| Previous changeset 22:2ddd41a0c2d5 (2024-02-01) Next changeset 24:fb6cc7bc24df (2024-02-03) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty |
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modified:
gff3_rebase.py jbrowse2.py jbrowse2.xml macros.xml pafcount.py |
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removed:
4DNFIQWS3632.hic Dockerfile hummingbird.chromosomes lancet.chromosomes peachgrape.paf |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 4DNFIQWS3632.hic |
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| Binary file 4DNFIQWS3632.hic has changed |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 Dockerfile --- a/Dockerfile Thu Feb 01 01:58:58 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -FROM quay.io/bioconda/base-glibc-busybox-bash:3.0 - -RUN adduser -u 1000 user1000 -D && adduser -u 1001 user1001 -D |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 gff3_rebase.py --- a/gff3_rebase.py Thu Feb 01 01:58:58 2024 +0000 +++ b/gff3_rebase.py Sat Feb 03 10:17:27 2024 +0000 |
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| @@ -117,7 +117,7 @@ start *= 3 end *= 3 - if parent.location.strand !=None and parent.location.strand >= 0: + if parent.location.strand != None and parent.location.strand >= 0: ns = parent.location.start + start ne = parent.location.start + end st = +1 @@ -137,7 +137,7 @@ if ne < 0: ne %= 3 if ns > ne: - ne, ns = ns, ne # dunno why but sometimes happens + ne, ns = ns, ne # dunno why but sometimes happens feature.location = FeatureLocation(ns, ne, strand=st) if hasattr(feature, "sub_features"): |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 hummingbird.chromosomes --- a/hummingbird.chromosomes Thu Feb 01 01:58:58 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,159 +0,0 @@ -Superscaffold_1 197551010 -Superscaffold_2 151342139 -Superscaffold_3 114810999 -Superscaffold_4 18597117 -Superscaffold_4A 44745344 -Superscaffold_4B 23291945 -Superscaffold_5 16645885 -Superscaffold_5A 43880846 -Superscaffold_6 35401958 -Superscaffold_7 39139214 -Superscaffold_8 31090148 -Superscaffold_9 25686456 -Superscaffold_10 22664390 -Superscaffold_11 20302349 -Superscaffold_12 21352500 -Superscaffold_13 17696115 -Superscaffold_14 15497061 -Superscaffold_15 13887164 -Superscaffold_17 10473655 -Superscaffold_18 11617720 -Superscaffold_19 11166003 -Superscaffold_20 15116875 -Superscaffold_21 7710055 -Superscaffold_22 5198135 -Superscaffold_23 6423903 -Superscaffold_24 6461084 -Superscaffold_25 2161911 -Superscaffold_26 6306732 -Superscaffold_27 5749075 -Superscaffold_28 5713987 -Superscaffold_33 1888140 -Superscaffold_Z 74081004 -scaffold_176_arrow_ctg1 26448777 -scaffold_100_arrow_ctg1 89391 -scaffold_101_arrow_ctg1 27420 -scaffold_102_arrow_ctg1 88291 -scaffold_103_arrow_ctg1 52293 -scaffold_105_arrow_ctg1 117061 -scaffold_108_arrow_ctg1 92013 -scaffold_109_arrow_ctg1 58627 -scaffold_110_arrow_ctg1 47716 -scaffold_113_arrow_ctg1 50750 -scaffold_114_arrow_ctg1 21565 -scaffold_116_arrow_ctg1 49460 -scaffold_117_arrow_ctg1 41171 -scaffold_118_arrow_ctg1 27591 -scaffold_119_arrow_ctg1 35133 -scaffold_11_arrow_ctg1 20442 -scaffold_121_arrow_ctg1 33689 -scaffold_122_arrow_ctg1 21202 -scaffold_123_arrow_ctg1 77962 -scaffold_129_arrow_ctg1 39186 -scaffold_12_arrow_ctg1 21624 -scaffold_131_arrow_ctg1 25182 -scaffold_132_arrow_ctg1 34049 -scaffold_133_arrow_ctg1 51633 -scaffold_134_arrow_ctg1 21742 -scaffold_135_arrow_ctg1 22491 -scaffold_138_arrow_ctg1 71357 -scaffold_139_arrow_ctg1 22556 -scaffold_142_arrow_ctg1 31870 -scaffold_143_arrow_ctg1 49694 -scaffold_145_arrow_ctg1 116243 -scaffold_146_arrow_ctg1 103453 -scaffold_147_arrow_ctg1 766393 -scaffold_148_arrow_ctg1 78695 -scaffold_150_arrow_ctg1 93154 -scaffold_151_arrow_ctg1 28870 -scaffold_153_arrow_ctg1 84999 -scaffold_156_arrow_ctg1 21911 -scaffold_158_arrow_ctg1 90337 -scaffold_159_arrow_ctg1 21208 -scaffold_161_arrow_ctg1 40230 -scaffold_162_arrow_ctg1 38283 -scaffold_163_arrow_ctg1 28592 -scaffold_167_arrow_ctg1 40388 -scaffold_168_arrow_ctg1 58669 -scaffold_173_arrow_ctg1 40534 -scaffold_177_arrow_ctg1 65243 -scaffold_178_arrow_ctg1 21095 -scaffold_179_arrow_ctg1 35229 -scaffold_180_arrow_ctg1 20398 -scaffold_181_arrow_ctg1 22300 -scaffold_182_arrow_ctg1 20570 -scaffold_183_arrow_ctg1 433116 -scaffold_188_arrow_ctg1 41118 -scaffold_189_arrow_ctg1 53824 -scaffold_18_arrow_ctg1 49594 -scaffold_190_arrow_ctg1 46001 -scaffold_192_arrow_ctg1 24118 -scaffold_193_arrow_ctg1 53560 -scaffold_194_arrow_ctg1 32702 -scaffold_199_arrow_ctg1 23307 -scaffold_19_arrow_ctg1 27865 -scaffold_203_arrow_ctg1 52906 -scaffold_205_arrow_ctg1 32166 -scaffold_206_arrow_ctg1 45797 -scaffold_208_arrow_ctg1 249319 -scaffold_211_arrow_ctg1 308288 -scaffold_212_arrow_ctg1 51160 -scaffold_213_arrow_ctg1 44165 -scaffold_215_arrow_ctg1 35631 -scaffold_216_arrow_ctg1 33371 -scaffold_217_arrow_ctg1 44418 -scaffold_219_arrow_ctg1 20621 -scaffold_21_arrow_ctg1 55185 -scaffold_220_arrow_ctg1 35027 -scaffold_221_arrow_ctg1 33193 -scaffold_224_arrow_ctg1 47771 -scaffold_227_arrow_ctg1 21147 -scaffold_22_arrow_ctg1 86944 -scaffold_230_arrow_ctg1 21451 -scaffold_232_arrow_ctg1 80082 -scaffold_234_arrow_ctg1 44937 -scaffold_235_arrow_ctg1 21900 -scaffold_23_arrow_ctg1 64517 -scaffold_25_arrow_ctg1 72196 -scaffold_26_arrow_ctg1 114866 -scaffold_27_arrow_ctg1 150140 -scaffold_29_arrow_ctg1 44491 -scaffold_31_arrow_ctg1 4777 -scaffold_32_arrow_ctg1 22773 -scaffold_33_arrow_ctg1 31849 -scaffold_38_arrow_ctg1 29917 -scaffold_39_arrow_ctg1 23626 -scaffold_3_arrow_ctg1 28703 -scaffold_41_arrow_ctg1 34025 -scaffold_44_arrow_ctg1 95945 -scaffold_45_arrow_ctg1 63497 -scaffold_46_arrow_ctg1 51536 -scaffold_47_arrow_ctg1 16959 -scaffold_48_arrow_ctg1 28674 -scaffold_4_arrow_ctg1 44112 -scaffold_56_arrow_ctg1 47374 -scaffold_59_arrow_ctg1 46574 -scaffold_61_arrow_ctg1 29997 -scaffold_63_arrow_ctg1 39109 -scaffold_65_arrow_ctg1 22524 -scaffold_67_arrow_ctg1 73637 -scaffold_68_arrow_ctg1 98386 -scaffold_71_arrow_ctg1 35194 -scaffold_72_arrow_ctg1 486644 -scaffold_75_arrow_ctg1 64650 -scaffold_76_arrow_ctg1 97557 -scaffold_79_arrow_ctg1 222555 -scaffold_81_arrow_ctg1 192870 -scaffold_82_arrow_ctg1 36996 -scaffold_83_arrow_ctg1 24473 -scaffold_84_arrow_ctg1 26327 -scaffold_86_arrow_ctg1 944055 -scaffold_87_arrow_ctg1 361110 -scaffold_89_arrow_ctg1 93331 -scaffold_8_arrow_ctg1 57289 -scaffold_90_arrow_ctg1 73378 -scaffold_91_arrow_ctg1 75794 -scaffold_92_arrow_ctg1 79498 -scaffold_98_arrow_ctg1 26696 -scaffold_99_arrow_ctg1 34028 -scaffold_9_arrow_ctg1 44275 |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 jbrowse2.py --- a/jbrowse2.py Thu Feb 01 01:58:58 2024 +0000 +++ b/jbrowse2.py Sat Feb 03 10:17:27 2024 +0000 |
| [ |
| b'@@ -231,9 +231,7 @@\n elif "scaling" in track:\n if track["scaling"]["method"] == "ignore":\n if track["scaling"]["scheme"]["color"] != "__auto__":\n- trackConfig["style"]["color"] = track["scaling"]["scheme"][\n- "color"\n- ]\n+ trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"]\n else:\n trackConfig["style"]["color"] = self.hex_from_rgb(\n *self._get_colours()\n@@ -260,18 +258,13 @@\n "blue": blue,\n }\n )\n- trackConfig["style"]["color"] = color_function.replace(\n- "\\n", ""\n- )\n+ trackConfig["style"]["color"] = color_function.replace("\\n", "")\n elif trackFormat == "gene_calls":\n # Default values, based on GFF3 spec\n min_val = 0\n max_val = 1000\n # Get min/max and build a scoring function since JBrowse doesn\'t\n- if (\n- scales["type"] == "automatic"\n- or scales["type"] == "__auto__"\n- ):\n+ if scales["type"] == "automatic" or scales["type"] == "__auto__":\n min_val, max_val = self.min_max_gff(gff3)\n else:\n min_val = scales.get("min", 0)\n@@ -279,9 +272,7 @@\n \n if scheme["color"] == "__auto__":\n user_color = "undefined"\n- auto_color = "\'%s\'" % self.hex_from_rgb(\n- *self._get_colours()\n- )\n+ auto_color = "\'%s\'" % self.hex_from_rgb(*self._get_colours())\n elif scheme["color"].startswith("#"):\n user_color = "\'%s\'" % self.hex_from_rgb(\n *self.rgb_from_hex(scheme["color"][1:])\n@@ -289,9 +280,7 @@\n auto_color = "undefined"\n else:\n user_color = "undefined"\n- auto_color = "\'%s\'" % self.hex_from_rgb(\n- *self._get_colours()\n- )\n+ auto_color = "\'%s\'" % self.hex_from_rgb(*self._get_colours())\n \n color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(\n **{\n@@ -303,9 +292,7 @@\n }\n )\n \n- trackConfig["style"]["color"] = color_function.replace(\n- "\\n", ""\n- )\n+ trackConfig["style"]["color"] = color_function.replace("\\n", "")\n return trackConfig\n \n \n@@ -381,7 +368,7 @@\n galaxy=GALAXY_INFRASTRUCTURE_URL,\n encoded_id=metadata.get("dataset_id", ""),\n tool_id=metadata.get("tool_tool_id", ""),\n- tool_version=metadata.get("tool_tool_version",""),\n+ tool_version=metadata.get("tool_tool_version", ""),\n )\n return metadata\n \n@@ -402,9 +389,7 @@\n \n def subprocess_check_call(self, command, output=None):\n if output:\n- log.debug(\n- "cd %s && %s > %s", self.outdir, " ".join(command), output\n- )\n+ log.debug("cd %s && %s > %s", self.outdir, " ".join(command), output)\n subprocess.check_call(command, cwd=self.outdir, stdout=output)\n else:\n log.debug("cd %s && %s", self.outdir, " ".join(command))\n@@ -615,7 +600,7 @@\n "plugins": [\n {\n "name": "MafViewer",\n- "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"\n+ "url": "https://unpkg.com/jbrowse'..b'ndex"]\n+ real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][\n+ "bam_index"\n+ ]\n if not isinstance(real_indexes, list):\n real_indexes = [real_indexes]\n \n@@ -1204,9 +1200,9 @@\n bam_index=real_indexes[i],\n )\n elif dataset_ext == "cram":\n- real_indexes = track["conf"]["options"]["cram"][\n- "cram_indices"\n- ]["cram_index"]\n+ real_indexes = track["conf"]["options"]["cram"]["cram_indices"][\n+ "cram_index"\n+ ]\n if not isinstance(real_indexes, list):\n real_indexes = [real_indexes]\n \n@@ -1282,7 +1278,7 @@\n \n if data.get("defaultLocation", ""):\n ddl = data["defaultLocation"]\n- loc_match = re.search(r"^([^:]+):(\\d*)\\.*(\\d*)$", ddl)\n+ loc_match = re.search(r"^([^:]+):([\\d,]*)\\.*([\\d,]*)$", ddl)\n if loc_match:\n refName = loc_match.group(1)\n drdict["refName"] = refName\n@@ -1349,18 +1345,14 @@\n config_json.update(self.config_json)\n config_data = {}\n \n- config_data["disableAnalytics"] = (\n- data.get("analytics", "false") == "true"\n- )\n+ config_data["disableAnalytics"] = data.get("analytics", "false") == "true"\n \n config_data["theme"] = {\n "palette": {\n "primary": {"main": data.get("primary_color", "#0D233F")},\n "secondary": {"main": data.get("secondary_color", "#721E63")},\n "tertiary": {"main": data.get("tertiary_color", "#135560")},\n- "quaternary": {\n- "main": data.get("quaternary_color", "#FFB11D")\n- },\n+ "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},\n },\n "typography": {"fontSize": int(data.get("font_size", 10))},\n }\n@@ -1414,9 +1406,7 @@\n parser = argparse.ArgumentParser(description="", epilog="")\n parser.add_argument("--xml", help="Track Configuration")\n parser.add_argument("--outdir", help="Output directory", default="out")\n- parser.add_argument(\n- "--version", "-V", action="version", version="%(prog)s 2.0.1"\n- )\n+ parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")\n args = parser.parse_args()\n tree = ET.parse(args.xml)\n root = tree.getroot()\n@@ -1512,8 +1502,7 @@\n track_conf["format"] = track.attrib["format"]\n if track.find("options/style"):\n track_conf["style"] = {\n- item.tag: parse_style_conf(item)\n- for item in track.find("options/style")\n+ item.tag: parse_style_conf(item) for item in track.find("options/style")\n }\n if track.find("options/style_labels"):\n track_conf["style_labels"] = {\n@@ -1526,9 +1515,7 @@\n track_conf["format"] = track.attrib["format"]\n try:\n # Only pertains to gff3 + blastxml. TODO?\n- track_conf["style"] = {\n- t.tag: t.text for t in track.find("options/style")\n- }\n+ track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}\n except TypeError:\n track_conf["style"] = {}\n pass\n@@ -1559,9 +1546,7 @@\n "primary_color": root.find("metadata/general/primary_color").text,\n "secondary_color": root.find("metadata/general/secondary_color").text,\n "tertiary_color": root.find("metadata/general/tertiary_color").text,\n- "quaternary_color": root.find(\n- "metadata/general/quaternary_color"\n- ).text,\n+ "quaternary_color": root.find("metadata/general/quaternary_color").text,\n "font_size": root.find("metadata/general/font_size").text,\n }\n jc.add_general_configuration(general_data)\n' |
| b |
| diff -r 2ddd41a0c2d5 -r 39b717d934a8 jbrowse2.xml --- a/jbrowse2.xml Thu Feb 01 01:58:58 2024 +0000 +++ b/jbrowse2.xml Sat Feb 03 10:17:27 2024 +0000 |
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| @@ -1,4 +1,4 @@ - <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_3" profile="22.05"> + <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" profile="22.05"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -173,6 +173,9 @@ #else if str($track.data_format.data_format_select) == "hic": <hic> </hic> + #else if str($track.data_format.data_format_select) == "cool": + <cool> + </cool> #else if str($track.data_format.data_format_select) == "sparql": <label>${track.data_format.label}</label> <sparql> @@ -231,6 +234,7 @@ <option value="pileup">BAM Pileup track</option> <option value="wiggle">BigWig track</option> <option value="blast">Blast XML track - converted to GFF</option> + <option value="cool">cool/mcool/scool data in hdf5 data</option> <option value="cram">CRAM</option> <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> @@ -315,7 +319,10 @@ <expand macro="input_conditional" label="HiC data" format="hic" /> <expand macro="track_visibility" /> </when> - + <when value="cool"> + <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" /> + <expand macro="track_visibility" /> + </when> <when value="sparql"> <param type="text" label="SPARQL Server URL" name="url" /> <param type="text" label="Track Label" name="label" value="SPARQL Genes" /> |
| b |
| diff -r 2ddd41a0c2d5 -r 39b717d934a8 lancet.chromosomes --- a/lancet.chromosomes Thu Feb 01 01:58:58 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,150 +0,0 @@ -H1.scaffold_1 44081015 -H1.scaffold_2 41097058 -H1.scaffold_3 34407287 -H1.scaffold_4 32212942 -H1.scaffold_5 25675203 -H1.scaffold_6 24043764 -H1.scaffold_7 23140439 -H1.scaffold_8 22936956 -H1.scaffold_9 21802644 -H1.scaffold_10 20716957 -H1.scaffold_11 19839374 -H1.scaffold_12 19575921 -H1.scaffold_13 18344658 -H1.scaffold_14 18274107 -H1.scaffold_15 18054619 -H1.scaffold_16 16412338 -H1.scaffold_17 16406862 -H1.scaffold_18 15759073 -H1.scaffold_19 14153004 -H1.scaffold_20 2916691 -H1.scaffold_21 2757211 -H1.scaffold_22 1634711 -H1.scaffold_23 497856 -H1.scaffold_24 313544 -H1.scaffold_25 283832 -H1.scaffold_26 100824 -H1.scaffold_27 84806 -H1.scaffold_28 77508 -H1.scaffold_29 68236 -H1.scaffold_30 67242 -H1.scaffold_31 64833 -H1.scaffold_32 64824 -H1.scaffold_33 64234 -H1.scaffold_34 62318 -H1.scaffold_35 62139 -H1.scaffold_36 61573 -H1.scaffold_37 58510 -H1.scaffold_38 56207 -H1.scaffold_39 54180 -H1.scaffold_40 53854 -H1.scaffold_41 53795 -H1.scaffold_42 52464 -H1.scaffold_43 52166 -H1.scaffold_44 49697 -H1.scaffold_45 49546 -H1.scaffold_46 49439 -H1.scaffold_47 48954 -H1.scaffold_48 48737 -H1.scaffold_49 48690 -H1.scaffold_50 47224 -H1.scaffold_51 47109 -H1.scaffold_52 47003 -H1.scaffold_53 46961 -H1.scaffold_54 45839 -H1.scaffold_55 45832 -H1.scaffold_56 44073 -H1.scaffold_57 43437 -H1.scaffold_58 43033 -H1.scaffold_59 42345 -H1.scaffold_60 42225 -H1.scaffold_61 40820 -H1.scaffold_62 40421 -H1.scaffold_63 40050 -H1.scaffold_65 39275 -H1.scaffold_66 38960 -H1.scaffold_67 38908 -H1.scaffold_68 37904 -H1.scaffold_69 37814 -H1.scaffold_70 37600 -H1.scaffold_71 36863 -H1.scaffold_72 36692 -H1.scaffold_73 36648 -H1.scaffold_74 36569 -H1.scaffold_75 36145 -H1.scaffold_76 35865 -H1.scaffold_77 35803 -H1.scaffold_78 35121 -H1.scaffold_79 34533 -H1.scaffold_80 34375 -H1.scaffold_81 33823 -H1.scaffold_82 33086 -H1.scaffold_83 32593 -H1.scaffold_84 32506 -H1.scaffold_85 29944 -H1.scaffold_86 29921 -H1.scaffold_87 29759 -H1.scaffold_88 28743 -H1.scaffold_89 28343 -H1.scaffold_90 27558 -H1.scaffold_91 26965 -H1.scaffold_92 26540 -H1.scaffold_93 25107 -H1.scaffold_94 24940 -H1.scaffold_95 24227 -H1.scaffold_96 22350 -H2.scaffold_1 44439011 -H2.scaffold_2 43350333 -H2.scaffold_3 40293604 -H2.scaffold_4 34253441 -H2.scaffold_5 32975783 -H2.scaffold_6 25723763 -H2.scaffold_7 23979314 -H2.scaffold_8 22323814 -H2.scaffold_9 22289062 -H2.scaffold_10 20566309 -H2.scaffold_11 20408427 -H2.scaffold_12 19950170 -H2.scaffold_13 18579514 -H2.scaffold_14 18547751 -H2.scaffold_15 17662894 -H2.scaffold_16 16774291 -H2.scaffold_17 16190743 -H2.scaffold_18 15895306 -H2.scaffold_19 1657473 -H2.scaffold_20 285499 -H2.scaffold_21 267671 -H2.scaffold_22 196008 -H2.scaffold_23 172711 -H2.scaffold_24 108077 -H2.scaffold_25 83925 -H2.scaffold_26 77522 -H2.scaffold_27 76518 -H2.scaffold_28 75954 -H2.scaffold_29 74048 -H2.scaffold_30 64571 -H2.scaffold_31 60839 -H2.scaffold_32 60704 -H2.scaffold_33 59025 -H2.scaffold_34 58664 -H2.scaffold_35 52625 -H2.scaffold_36 49637 -H2.scaffold_37 49477 -H2.scaffold_38 44953 -H2.scaffold_39 41175 -H2.scaffold_40 40519 -H2.scaffold_41 39976 -H2.scaffold_43 39061 -H2.scaffold_44 37325 -H2.scaffold_45 35941 -H2.scaffold_46 35888 -H2.scaffold_47 35858 -H2.scaffold_48 35116 -H2.scaffold_49 34268 -H2.scaffold_50 33528 -H2.scaffold_51 33484 -H2.scaffold_52 33071 -H2.scaffold_53 32811 -H2.scaffold_54 28588 -H2.scaffold_55 26455 -H2.scaffold_56 20418 |
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| diff -r 2ddd41a0c2d5 -r 39b717d934a8 macros.xml --- a/macros.xml Thu Feb 01 01:58:58 2024 +0000 +++ b/macros.xml Sat Feb 03 10:17:27 2024 +0000 |
| b |
| @@ -20,6 +20,7 @@ <requirement type="package" version="6.0.1">pyyaml</requirement> <requirement type="package" version="1.11">tabix</requirement> <requirement type="package" version="4.6.0">findutils</requirement> + <requirement type="package" version="0.0.8">hictk</requirement> <yield/> </requirements> </xml> |
| b |
| diff -r 2ddd41a0c2d5 -r 39b717d934a8 pafcount.py --- a/pafcount.py Thu Feb 01 01:58:58 2024 +0000 +++ b/pafcount.py Sat Feb 03 10:17:27 2024 +0000 |
| [ |
| @@ -1,4 +1,5 @@ import sys + """ Col Type Description @@ -21,29 +22,29 @@ qtrans = {} ttrans = {} pafname = sys.argv[1] -pf = open(pafname, 'r').readlines() +pf = open(pafname, "r").readlines() for row in pf: - qn,ql,qs,qe,qrs,tn,tl,ts,te,nm,abl,mq = row.strip().split("\t")[:12] + qn, ql, qs, qe, qrs, tn, tl, ts, te, nm, abl, mq = row.strip().split("\t")[:12] - if (qn == tn): # cis - print('cis', qn,tn) + if qn == tn: # cis + print("cis", qn, tn) tcis.setdefault(tn, 0) tcis[tn] = tcis[tn] + 1 qcis.setdefault(qn, 0) qcis[qn] = qcis[qn] + 1 - else: # trans - print('trans', qn,tn) - k = '%s_%s' % (qn,tn) + else: # trans + print("trans", qn, tn) + k = "%s_%s" % (qn, tn) ttrans.setdefault(k, 0) - ttrans[k] = ttrans[k]+ 1 + ttrans[k] = ttrans[k] + 1 qtrans.setdefault(k, 0) - qtrans[k] = qtrans[k] + 1 -#print('qcis', qcis,'\nqtrans', qtrans,'\ntcis', tcis,'\ntt', ttrans) -#print('\nqtrans', qtrans,'\nttrans', ttrans) + qtrans[k] = qtrans[k] + 1 +# print('qcis', qcis,'\nqtrans', qtrans,'\ntcis', tcis,'\ntt', ttrans) +# print('\nqtrans', qtrans,'\nttrans', ttrans) chroms = list(qtrans.keys()) -print('chroms=', chroms) -#print('chrom\tqcis\ttcis\tqtrans\tttrans') -print('chrom\tqtrans\tttrans') +print("chroms=", chroms) +# print('chrom\tqcis\ttcis\tqtrans\tttrans') +print("chrom\tqtrans\tttrans") for cr in chroms: - #print('%s\t%d\t%d\t%d\t%d' % (cr, qcis[cr], tcis[cr], qtrans[cr], ttrans[cr])) - print('%s\t%d\t%d' % (cr, qtrans[cr], ttrans[cr])) + # print('%s\t%d\t%d\t%d\t%d' % (cr, qcis[cr], tcis[cr], qtrans[cr], ttrans[cr])) + print("%s\t%d\t%d" % (cr, qtrans[cr], ttrans[cr])) |
| b |
| diff -r 2ddd41a0c2d5 -r 39b717d934a8 peachgrape.paf --- a/peachgrape.paf Thu Feb 01 01:58:58 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,16985 +0,0 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|