym=ECK0023;locus_tag=b0022
+NC_000913.3 RefSeq CDS 20233 20508 . - 0 ID=cds-NP_414563.1;Parent=gene-b0022;Dbxref=UniProtKB/Swiss-Prot:P0CF07,Genbank:NP_414563.1,ASAP:ABE-0000078,ECOCYC:G6086,EcoGene:EG40001,GeneID:948449;Name=NP_414563.1;gbkey=CDS;gene=insA-1;locus_tag=b0022;orig_transcript_id=gnl|b0022|mrna.b0022;product=IS1 protein InsA;protein_id=NP_414563.1;transl_table=11
+NC_000913.3 RefSeq gene 20815 21078 . - . ID=gene-b0023;Dbxref=ASAP:ABE-0000082,ECOCYC:EG10919,EcoGene:EG10919,GeneID:944759;Name=rpsT;gbkey=Gene;gene=rpsT;gene_biotype=protein_coding;gene_synonym=ECK0024,sup(s20),supS,supS20;locus_tag=b0023
+NC_000913.3 RefSeq CDS 20815 21078 . - 0 ID=cds-NP_414564.1;Parent=gene-b0023;Dbxref=UniProtKB/Swiss-Prot:P0A7U7,Genbank:NP_414564.1,ASAP:ABE-0000082,ECOCYC:EG10919,EcoGene:EG10919,GeneID:944759;Name=NP_414564.1;gbkey=CDS;gene=rpsT;locus_tag=b0023;orig_transcript_id=gnl|b0023|mrna.b0023;product=30S ribosomal subunit protein S20;protein_id=NP_414564.1;transl_table=11
+NC_000913.3 RefSeq gene 21181 21399 . + . ID=gene-b0024;Dbxref=ASAP:ABE-0000089,ECOCYC:G6087,EcoGene:EG14386,GeneID:949128;Name=yaaY;gbkey=Gene;gene=yaaY;gene_biotype=protein_coding;gene_synonym=ECK0025;locus_tag=b0024
+NC_000913.3 RefSeq CDS 21181 21399 . + 0 ID=cds-NP_414565.1;Parent=gene-b0024;Dbxref=UniProtKB/Swiss-Prot:P75620,Genbank:NP_414565.1,ASAP:ABE-0000089,ECOCYC:G6087,EcoGene:EG14386,GeneID:949128;Name=NP_414565.1;gbkey=CDS;gene=yaaY;locus_tag=b0024;orig_transcript_id=gnl|b0024|mrna.b0024;product=DUF2575 domain-containing protein YaaY;protein_id=NP_414565.1;transl_table=11
+NC_000913.3 RefSeq gene 21407 22348 . + . ID=gene-b0025;Dbxref=ASAP:ABE-0000091,ECOCYC:EG11079,EcoGene:EG11079,GeneID:949129;Name=ribF;gbkey=Gene;gene=ribF;gene_biotype=protein_coding;gene_synonym=ECK0026,yaaC;locus_tag=b0025
+NC_000913.3 RefSeq CDS 21407 22348 . + 0 ID=cds-NP_414566.1;Parent=gene-b0025;Dbxref=UniProtKB/Swiss-Prot:P0AG40,Genbank:NP_414566.1,ASAP:ABE-0000091,ECOCYC:EG11079,EcoGene:EG11079,GeneID:949129;Name=NP_414566.1;gbkey=CDS;gene=ribF;locus_tag=b0025;orig_transcript_id=gnl|b0025|mrna.b0025;product=bifunctional riboflavin kinase/FMN adenylyltransferase;protein_id=NP_414566.1;transl_table=11
+NC_000913.3 RefSeq gene 22391 25207 . + . ID=gene-b0026;Dbxref=ASAP:ABE-0000094,ECOCYC:EG10492,EcoGene:EG10492,GeneID:944761;Name=ileS;gbkey=Gene;gene=ileS;gene_biotype=protein_coding;gene_synonym=ECK0027,ilvS;locus_tag=b0026
+NC_000913.3 RefSeq CDS 22391 25207 . + 0 ID=cds-NP_414567.1;Parent=gene-b0026;Dbxref=UniProtKB/Swiss-Prot:P00956,Genbank:NP_414567.1,ASAP:ABE-0000094,ECOCYC:EG10492,EcoGene:EG10492,GeneID:944761;Name=NP_414567.1;gbkey=CDS;gene=ileS;locus_tag=b0026;orig_transcript_id=gnl|b0026|mrna.b0026;product=isoleucine--tRNA ligase;protein_id=NP_414567.1;transl_table=11
+NC_000913.3 RefSeq gene 25207 25701 . + . ID=gene-b0027;Dbxref=ASAP:ABE-0000096,ECOCYC:EG10548,EcoGene:EG10548,GeneID:944800;Name=lspA;gbkey=Gene;gene=lspA;gene_biotype=protein_coding;gene_synonym=ECK0028,lsp;locus_tag=b0027
+NC_000913.3 RefSeq CDS 25207 25701 . + 0 ID=cds-NP_414568.1;Parent=gene-b0027;Dbxref=UniProtKB/Swiss-Prot:P00804,Genbank:NP_414568.1,ASAP:ABE-0000096,ECOCYC:EG10548,EcoGene:EG10548,GeneID:944800;Name=NP_414568.1;gbkey=CDS;gene=lspA;locus_tag=b0027;orig_transcript_id=gnl|b0027|mrna.b0027;product=lipoprotein signal peptidase;protein_id=NP_414568.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 25711 25746 . + . ID=id-62;Note=REP2a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 25763 25796 . - . ID=id-63;Note=REP2b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 25826 26275 . + . ID=gene-b0028;Dbxref=ASAP:ABE-0000101,ECOCYC:EG11080,EcoGene:EG11080,GeneID:944807;Name=fkpB;gbkey=Gene;gene=fkpB;gene_biotype=protein_coding;gene_synonym=ECK0029,slpA,yaaD;locus_tag=b0028
+NC_000913.3 RefSeq CDS 25826 26275 . + 0 ID=cds-NP_414569.1;Parent=gene-b0028;Dbxref=UniProtKB/Swiss-Prot:P0AEM0,Genbank:NP_414569.1,ASAP:ABE-0000101,ECOCYC:EG11080,EcoGene:EG11080,GeneID:944807;Name=NP_414569.1;gbkey=CDS;gene=fkpB;locus_tag=b0028;orig_transcript_id=gnl|b0028|mrna.b0028;product=peptidyl-prolyl cis-trans isomerase FkpB;protein_id=NP_414569.1;transl_table=11
+NC_000913.3 RefSeq gene 26277 27227 . + . ID=gene-b0029;Dbxref=ASAP:ABE-0000103,ECOCYC:EG11081,EcoGene:EG11081,GeneID:944777;Name=ispH;gbkey=Gene;gene=ispH;gene_biotype=protein_coding;gene_synonym=ECK0030,lytB,yaaE;locus_tag=b0029
+NC_000913.3 RefSeq CDS 26277 27227 . + 0 ID=cds-NP_414570.1;Parent=gene-b0029;Dbxref=UniProtKB/Swiss-Prot:P62623,Genbank:NP_414570.1,ASAP:ABE-0000103,ECOCYC:EG11081,EcoGene:EG11081,GeneID:944777;Name=NP_414570.1;gbkey=CDS;gene=ispH;locus_tag=b0029;orig_transcript_id=gnl|b0029|mrna.b0029;product=1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase;protein_id=NP_414570.1;transl_table=11
+NC_000913.3 RefSeq gene 27293 28207 . + . ID=gene-b0030;Dbxref=ASAP:ABE-0000109,ECOCYC:EG11082,EcoGene:EG11082,GeneID:944796;Name=rihC;gbkey=Gene;gene=rihC;gene_biotype=protein_coding;gene_synonym=ECK0031,yaaF;locus_tag=b0030
+NC_000913.3 RefSeq CDS 27293 28207 . + 0 ID=cds-NP_414571.1;Parent=gene-b0030;Dbxref=UniProtKB/Swiss-Prot:P22564,Genbank:NP_414571.1,ASAP:ABE-0000109,ECOCYC:EG11082,EcoGene:EG11082,GeneID:944796;Name=NP_414571.1;gbkey=CDS;gene=rihC;locus_tag=b0030;orig_transcript_id=gnl|b0030|mrna.b0030;product=ribonucleoside hydrolase RihC;protein_id=NP_414571.1;transl_table=11
+NC_000913.3 RefSeq gene 28374 29195 . + . ID=gene-b0031;Dbxref=ASAP:ABE-0000112,ECOCYC:EG10206,EcoGene:EG10206,GeneID:944762;Name=dapB;gbkey=Gene;gene=dapB;gene_biotype=protein_coding;gene_synonym=ECK0032;locus_tag=b0031
+NC_000913.3 RefSeq CDS 28374 29195 . + 0 ID=cds-NP_414572.1;Parent=gene-b0031;Dbxref=UniProtKB/Swiss-Prot:P04036,Genbank:NP_414572.1,ASAP:ABE-0000112,ECOCYC:EG10206,EcoGene:EG10206,GeneID:944762;Name=NP_414572.1;gbkey=CDS;gene=dapB;locus_tag=b0031;orig_transcript_id=gnl|b0031|mrna.b0031;product=4-hydroxy-tetrahydrodipicolinate reductase;protein_id=NP_414572.1;transl_table=11
+NC_000913.3 RefSeq gene 29651 30799 . + . ID=gene-b0032;Dbxref=ASAP:ABE-0000118,ECOCYC:EG10134,EcoGene:EG10134,GeneID:949025;Name=carA;gbkey=Gene;gene=carA;gene_biotype=protein_coding;gene_synonym=arg,cap,ECK0033,pyrA;locus_tag=b0032
+NC_000913.3 RefSeq CDS 29651 30799 . + 0 ID=cds-NP_414573.1;Parent=gene-b0032;Dbxref=UniProtKB/Swiss-Prot:P0A6F1,Genbank:NP_414573.1,ASAP:ABE-0000118,ECOCYC:EG10134,EcoGene:EG10134,GeneID:949025;Name=NP_414573.1;gbkey=CDS;gene=carA;locus_tag=b0032;orig_transcript_id=gnl|b0032|mrna.b0032;product=carbamoyl phosphate synthetase subunit alpha;protein_id=NP_414573.1;transl_table=11
+NC_000913.3 RefSeq gene 30817 34038 . + . ID=gene-b0033;Dbxref=ASAP:ABE-0000121,ECOCYC:EG10135,EcoGene:EG10135,GeneID:944775;Name=carB;gbkey=Gene;gene=carB;gene_biotype=protein_coding;gene_synonym=cap,ECK0034,pyrA;locus_tag=b0033
+NC_000913.3 RefSeq CDS 30817 34038 . + 0 ID=cds-NP_414574.1;Parent=gene-b0033;Dbxref=UniProtKB/Swiss-Prot:P00968,Genbank:NP_414574.1,ASAP:ABE-0000121,ECOCYC:EG10135,EcoGene:EG10135,GeneID:944775;Name=NP_414574.1;gbkey=CDS;gene=carB;locus_tag=b0033;orig_transcript_id=gnl|b0033|mrna.b0033;product=carbamoyl phosphate synthetase subunit beta;protein_id=NP_414574.1;transl_table=11
+NC_000913.3 RefSeq gene 34300 34695 . + . ID=gene-b0034;Dbxref=ASAP:ABE-0000125,ECOCYC:G6088,EcoGene:EG13451,GeneID:944795;Name=caiF;gbkey=Gene;gene=caiF;gene_biotype=protein_coding;gene_synonym=ECK0035;locus_tag=b0034
+NC_000913.3 RefSeq CDS 34300 34695 . + 0 ID=cds-NP_414576.4;Parent=gene-b0034;Dbxref=UniProtKB/Swiss-Prot:P0AE58,Genbank:NP_414576.4,ASAP:ABE-0000125,ECOCYC:G6088,EcoGene:EG13451,GeneID:944795;Name=NP_414576.4;gbkey=CDS;gene=caiF;locus_tag=b0034;orig_transcript_id=gnl|b0034|mrna.b0034;product=DNA-binding transcriptional activator CaiF;protein_id=NP_414576.4;transl_table=11
+NC_000913.3 RefSeq repeat_region 34728 34763 . + . ID=id-78;Note=REP3;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 34781 35371 . - . ID=gene-b0035;Dbxref=ASAP:ABE-0000128,ECOCYC:EG12608,EcoGene:EG12608,GeneID:948999;Name=caiE;gbkey=Gene;gene=caiE;gene_biotype=protein_coding;gene_synonym=ECK0036;locus_tag=b0035
+NC_000913.3 RefSeq CDS 34781 35371 . - 0 ID=cds-NP_414577.2;Parent=gene-b0035;Dbxref=UniProtKB/Swiss-Prot:P39206,Genbank:NP_414577.2,ASAP:ABE-0000128,ECOCYC:EG12608,EcoGene:EG12608,GeneID:948999;Name=NP_414577.2;gbkey=CDS;gene=caiE;locus_tag=b0035;orig_transcript_id=gnl|b0035|mrna.b0035;product=putative transferase CaiE;protein_id=NP_414577.2;transl_table=11
+NC_000913.3 RefSeq gene 35377 36162 . - . ID=gene-b0036;Dbxref=ASAP:ABE-0000130,ECOCYC:EG11557,EcoGene:EG11557,GeneID:948995;Name=caiD;gbkey=Gene;gene=caiD;gene_biotype=protein_coding;gene_synonym=ECK0037,yaaL;locus_tag=b0036
+NC_000913.3 RefSeq CDS 35377 36162 . - 0 ID=cds-NP_414578.2;Parent=gene-b0036;Dbxref=UniProtKB/Swiss-Prot:P31551,Genbank:NP_414578.2,ASAP:ABE-0000130,ECOCYC:EG11557,EcoGene:EG11557,GeneID:948995;Name=NP_414578.2;gbkey=CDS;gene=caiD;locus_tag=b0036;orig_transcript_id=gnl|b0036|mrna.b0036;product=crotonobetainyl-CoA hydratase;protein_id=NP_414578.2;transl_table=11
+NC_000913.3 RefSeq gene 36271 37824 . - . ID=gene-b0037;Dbxref=ASAP:ABE-0000133,ECOCYC:EG11558,EcoGene:EG11558,GeneID:944886;Name=caiC;gbkey=Gene;gene=caiC;gene_biotype=protein_coding;gene_synonym=ECK0038,yaaM;locus_tag=b0037
+NC_000913.3 RefSeq CDS 36271 37824 . - 0 ID=cds-NP_414579.4;Parent=gene-b0037;Dbxref=UniProtKB/Swiss-Prot:P31552,Genbank:NP_414579.4,ASAP:ABE-0000133,ECOCYC:EG11558,EcoGene:EG11558,GeneID:944886;Name=NP_414579.4;gbkey=CDS;gene=caiC;locus_tag=b0037;orig_transcript_id=gnl|b0037|mrna.b0037;product=carnitine-CoA ligase;protein_id=NP_414579.4;transl_table=11
+NC_000913.3 RefSeq gene 37898 39115 . - . ID=gene-b0038;Dbxref=ASAP:ABE-0000136,ECOCYC:EG11559,EcoGene:EG11559,GeneID:948997;Name=caiB;gbkey=Gene;gene=caiB;gene_biotype=protein_coding;gene_synonym=ECK0039,yaaN;locus_tag=b0038
+NC_000913.3 RefSeq CDS 37898 39115 . - 0 ID=cds-NP_414580.1;Parent=gene-b0038;Dbxref=UniProtKB/Swiss-Prot:P31572,Genbank:NP_414580.1,ASAP:ABE-0000136,ECOCYC:EG11559,EcoGene:EG11559,GeneID:948997;Name=NP_414580.1;gbkey=CDS;gene=caiB;locus_tag=b0038;orig_transcript_id=gnl|b0038|mrna.b0038;product=gamma-butyrobetainyl-CoA:carnitine CoA transferase;protein_id=NP_414580.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 39152 39185 . + . ID=id-87;Note=REP4a;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq repeat_region 39198 39233 . - . ID=id-88;Note=REP4b;gbkey=repeat_region;rpt_type=other
+NC_000913.3 RefSeq gene 39244 40386 . - . ID=gene-b0039;Dbxref=ASAP:ABE-0000139,ECOCYC:EG11560,EcoGene:EG11560,GeneID:949064;Name=caiA;gbkey=Gene;gene=caiA;gene_biotype=protein_coding;gene_synonym=ECK0040,yaaO;locus_tag=b0039
+NC_000913.3 RefSeq CDS 39244 40386 . - 0 ID=cds-NP_414581.1;Parent=gene-b0039;Dbxref=UniProtKB/Swiss-Prot:P60584,Genbank:NP_414581.1,ASAP:ABE-0000139,ECOCYC:EG11560,EcoGene:EG11560,GeneID:949064;Name=NP_414581.1;gbkey=CDS;gene=caiA;locus_tag=b0039;orig_transcript_id=gnl|b0039|mrna.b0039;product=crotonobetainyl-CoA reductase;protein_id=NP_414581.1;transl_table=11
+NC_000913.3 RefSeq gene 40417 41931 . - . ID=gene-b0040;Dbxref=ASAP:ABE-0000141,ECOCYC:EG11561,EcoGene:EG11561,GeneID:944765;Name=caiT;gbkey=Gene;gene=caiT;gene_biotype=protein_coding;gene_synonym=ECK0041,yaaP;locus_tag=b0040
+NC_000913.3 RefSeq CDS 40417 41931 . - 0 ID=cds-NP_414582.1;Parent=gene-b0040;Dbxref=UniProtKB/Swiss-Prot:P31553,Genbank:NP_414582.1,ASAP:ABE-0000141,ECOCYC:EG11561,EcoGene:EG11561,GeneID:944765;Name=NP_414582.1;gbkey=CDS;gene=caiT;locus_tag=b0040;orig_transcript_id=gnl|b0040|mrna.b0040;product=L-carnitine:gamma-butyrobetaine antiporter;protein_id=NP_414582.1;transl_table=11
diff -r ae9994cf526f -r 014a21767ac4 test-data/tiles/2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tiles/2.out Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,51 @@
+NC_000913.3 0 4641652 name=ANONYMOUS,strand=1,value=0
+NC_000913.3 189 255 name=thrL,strand=1,value=0
+NC_000913.3 336 2799 name=thrA,strand=1,value=0
+NC_000913.3 2800 3733 name=thrB,strand=1,value=0
+NC_000913.3 3733 5020 name=thrC,strand=1,value=0
+NC_000913.3 5233 5530 name=yaaX,strand=1,value=0
+NC_000913.3 5565 5601 name=None,strand=1,value=0
+NC_000913.3 5636 5670 name=None,strand=-1,value=0
+NC_000913.3 5682 6459 name=yaaA,strand=-1,value=0
+NC_000913.3 6528 7959 name=yaaJ,strand=-1,value=0
+NC_000913.3 8237 9191 name=talB,strand=1,value=0
+NC_000913.3 9305 9893 name=mog,strand=1,value=0
+NC_000913.3 9927 10494 name=satP,strand=-1,value=0
+NC_000913.3 10642 11356 name=yaaW,strand=-1,value=0
+NC_000913.3 10829 11315 name=mbiA,strand=1,value=0
+NC_000913.3 11381 11786 name=yaaI,strand=-1,value=0
+NC_000913.3 12162 14079 name=dnaK,strand=1,value=0
+NC_000913.3 14167 15298 name=dnaJ,strand=1,value=0
+NC_000913.3 15386 16731 name=None,strand=1,value=0
+NC_000913.3 15444 16557 name=insL-1,strand=1,value=0
+NC_000913.3 16750 16960 name=mokC,strand=-1,value=0
+NC_000913.3 16750 16903 name=hokC,strand=-1,value=0
+NC_000913.3 16951 17006 name=sokC,strand=1,value=0
+NC_000913.3 17488 18655 name=nhaA,strand=1,value=0
+NC_000913.3 18714 19620 name=nhaR,strand=1,value=0
+NC_000913.3 19795 20563 name=None,strand=-1,value=0
+NC_000913.3 19810 20314 name=insB-1,strand=-1,value=0
+NC_000913.3 20232 20508 name=insA-1,strand=-1,value=0
+NC_000913.3 20814 21078 name=rpsT,strand=-1,value=0
+NC_000913.3 21180 21399 name=yaaY,strand=1,value=0
+NC_000913.3 21406 22348 name=ribF,strand=1,value=0
+NC_000913.3 22390 25207 name=ileS,strand=1,value=0
+NC_000913.3 25206 25701 name=lspA,strand=1,value=0
+NC_000913.3 25710 25746 name=None,strand=1,value=0
+NC_000913.3 25762 25796 name=None,strand=-1,value=0
+NC_000913.3 25825 26275 name=fkpB,strand=1,value=0
+NC_000913.3 26276 27227 name=ispH,strand=1,value=0
+NC_000913.3 27292 28207 name=rihC,strand=1,value=0
+NC_000913.3 28373 29195 name=dapB,strand=1,value=0
+NC_000913.3 29650 30799 name=carA,strand=1,value=0
+NC_000913.3 30816 34038 name=carB,strand=1,value=0
+NC_000913.3 34299 34695 name=caiF,strand=1,value=0
+NC_000913.3 34727 34763 name=None,strand=1,value=0
+NC_000913.3 34780 35371 name=caiE,strand=-1,value=0
+NC_000913.3 35376 36162 name=caiD,strand=-1,value=0
+NC_000913.3 36270 37824 name=caiC,strand=-1,value=0
+NC_000913.3 37897 39115 name=caiB,strand=-1,value=0
+NC_000913.3 39151 39185 name=None,strand=1,value=0
+NC_000913.3 39197 39233 name=None,strand=-1,value=0
+NC_000913.3 39243 40386 name=caiA,strand=-1,value=0
+NC_000913.3 40416 41931 name=caiT,strand=-1,value=0
diff -r ae9994cf526f -r 014a21767ac4 text-from-bed.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/text-from-bed.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+import logging
+import sys
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger()
+
+
+if __name__ == "__main__":
+ with open(sys.argv[1], "r") as handle:
+ for line in handle:
+ lineData = line.strip().split()
+ # BED3+ chrom chromStart chromEnd
+ # BED6+ name score strand
+ # BED9+ thickStart thickEnd itemRgb
+ kv = {}
+ if len(lineData) >= 6:
+ kv["strand"] = lineData[5].replace("+", "1").replace("-", "-1")
+ kv["value"] = lineData[4]
+ else:
+ sys.exit("Must be BED6+")
+
+ line = [
+ lineData[0], # chrom
+ lineData[1], # chromStart
+ lineData[2], # chromEnd
+ lineData[3],
+ ",".join(["%s=%s" % x for x in sorted(kv.items())]),
+ ]
+
+ sys.stdout.write("\t".join(line))
+ sys.stdout.write("\n")
diff -r ae9994cf526f -r 014a21767ac4 text-from-gff3.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/text-from-gff3.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+import logging
+import sys
+
+from BCBio import GFF
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger()
+
+
+if __name__ == "__main__":
+ attr = sys.argv[2]
+
+ for record in GFF.parse(sys.argv[1]):
+ if len(record.features) == 0:
+ continue
+
+ for feature in sorted(record.features, key=lambda x: x.location.start):
+ # chrom chromStart chromEnd
+ # name score strand
+ # thickStart thickEnd itemRgb
+
+ kv = {
+ "strand": 0 if not feature.location.strand else feature.location.strand,
+ "value": feature.qualifiers.get("score", [0])[0],
+ }
+
+ if attr not in feature.qualifiers:
+ continue
+
+ name = feature.qualifiers[attr][0]
+
+ line = [
+ record.id,
+ str(int(feature.location.start)),
+ str(int(feature.location.end)),
+ name,
+ ",".join(["%s=%s" % x for x in sorted(kv.items())]),
+ ]
+
+ sys.stdout.write("\t".join(line))
+ sys.stdout.write("\n")
diff -r ae9994cf526f -r 014a21767ac4 text-from-interval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/text-from-interval.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,59 @@
+
+
+ reformats interval files to prepare for Circos text labels
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 tiles-from-bed.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tiles-from-bed.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+import logging
+import sys
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger()
+
+
+if __name__ == "__main__":
+ with open(sys.argv[1], "r") as handle:
+ for line in handle:
+ lineData = line.strip().split()
+ # BED3+ chrom chromStart chromEnd
+ # BED6+ name score strand
+ # BED9+ thickStart thickEnd itemRgb
+ kv = {}
+ if len(lineData) >= 6:
+ kv["strand"] = lineData[5].replace("+", "1").replace("-", "-1")
+ kv["name"] = lineData[3]
+ kv["value"] = lineData[4]
+
+ line = [
+ lineData[0], # chrom
+ lineData[1], # chromStart
+ lineData[2], # chromEnd
+ ",".join(["%s=%s" % x for x in sorted(kv.items())]),
+ ]
+
+ sys.stdout.write("\t".join(line))
+ sys.stdout.write("\n")
diff -r ae9994cf526f -r 014a21767ac4 tiles-from-gff3.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tiles-from-gff3.py Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+import logging
+import sys
+
+from BCBio import GFF
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger()
+
+
+if __name__ == "__main__":
+ attr = sys.argv[2]
+
+ for record in GFF.parse(sys.argv[1]):
+ if len(record.features) == 0:
+ continue
+
+ for feature in sorted(record.features, key=lambda x: x.location.start):
+ # chrom chromStart chromEnd
+ # name score strand
+ # thickStart thickEnd itemRgb
+
+ kv = {
+ "strand": 0 if not feature.location.strand else feature.location.strand,
+ "name": feature.qualifiers.get(attr, ["None"])[0] or feature.id,
+ "value": feature.qualifiers.get("score", [0])[0],
+ }
+
+ line = [
+ record.id,
+ str(int(feature.location.start)),
+ str(int(feature.location.end)),
+ ",".join(["%s=%s" % x for x in sorted(kv.items())]),
+ ]
+
+ sys.stdout.write("\t".join(line))
+ sys.stdout.write("\n")
diff -r ae9994cf526f -r 014a21767ac4 tiles-from-interval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tiles-from-interval.xml Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,59 @@
+
+
+ reformats interval files to prepare for Circos tile plots
+
+ macros.xml
+
+
+
+ '$output'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r ae9994cf526f -r 014a21767ac4 unified-histogram.py
--- a/unified-histogram.py Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-#!/usr/bin/env python
-import logging
-import sys
-
-import wiggle
-from BCBio import GFF
-
-logging.basicConfig(level=logging.INFO)
-log = logging.getLogger()
-
-
-MODE = sys.argv[1]
-
-# Pair up (file, extension) pairs from sys.argv
-files = zip(sys.argv[2:][0::2], sys.argv[2:][1::2])
-
-# Our output data structure. This could be much more efficient.
-data = {}
-
-
-def bed(idx, path):
- # chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
- # chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
- # chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
- # name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
- # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
- # strand - Defines the strand - either '+' or '-'.
- # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
- # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
- # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
-
- with open(path, 'r') as handle:
- for line in handle:
- lineData = line.strip().split()
- chrom = lineData[0]
- chromStart = lineData[1]
- chromEnd = lineData[2]
-
- if chrom not in data:
- data[chrom] = {}
-
- for i in range(chromStart, chromEnd):
- if i not in data[chrom]:
- data[chrom][i] = {}
-
- data[chrom][i][idx] = lineData[5]
-
-
-# Handlers
-def gff3(idx, path):
- for record in GFF.parse(path):
- if len(record.features) == 0:
- continue
-
- if record.id not in data:
- data[record.id] = {}
-
- for feature in record.features:
- if 'score' in feature.qualifiers:
- for i in range(feature.location.start, feature.location.end):
- if i not in data[record.id]:
- data[record.id][i] = {}
-
- data[record.id][i][idx] = feature.qualifiers['score'][0]
-
-
-def wig(idx, path):
- walker = wiggle.Wiggle()
- with open(path, 'r') as handle:
- for region, position, value in walker.walk(handle):
- if region not in data:
- data[region] = {}
-
- if position not in data[region]:
- data[region][position] = {}
-
- data[region][position][idx] = value
-
-
-if __name__ == '__main__':
- mode_tiles_possible = True
-
- for idx, (file_path, file_type) in enumerate(files):
- log.info("Processing %s.%s", file_path, file_type)
-
- if file_type in globals():
- func = globals()[file_type]
- func(idx, file_path)
-
- if file_type == 'wig':
- mode_tiles_possible = False
-
- if MODE == 'tile' and not mode_tiles_possible:
- raise Exception("You requested a 'tile' plot with wig data, which is impossible")
-
- # Max number of files
- max_idx = range(len(files))
-
- serialized_values = None
- region_start, region_end = (None, None)
-
- for genome in data:
- for position in sorted(data[genome]):
- values = [
- '' if x not in data[genome][position] else data[genome][position][x]
- for x in max_idx
- ]
- if serialized_values is None:
- serialized_values = values
- if region_start is None:
- region_start = position
- region_end = position
-
- if values == serialized_values:
- region_end = position
- else:
- if MODE == 'histogram':
- # histogram
- # hs4 0 1999999 5.0000,3.0000,1.0000,19.0000
- sys.stdout.write(' '.join(
- (genome, str(region_start), str(region_end), ','.join(map(str, values)))
- ) + '\n')
- elif MODE == 'heatmap':
- # heatmap
- # hs1 2000000 3999999 0.0000 id=hs4
- # hs1 4000000 5999999 2.0000 id=hs1
- # hs1 4000000 5999999 0.0000 id=hs2
- # hs1 4000000 5999999 0.0000 id=hs3
- # hs1 4000000 5999999 0.0000 id=hs4
- # hs1 6000000 7999999 4.0000 id=hs2
- for x in max_idx:
- if x in data[genome][position]:
- sys.stdout.write(' '.join(
- (genome, str(region_start), str(region_end), data[genome][position][x], 'id=hm%s' % x)
- ) + '\n')
- else:
- sys.stdout.write(' '.join(
- (genome, str(region_start), str(region_end), 0.0, 'id=hm%s' % x)
- ) + '\n')
- elif MODE == 'line':
- # multiple=False
- sys.stdout.write(' '.join(
- (genome, str(region_start), str(region_end), data[genome][position][0])
- ) + '\n')
- elif MODE == 'scatter':
- # multiple=False
- sys.stdout.write(' '.join(
- (genome, str(region_start), str(region_end), data[genome][position][0])
- ) + '\n')
-
- # Update start of next array
- region_start = position
- region_end = position
- # And update with new array
- serialized_values = values
diff -r ae9994cf526f -r 014a21767ac4 unified-tiles.py
--- a/unified-tiles.py Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-#!/usr/bin/env python
-import logging
-import sys
-
-from BCBio import GFF
-
-logging.basicConfig(level=logging.INFO)
-log = logging.getLogger()
-
-
-# Pair up (file, extension) pairs from sys.argv
-files = zip(sys.argv[1:][0::2], sys.argv[1:][1::2])
-
-
-# Handlers
-def bed(idx, path):
- # chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
- # chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
- # chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
- # name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
- # score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray:
- # strand - Defines the strand - either '+' or '-'.
- # thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). When there is no thick part, thickStart and thickEnd are usually set to the chromStart position.
- # thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
- # itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
-
- with open(path, 'r') as handle:
- for line in handle:
- lineData = line.strip().split()
- chrom = lineData[0]
- chromStart = lineData[1]
- chromEnd = lineData[2]
-
- yield (chrom, chromStart, chromEnd, lineData[4], lineData[6], lineData[5], lineData[9])
-
-
-def gff3(idx, path):
- for record in GFF.parse(path):
- if len(record.features) == 0:
- continue
-
- for feature in sorted(record.features, key=lambda x: x.location.start):
- yield (
- record.id,
- feature.location.start,
- feature.location.end,
- feature.id or feature.qualifiers.get('Name', [None])[0],
- feature.location.strand,
- feature.qualifiers.get('score', [0.0])[0],
- feature.qualifiers.get('color', [None])[0]
- )
-
-
-if __name__ == '__main__':
- for idx, (file_path, file_type) in enumerate(files):
- log.info("Processing %s.%s", file_path, file_type)
-
- if file_type in globals():
- func = globals()[file_type]
- for item in func(idx, file_path):
- # multiple=False
- # hs1 10292899 10301003 id=Conrad_993
- # hs1 10297766 10301003 id=Conrad_994
- lineExtra = [
- 'strand=%s' % item[4],
- 'score=%s' % item[5],
- 'value=%s' % item[5],
- ]
- if item[3] is not None:
- lineExtra.append('id=%s' % item[3])
- if item[6] is not None:
- lineExtra.append('color=%s' % item[6])
-
- sys.stdout.write(' '.join((str(item[0]), str(item[1]), str(item[2]), ','.join(lineExtra))) + '\n')
diff -r ae9994cf526f -r 014a21767ac4 wiggle.py
--- a/wiggle.py Thu Oct 04 06:05:31 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-class Wiggle:
-
- def fixedStepParser(self, line):
- value = line.strip()
- start_position = self.stepIdx * self.parserConfig['step'] + self.parserConfig['start']
- stop_position = start_position + self.parserConfig['span'] - 1
- self.stepIdx += 1
-
- for position in range(start_position, stop_position):
- yield (self.parserConfig['chrom'], position, value)
-
- def variableStepParser(self, line):
- (start, value) = line.strip().split()
- start = int(start)
- start_position = start
- stop_position = start + self.parserConfig['span']
-
- for position in range(start_position, stop_position):
- yield (self.parserConfig['chrom'], position, value)
-
- def walk(self, handle):
-
- parser = None
- for line in handle:
- if line.startswith('track'):
- continue
- elif line.startswith('fixedStep'):
- parser = self.fixedStepParser
- lineData = line.split()
- fields = {x.split('=')[0]: x.split('=')[1] for x in lineData[1:]}
- self.parserConfig = fields
-
- for numField in ('step', 'start', 'span'):
- if numField in self.parserConfig:
- self.parserConfig[numField] = int(self.parserConfig[numField])
- self.stepIdx = 0
- elif line.startswith('variableStep'):
- parser = self.variableStepParser
- lineData = line.split()
- fields = {x.split('=')[0]: x.split('=')[1] for x in lineData[1:]}
- # Default value
- if 'span' not in fields:
- fields['span'] = 1
- self.parserConfig = fields
-
- for numField in ('span',):
- if numField in self.parserConfig:
- self.parserConfig[numField] = int(self.parserConfig[numField])
-
- self.stepIdx = 0
- elif len(line.strip()) == 0:
- continue
- else:
- for data in parser(line):
- yield data