Add "--fasta" argument to replace positional "fasta" argument.

igvteam · Sep 1, 2023 · dcec933 · dcec933
1 parent 14d3418
commit dcec933
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diff --git a/.gitignore b/.gitignore
@@ -115,3 +115,4 @@ venv.bak/
 
 
 /publish_examples.sh
+/issue_82/
diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@ The generated HTML page contains all data neccessary for IGV as uuencoded blobs.
 
 #### Prerequisites
 
-igv-reports __requires Python 3.6__ or greater.  
+igv-reports __requires Python 3.8__ or greater.  
 
 
 #### Installing igv-reports
@@ -39,7 +39,8 @@ Although _--tracks_ is optional, a typical report will include at least an align
 **Arguments:**
 * Required
     * __sites__   VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites.  Tabix indexed files are supported and strongly recommended for large files.
-    * __fasta__   Reference fasta file; must be indexed.  This argument should be ommited if --genome is used, otherwise it is required.  
+    * __--fasta__   Reference fasta file; must be indexed.  This argument should be ommited if --genome is used, otherwise it is required.  
+    * __--genome__  An igv.js genome identifier (e.g. hg38).  If supplied fasta, ideogram, and the default annotation track for the specified genome will be used.* 
 
 * The arguments _begin_, _end_, and _sequence_ are required for a generic tab delimited __sites__ file.
     * __--begin__ INT.   Column of start chromosomal position for __sites__ file.  Used for generic tab delimited input.
@@ -50,7 +51,6 @@ Although _--tracks_ is optional, a typical report will include at least an align
     * __--zero-based__  Specify that the position in the __sites__ file is 0-based (e.g. UCSC files) rather than 1-based.  Default is ```false```.
 
 * Optional
-    * __--genome__ **_New_** An igv.js genome identifier (e.g. hg38).  If supplied fasta, ideogram, and the default annotation track for the specified genome will be used.
     * __--ideogram__ FILE. Ideogram file in UCSC cytoIdeo format.  Useful when __fasta__ is used to specify the reference.
     * __--tracks__ LIST.  Space-delimited list of track files, see below for supported formats.  If both *tracks* and *track-config* are specified *tracks* will appear first by default.
     * __--track-config__  FILE.  File containing array of json configuration objects for igv.js tracks.  See the [igv.js wiki](https://github.com/igvteam/igv.js/wiki/Tracks-2.0) for more details.  This option allows customization of track parameters.  When using this option, the track ```url``` and ```indexURL``` properties should be set to the paths of the respective files.
@@ -78,21 +78,10 @@ files must be indexed.  Tabix is supported and it is recommended that all large
 Data for the examples are available in the github repository [https://github.com/igvteam/igv-reports](https://github.com/igvteam/igv-reports).  The repository can be
 downloaded as a zip archive here [https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip](https://github.com/igvteam/igv-reports/archive/refs/heads/master.zip).
 It is assumed that the examples are run from the root directory of the repository.  Output html is written to the [examples directory](https://github.com/igvteam/igv-reports/tree/master/examples) 
-and can be viewed [here](https://igv.org/igv-reports/examples/1.5.1).
+and can be viewed [here](https://igv.org/igv-reports/examples/1.8.1).
 
-#### NEW (version 1.5.0) - Create a report using a genome identifier: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_genome.html)\)
-
-```bash
-create_report test/data/variants/variants.vcf.gz \
---genome hg38 \
---flanking 1000 \
---info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
---tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam \
---output examples/example_genome.html
-```
 
-
-#### Create a variant report from a VCF file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_vcf.html))
+#### Create a variant report from a VCF file: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_vcf.html))
 
 ```bash
 
@@ -108,22 +97,19 @@ create_report test/data/variants/variants.vcf.gz \
 
 ```
 
+#### Create a variant report from a BED  file: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_bed.html))
 
-
-#### Create a variant report with tracks defined in an [igv.js track config json file](https://github.com/igvteam/igv-reports/tree/master/test/data/variants/trackConfigs.json): ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_config.html))
-
-``` bash
-create_report test/data/variants/variants.vcf.gz \
---fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
---ideogram test/data/hg38/cytoBandIdeo.txt \
+```bash
+echo bed
+create_report test/data/variants/variants.bed \
+--genome hg38 \
 --flanking 1000 \
 --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
---track-config test/data/variants/trackConfigs.json \
---output examples/example_config.html
+--tracks test/data/variants/variants.bed test/data/variants/recalibrated.bam \
+--output examples/example_genome.html
 ```
 
-
-#### Create a variant report from a TCGA MAF file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_maf.html))
+#### Create a variant report from a TCGA MAF file: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_maf.html))
 
 ```bash
 
@@ -136,7 +122,7 @@ create_report test/data/variants/tcga_test.maf \
 
 ```
 
-#### Create a variant report from a generic tab-delimited file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_tab.html))
+#### Create a variant report from a generic tab-delimited file: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_tab.html))
 
 ```bash
 
@@ -148,7 +134,7 @@ create_report test/data/variants/test.maflite.tsv \
 --output examples/example_tab.html
 
 ```
-####  Create a structural variant report from a bedpe file with two locations (BEDPE format): ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_bedpe.html))
+####  Create a structural variant report from a bedpe file with two locations (BEDPE format): ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_bedpe.html))
 
 ```bash
 
@@ -159,7 +145,30 @@ create_report test/data/variants/SKBR3_Sniffles_tra.bedpe \
 --output examples/example_bedpe.html
 ```
 
-#### Create a variant report with custom ID link urls: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_idlink.html))
+#### Create a report using a genome identifier: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_genome.html)\)
+
+```bash
+create_report test/data/variants/variants.vcf.gz \
+--genome hg38 \
+--flanking 1000 \
+--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
+--tracks test/data/variants/variants.vcf.gz test/data/variants/recalibrated.bam \
+--output examples/example_genome.html
+```
+
+#### Create a variant report with tracks defined in an [igv.js track config json file](https://github.com/igvteam/igv-reports/tree/master/test/data/variants/trackConfigs.json): ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_config.html))
+
+``` bash
+create_report test/data/variants/variants.vcf.gz \
+--fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
+--ideogram test/data/hg38/cytoBandIdeo.txt \
+--flanking 1000 \
+--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
+--track-config test/data/variants/trackConfigs.json \
+--output examples/example_config.html
+```
+
+#### Create a variant report with custom ID link urls: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_idlink.html))
 
 ```bash
 
@@ -172,7 +181,7 @@ create_report test/data/variants/1kg_phase3_sites.vcf.gz \
 
 ```
 
-#### Create a junction report from a splice-junction bed file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_junctions.html))
+#### Create a junction report from a splice-junction bed file: ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_junctions.html))
 
 ```bash
 create_report test/data/junctions/Introns.38.bed \
@@ -205,7 +214,7 @@ create_report test/data/wig/regions.bed \
 
 ```
 
-#### Use of ```info-columns-prefixes``` option.  Variant track only, no alignments. ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_ann.html))
+#### Use of ```info-columns-prefixes``` option.  Variant track only, no alignments. ([Example output](https://igv.org/igv-reports/examples/1.8.1/example_ann.html))
 
 
 ```bash
@@ -218,7 +227,7 @@ python igv_reports/report.py test/data/annotated_vcf/consensus.filtered.ann.vcf
 --output examples/example_ann.html 
 ```
 
-#### Use ```--exclude-flags``` option to include duplicate alignments in report.  Default value is 1536 which filters duplicates and vendor-failed reads.
+#### Use ```--exclude-flags``` option to include duplicate alignments in report by specifying a samtools `--exclude-flags` value.  Default value is 1536 which filters duplicates and vendor-failed reads.
 
 ```bash
 create_report test/data/dups/dups.bed \

diff --git a/examples/example_ann.html b/examples/example_ann.html
diff --git a/examples/example_bed.html b/examples/example_bed.html
diff --git a/examples/example_bedpe.html b/examples/example_bedpe.html
diff --git a/examples/example_config.html b/examples/example_config.html
diff --git a/examples/example_dups.html b/examples/example_dups.html
diff --git a/examples/example_fusions.html b/examples/example_fusions.html
diff --git a/examples/example_genome.html b/examples/example_genome.html
diff --git a/examples/example_idlink.html b/examples/example_idlink.html
diff --git a/examples/example_junctions.html b/examples/example_junctions.html
diff --git a/examples/example_maf.html b/examples/example_maf.html
diff --git a/examples/example_noembed.html b/examples/example_noembed.html
@@ -172,7 +172,7 @@
         var igvDiv;
 
         igvDiv = document.getElementById("igvDiv");
-        var options = {"reference": {"fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz"}, "tracks": [{"name": "Refseq Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz", "indexed": false, "removable": false, "order": 1000000, "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$", "type": "annotation"}, {"name": "variants.vcf", "url": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/variants.vcf.gz", "type": "variant", "format": "vcf"}, {"name": "recalibrated", "url": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam", "type": "alignment", "format": "bam", "height": 500, "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam.bai"}]}
+        var options = {"reference": {"fastaURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai", "cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz"}, "tracks": [{"name": "Refseq Genes", "format": "refgene", "url": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz", "indexed": false, "removable": false, "order": 1000000, "infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$", "type": "annotation"}, {"name": "variants.vcf", "url": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/variants.vcf.gz", "type": "variant", "format": "vcf", "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/variants.vcf.gz.tbi"}, {"name": "recalibrated", "url": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam", "type": "alignment", "format": "bam", "height": 500, "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/reports/recalibrated.bam.bai"}]}
 
         igv.createBrowser(igvDiv, options)
             .then(function (b) {

diff --git a/examples/example_tab.html b/examples/example_tab.html
diff --git a/examples/example_vcf.html b/examples/example_vcf.html
diff --git a/examples/example_wig.html b/examples/example_wig.html
diff --git a/igv_reports/report.py b/igv_reports/report.py
@@ -49,7 +49,7 @@ def create_report(args):
     elif variants_file.endswith(".json"):
         table = GenericTable.from_fusionjson(variants_file)
 
-    # Track json array.  Tracks can come from (1) tracks CL argument, (2) genome CL argument, and (3) track_config Cl argument
+    # Track json array.  Tracks can come from (1) --tracks argument, (2) --genome  argument, and (3) --track_config argument
     trackjson = []
 
     # Check for optional genome argument.  If supplied an igv.js genome json definition is used in lieu of a fasta file
@@ -65,9 +65,6 @@ def create_report(args):
                     config["format"] = feature.infer_format(config["url"])
                 if "type" not in config:
                     config["type"] = get_track_type(config["format"])
-
-                # Add potential index references
-
                 trackjson.append(config)
 
     # --tracks argument
@@ -424,6 +421,7 @@ def locus_string(chr, start, end):
 
 # Potentially add an index URL to a track config.  The "format" field must be set before calling this function
 def add_index(config):
+
     if "url" not in config or "indexURL" in config:
         return
 
@@ -440,7 +438,7 @@ def add_index(config):
     # Check potential bam/cram files
     if "format" in config:
         format = config["format"]
-        if format == "bam" or format == "cram":
+        if format == "bam":
             if resource_exists(url + ".bai"):
                 indexURL = url + ".bai"
             elif resource_exists(format + ".csi"):

diff --git a/run_examples.sh b/run_examples.sh
@@ -29,8 +29,17 @@ python igv_reports/report.py test/data/variants/variants.vcf.gz \
 --track-config test/data/variants/trackConfigs.json \
 --output examples/example_config.html
 
+#### Create a variant report from a BED  file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_bed.html))
+echo bed
+python igv_reports/report.py test/data/variants/variants.bed \
+--genome hg38 \
+--flanking 1000 \
+--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
+--tracks test/data/variants/variants.bed test/data/variants/recalibrated.bam \
+--output examples/example_bed.html
 
-#### Create a variant report from a TCGA MAF file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_maf.html))
+
+#### Create a variant report from a TCGA MAF file: ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_bed.html))
 echo maf
 python igv_reports/report.py test/data/variants/tcga_test.maf \
 --genome hg19 \
@@ -50,7 +59,6 @@ python igv_reports/report.py test/data/variants/test.maflite.tsv \
 --output examples/example_tab.html
 
 ####  Create a structural variant report from a bedpe file with two locations (BEDPE format): ([Example output](https://igv.org/igv-reports/examples/1.5.1/example_bedpe.html))
-
 echo bedpe
 python igv_reports/report.py test/data/variants/SKBR3_Sniffles_tra.bedpe \
 --genome hg19 \

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(name='igv-reports',
                  packages=['igv_reports'],
-                 version='1.8.0',
+                 version='1.8.1',
                  description='Creates self-contained html pages for visual variant review with IGV (igv.js).',
                  long_description=long_description,
                  long_description_content_type="text/markdown",
Original file line number	Diff line number	Diff line change
Expand Up		@@ -115,3 +115,4 @@ venv.bak/


		/publish_examples.sh
		/issue_82/