get Snakemake input from LabKey API

- add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table
- script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file
- add tests for both use cases
- common input files for tests now in 'tests/input_files'
- update all other tests to account for new file locations
- update documentation

.gitlab-ci.yml

@@ -10,6 +10,7 @@ test:
     # add code quality tests here
     # add unit tests here
     # add script tests here
+    - bash tests/test_scripts_table_to_snakemake/test.sh
     - bash tests/test_scripts_labkey_to_snakemake/test.sh
     # add integration tests here
     - bash tests/test_create_dag_image/test.sh

README.md

@@ -117,8 +117,8 @@ bash tests/test_integration_workflow/test.slurm.sh
 create a directory for your workflow run and traverse inside it with:
 
     ```bash
-    mkdir runs/my_run
-    cd runs/my_run
+    mkdir config/my_run
+    cd config/my_run
     ```
 
 2. Create empty sample table, workflow configuration and, if necessary, cluster
@@ -224,28 +224,19 @@ you do not have these):
     EOF
     ```
 
-3. Run the LabKey API client script:
+3. Generate the workflow configuration with the following command, after
+replacing the placeholders with the appropriate values (check out the
+help screen with option '--help' for further options and information):
 
     ```bash
-    python scripts/labkey_api.py <project_name> <labkey_table_nane>
-    ```
-
-    > **NOTE:** Right now the script only prints a `pandas` data frame
-    > representation of the LabKey table on the screen and manually needs to be
-    > saved to a file for the next step. Ultimately the script will produce
-    > either a file in table format or will be merged with the following
-    > script.
-
-4. Generate the workflow configuration with the following command, after
-replacing the placeholders with the appropriate values:
-
-    ```bash
-    python scripts scripts/labkey_to_snakemake.py \
-        --input_table=<labkey_output_table> \
-        --input_dict="scripts/input_dict.tsv" \
-        --config_file="runs/my_run/config.yaml" \
-        --samples_table="runs/my_run/samples.tsv" \
-        --genomes_path=<path_to_annotation_files>
+    python scripts/labkey_to_snakemake.py \
+        --input_dict="scripts/labkey_to_snakemake.dict.tsv" \
+        --config_file="config/my_run/config.yaml" \
+        --samples_table="config/my_run/samples.tsv" \
+        --remote \
+        --project-name="project_name" \
+        --table-name="table_name" \
+        <path_to_annotation_files>
     ```
 
 #### Additional information

Snakefile

-configfile: "config.yaml"
-
 ################################################################################
 ### python modules
 ################################################################################

scripts/input_dict_caption.tsv

-labkey	snakemake
-Entry date	entry_date
-Path to FASTQ file(s)	fastq_path
-Condition name	condition
-Replicate name	replicate_name
-End type (PAIRED or SINGLE)	seqmode
-Name of Mate1 FASTQ file	fq1
-Name of Mate2 FASTQ file	fq2
-Direction of Mate1 (SENSE, ANTISENSE or RANDOM)	mate1_direction
-Direction of Mate2 (SENSE, ANTISENSE or RANDOM)	mate2_direction
-5' adapter of Mate1	fq1_5p
-3' adapter of Mate1	fq1_3p
-5' adapter of Mate2	fq2_5p
-3' adapter of Mate2	fq2_3p
-Fragment length mean	mean
-Fragment length SD	sd
-Quality control flag (PASSED or FAILED)	quality_control_flag
-Checksum of raw Mate1 FASTQ file	mate1_checksum
-Checksum of raw Mate2 FASTQ file	mate2_checksum
-Name of metadata file	metadata
-Name of quality control file for Mate1	mate1_quality
-Name of quality control file for Mate2	mate2_quality
-Organism	organism
-Taxon ID	taxon_id
-Name of Strain / Isolate / Breed / Ecotype	strain_name
-Strain / Isolate / Breed / Ecotype ID	strain_id
-Biomaterial provider	biomaterial_provider
-Source / tissue name	source_name
-Tissue code	tissue_code
-Additional tissue description	tissue_description
-Genotype short name	genotype_name
-Genotype description	genotype_description
-Disease short name	disease_name
-Disease description	disease_description
-Abbreviation for treatment	treatment
-Treatment description	treatment_description
-Gender	gender
-Age	age
-Developmental stage	development_stage
-Passage number	passage_number
-Sample preparation date (YYYY-MM-DD)	sample_prep_date
-Prepared by	prepared_by
-Documentation	documentation
-Name of protocol file	protocol_file
-Sequencing date (YYYY-MM-DD)	seq_date
-Sequencing instrument	seq_instrument
-Library preparation kit	library_kit
-Cycles	cycles
-Molecule	molecule
-Contaminant sequences	contaminant_seqs
-Name of BioAnalyzer file	bioanalyser_file

scripts/labkey_to_snakemake.py

+#!/usr/bin/env python3
+
 ## -----------------------------------------------------------------------------
 # Author : Katsantoni Maria, Christina Herrmann
 # Company: Mihaela Zavolan, Biozentrum, Basel
@@ -35,85 +37,98 @@ def main():
         formatter_class=RawTextHelpFormatter)
 
     parser.add_argument(
-        "--samples_table",
-        dest="samples_table",
-        help="Output table compatible to snakemake",
-        required=True)
-
-    parser.add_argument(
-        "--input_table",
-        dest="input_table",
-        help="input table containing the sample information (labkey format)",
-        required=True,
-        metavar="FILE")
+        "genomes_path",
+        help="Path containing the FASTA and GTF files for all organisms",
+        metavar="GENOMES PATH"
+    )
 
     parser.add_argument(
-        "--input_dict",
-        dest="input_dict",
-        help="input dictionary containing the feature name \
-              conversion from labkey to snakemake",
-        required=True,
-        metavar="FILE")
+        "--input-table",
+        type=str,
+        default=None,
+        help=(
+            "Input table in LabKey format containing the sample information;"
+            "\nexactly one of '--input-table' and '--remote' is required."
+        ),
+        metavar="FILE",
+    )
 
     parser.add_argument(
         "--remote",
-        help="Fetch labkey table via API",
-        action='store_true')
+        action="store_true",
+        help=(
+            "Fetch LabKey table via API; exactly one of '--input-table' and"
+            "\n'--remote' is required."
+        ),
+    )
 
     parser.add_argument(
-        "--project_name",
-        help="Name of labkey folder containing the labkey table (remote mode)",
-        required = False)
+        "--project-name",
+        help=(
+            "Name of LabKey project containing table '--table-name'; required"
+            "\nif '--remote' is specified."
+        ),
+        metavar="STR",
+    )
 
     parser.add_argument(
-        "--query_name",
-        help="Name of labkey table (remote mode)",
-        required = False)
-
+        "--table-name",
+        help="Name of LabKey table; required if '--remote' is specified.",
+        metavar="STR",
+    )
+    parser.add_argument(
+        "--input-dict",
+        help=(
+            "Input dictionary containing the feature name conversion from \n"
+            "LabKey to Snakemake; default: '%(default)s'"
+        ),
+        default=os.path.join(
+            os.path.dirname(__file__),
+            'labkey_to_snakemake.dict.tsv'
+        ),
+        metavar="FILE"
+    )
 
     parser.add_argument(
-        "--genomes_path",
-        dest="genomes_path",
-        help="path containing the fasta and gtf files for all organisms",
-        required=True)
+        "--samples-table",
+        help="Output table compatible to snakemake; default: '%(default)s'",
+        default='samples.tsv',
+        metavar="FILE"
+    )
 
     parser.add_argument(
         "--multimappers",
-        dest="multimappers",
-        help="number of mulitmappers allowed",
-        required=False,
         type=int,
-        metavar='value',
-        default=1)
+        default=100,
+        help="Number of allowed multimappers",
+        metavar='INT',
+    )
 
     parser.add_argument(
-        "--soft_clip",
-        dest="soft_clip",
-        help="soft-clipping option of STAR",
-        required=False,
+        "--soft-clip",
         choices=['EndToEnd','Local'],
-        default='EndToEnd')
+        default='EndToEnd',
+        help="Soft-clipping option for STAR",
+    )
 
     parser.add_argument(
-        "--pass_mode",
-        dest="pass_mode",
-        help="STAR option pass_mode",
-        required=False,
+        "--pass-mode",
         choices=['None','Basic'],
-        default='None')
+        default='None',
+        help="2-pass mode option for STAR",
+    )
 
     parser.add_argument(
         "--libtype",
-        dest="libtype",
+        default='A',
         help="Library type for salmon",
-        required=False,
-        default='A')
+        metavar="STR",
+    )
 
     parser.add_argument(
-        "--config_file",
-        dest="config_file",
+        "--config-file",
         help="Configuration file to be used by Snakemake",
-        required=False)
+    )
 
 
     # __________________________________________________________________________________________________________________
@@ -129,13 +144,33 @@ def main():
         parser.print_help()
         sys.exit(1)
 
+    if options.remote and options.input_table:
+        parser.print_help()
+        print("\n[ERROR] Options '--input-table' and '--remote' are mutually exclusive.")
+        sys.exit(1)
+
+    if not options.remote and not options.input_table:
+        parser.print_help()
+        print("\n[ERROR] At least one of '--input-table' and '--remote' is required.")
+        sys.exit(1)
+
+    if options.remote and not options.project_name:
+        parser.print_help()
+        print("\n[ERROR] If option '--remote' is specified, option '--project-name' is required.")
+        sys.exit(1)
+
+    if options.remote and not options.table_name:
+        parser.print_help()
+        print("\n[ERROR] If option '--remote' is specified, option '--table-name' is required.")
+        sys.exit(1)
+
     sys.stdout.write('Reading input file...\n')
 
     if options.remote == True:
         input_table = api_fetch_labkey_table(
             project_name=options.project_name,
-            query_name=options.query_name)
-
+            query_name=options.table_name)
+        input_table.to_csv(options.input_table, sep='\t', index=False)
     else:
         input_table = pd.read_csv(
             options.input_table,
@@ -157,7 +192,7 @@ def main():
     sys.stdout.write('Create snakemake table...\n')
     snakemake_table = pd.DataFrame()
     for index, row in input_table.iterrows():
-        snakemake_table.loc[index, 'sample'] = row[input_dict.loc['replicate_name', 'labkey']] + row[input_dict.loc['condition', 'labkey']]
+        snakemake_table.loc[index, 'sample'] = row[input_dict.loc['replicate_name', 'labkey']] + "_" + row[input_dict.loc['condition', 'labkey']]
         if row[input_dict.loc['seqmode', 'labkey']] == 'PAIRED':
             snakemake_table.loc[index, 'seqmode'] = 'paired_end'
         elif row[input_dict.loc['seqmode', 'labkey']] == 'SINGLE':
@@ -173,7 +208,7 @@ def main():
             for record in SeqIO.parse(handle, "fastq"):
                 read_length = len(record.seq)
                 break
-        
+
         snakemake_table.loc[index, 'index_size'] = read_length
         if read_length <= 50:
             snakemake_table.loc[index, 'kmer'] = 21
@@ -195,7 +230,7 @@ def main():
 
         organism = row[input_dict.loc['organism', 'labkey']].replace(' ', '_').lower()
         snakemake_table.loc[index, 'organism'] = organism
-        
+
         snakemake_table.loc[index, 'gtf'] = os.path.join(
             options.genomes_path,
             organism,
@@ -251,6 +286,15 @@ def main():
 
 
     snakemake_table.fillna('XXXXXXXXXXXXX', inplace=True)
+    snakemake_table = snakemake_table.astype(
+        {
+            "sd": int,
+            "mean": int,
+            "multimappers": int,
+            "kmer": int,
+            "index_size": int,
+        }
+    )
     snakemake_table.to_csv(
         options.samples_table,
         sep='\t',

tests/input_files/config.yaml

+---
+  output_dir: "results"
+  local_log: "local_log"
+  star_indexes: "results/star_indexes"
+  kallisto_indexes: "results/kallisto_indexes"
+  samples: "../input_files/samples.tsv"
+  salmon_indexes: "results/salmon_indexes"
+...

tests/input_files/samples.tsv

+sample	seqmode	fq1	index_size	kmer	fq2	fq1_3p	fq1_5p	fq2_3p	fq2_5p	organism	gtf	gtf_filtered	genome	tr_fasta_filtered	sd	mean	multimappers	soft_clip	pass_mode	libtype	kallisto_directionality	fq1_polya	fq2_polya
+synthetic_10_reads_paired_synthetic_10_reads_paired	paired_end	../input_files/project1/synthetic.mate_1.fastq.gz	75	31	../input_files/project1/synthetic.mate_2.fastq.gz	AGATCGGAAGAGCACA	XXXXXXXXXXXXX	AGATCGGAAGAGCGT	XXXXXXXXXXXXX	homo_sapiens	../input_files/homo_sapiens/annotation.gtf	../input_files/homo_sapiens/annotation.gtf	../input_files/homo_sapiens/genome.fa	../input_files/homo_sapiens/transcriptome.fa	100	250	10	EndToEnd	None	A	--fr	AAAAAAAAAAAAAAAAA	TTTTTTTTTTTTTTTTT
+synthetic_10_reads_mate_1_synthetic_10_reads_mate_1	single_end	../input_files/project2/synthetic.mate_1.fastq.gz	75	31	XXXXXXXXXXXXX	AGATCGGAAGAGCACA	XXXXXXXXXXXXX	XXXXXXXXXXXXX	XXXXXXXXXXXXX	homo_sapiens	../input_files/homo_sapiens/annotation.gtf	../input_files/homo_sapiens/annotation.gtf	../input_files/homo_sapiens/genome.fa	../input_files/homo_sapiens/transcriptome.fa	100	250	10	EndToEnd	None	A	--fr	AAAAAAAAAAAAAAAAA	XXXXXXXXXXXXX

tests/input_files/synthetic.mate_1.bed

-1-10000-20000	3397	3472	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3249	3324	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3735	3810	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2055	2130	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3567	3642	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7920	7995	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6665	6740	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6915	6990	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5841	5916	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7929	8004	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P
+1-10000-20000	3397	3472	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	ENSG00000223972
+1-10000-20000	3249	3324	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	ENSG00000223972
+1-10000-20000	3735	3810	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	ENSG00000223972
+1-10000-20000	2055	2130	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	ENSG00000223972
+1-10000-20000	3567	3642	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	ENSG00000223972
+1-10000-20000	7945	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	ENSG00000227232
+1-10000-20000	6690	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	ENSG00000227232
+1-10000-20000	6940	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	ENSG00000227232
+1-10000-20000	5866	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	ENSG00000227232
+1-10000-20000	7954	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	ENSG00000227232

tests/input_files/synthetic.mate_2.bed

-1-10000-20000	3422	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3274	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3760	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2080	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3592	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7945	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6690	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6940	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5866	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7954	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P
+1-10000-20000	3422	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	ENSG00000223972
+1-10000-20000	3274	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	ENSG00000223972
+1-10000-20000	3760	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	ENSG00000223972
+1-10000-20000	2080	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	ENSG00000223972
+1-10000-20000	3592	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	ENSG00000223972
+1-10000-20000	7920	7995	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	ENSG00000227232
+1-10000-20000	6665	6740	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	ENSG00000227232
+1-10000-20000	6915	6990	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	ENSG00000227232
+1-10000-20000	5841	5916	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	ENSG00000227232
+1-10000-20000	7929	8004	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	ENSG00000227232

tests/input_files/synthetic.paired.bed

-1-10000-20000	3397	3497	NS500318:863:HY2KYBGXC:1:11101:14671:1067	0	+	DDX11L1
-1-10000-20000	3249	3349	NS500318:863:HY2KYBGXC:1:11101:24439:1068	0	+	DDX11L1
-1-10000-20000	3735	3835	NS500318:863:HY2KYBGXC:1:11101:14965:1069	0	+	DDX11L1
-1-10000-20000	2055	2155	NS500318:863:HY2KYBGXC:1:11101:21081:1069	0	+	DDX11L1
-1-10000-20000	3567	3667	NS500318:863:HY2KYBGXC:1:11101:18197:1070	0	+	DDX11L1
-1-10000-20000	7920	8020	NS500318:863:HY2KYBGXC:1:11101:4614:1071	0	-	WASH7P
-1-10000-20000	6665	6765	NS500318:863:HY2KYBGXC:1:11101:8467:1073	0	-	WASH7P
-1-10000-20000	6915	7015	NS500318:863:HY2KYBGXC:1:11101:18960:1076	0	-	WASH7P
-1-10000-20000	5841	5941	NS500318:863:HY2KYBGXC:1:11101:6851:1076	0	-	WASH7P
-1-10000-20000	7929	8029	NS500318:863:HY2KYBGXC:1:11101:14731:1078	0	-	WASH7P

tests/test_create_dag_image/config.yaml

----
-  ##############################################################################
-  ### Annotation
-  ##############################################################################
-  organism: "Homo_sapiens"
-  annotation: "../prepare_annotation/results/annotation.gtf"
-  genome: "../prepare_annotation/results/genome.fa"
-  annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
-  STAR_index: "../prepare_annotation/results/STAR_index/"
-  other_RNAs_sequence: "../prepare_annotation/other.fa"
-  other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
-  salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
-  ##############################################################################
-  ### Output and log directories
-  ##############################################################################
-  database_path: "/some/path"
-  STAR_idx_folder: "STAR_indices"
-  output_dir: "results"
-  star_indexes: "results"
-  salmon_indexes: "results"
-  kallisto_indexes: "results"
-  local_log: "logs/local_log"
-  cluster_log: "logs/cluster_log"
-  
-  ##############################################################################
-  ### Sample info
-  ##############################################################################
-  samples: "samples.tsv"
-...

tests/test_create_dag_image/input_files/chr1-10000-20000.fa

->1-10000-20000
-ntaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacc
-ctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccaaccctaaccc
-taaccctaaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctaacc
-taaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaacccctaacc
-ctaaccctaaaccctaaaccctaaccctaaccctaaccctaaccctaaccccaaccccaa
-ccccaaccccaaccccaaccccaaccctaacccctaaccctaaccctaaccctaccctaa
-ccctaaccctaaccctaaccctaaccctaacccctaacccctaaccctaaccctaaccct
-aaccctaaccctaaccctaacccctaaccctaaccctaaccctaaccctcgcggtaccct
-cagccggcccgcccgcccgggtctgacctgaggagaactgtgctccgccttcagagtacc
-accgaaatctgtgcagaggacaacgcagctccgccctcgcggtgctctccgggtctgtgc
-tgaggagaacgcaactccgccgttgcaaaggcgcgccgcgccggcgcaggcgcagagagg
-cgcgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcg
-cgccgcgccggcgcaggcgcagagaggcgcgccgcgccggcgcaggcgcagagaggcgcg
-ccgcgccggcgcaggcgcagacacatgctagcgcgtcggggtggaggcgtggcgcaggcg
-cagagaggcgcgccgcgccggcgcaggcgcagagacacatgctaccgcgtccaggggtgg
-aggcgtggcgcaggcgcagagaggcgcaccgcgccggcgcaggcgcagagacacatgcta
-gcgcgtccaggggtggaggcgtggcgcaggcgcagagacgcaagcctacgggcgggggtt
-gggggggcgtgtgttgcaggagcaaagtcgcacggcgccgggctggggcggggggagggt
-ggcgccgtgcacgcgcagaaactcacgtcacggtggcgcggcgcagagacgggtagaacc
-tcagtaatccgaaaagccgggatcgaccgccccttgcttgcagccgggcactacaggacc
-cgcttgctcacggtgctgtgccagggcgccccctgctggcgactagggcaactgcagggc
-tctcttgcttagagtggtggccagcgccccctgctggcgccggggcactgcagggccctc
-ttgcttactgtatagtggtggcacgccgcctgctggcagctagggacattgcagggtcct
-cttgctcaaggtgtagtggcagcacgcccacctgctggcagctggggacactgccgggcc
-ctcttgctcCAACAGTACTGGCGGATTATAGGGAAACACCCGGAGCATATGCTGTTTGGT
-CTCAGtagactcctaaatatgggattcctgggtttaaaagtaaaaaataaatatgtttaa
-tttgtgaactgattaccatcagaattgtactgttctgtatcccaccagcaatgtctagga
-atgcctgtttctccacaaagtgtttacttttggatttttgccagtctaacaggtgaAGcc
-ctggagattcttattagtgatttgggctggggcctggccatgtgtatttttttaaatttc
-cactgatgattttgctgcatggccggtgttgagaatgactgCGCAAATTTGCCGGATTTC
-CTTTGCTGTTCCTGCATGTAGTTTAAACGAGATTGCCAGCACCGGGTATCATTCACCATT
-TTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTA
-TTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACA
-GGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGT
-GCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGA
-GTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAACTTAATACCACA
-ACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAAC
-CTAGGCCAGTAAGTAGTGCTTGTGCTCATCTCCTTGGCTGTGATACGTGGCCGGCCCTCG
-CTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGCCATCGGAGCCCAAAGCCGGGCTGTG
-ACTGCTCAGACCAGCCGGCTGGAGGGAGGGGCTCAGCAGGTCTGGCTTTGGCCCTGGGAG
-AGCAGGTGGAAGATCAGGCAGGCCATCGCTGCCACAGAACCCAGTGGATTGGCCTAGGTG
-GGATCTCTGAGCTCAACAAGCCCTCTCTGGGTGGTAGGTGCAGAGACGGGAGGGGCAGAG
-CCGCAGGCACAGCCAAGAGGGCTGAAGAAATGGTAGAACGGAGCAGCTGGTGATGTGTGG
-GCCCACCGGCCCCAGGCTCCTGTCTCCCCCCAGGTGTGTGGTGATGCCAGGCATGCCCTT
-CCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTGT
-GAGTGTCCCCAGTGTTGCAGAGGTGAGAGGAGAGTAGACAGTGAGTGGGAGTGGCGTCGC
-CCCTAGGGCTCTACGGGGCCGGCGTCTCCTGTCTCCTGGAGAGGCTTCGATGCCCCTCCA
-CACCCTCTTGATCTTCCCTGTGATGTCATCTGGAGCCCTGCTGCTTGCGGTGGCCTATAA
-AGCCTCCTAGTCTGGCTCCAAGGCCTGGCAGAGTCTTTCCCAGGGAAAGCTACAAGCAGC
-AAACAGTCTGCATGGGTCATCCCCTTCACTCCCAGCTCAGAGCCCAGGCCAGGGGCCCCC
-AAGAAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAAGCC
-TGGCTGCCTCCAGCTGGGTCGACAGACAGGGGCTGGAGAAGGGGAGAAGAGGAAAGTGAG
-GTTGCCTGCCCTGTCTCCTACCTGAGGCTGAGGAAGGAGAAGGGGATGCACTGTTGGGGA
-GGCAGCTGTAACTCAAAGCCTTAGCCTCTGTTCCCACGAAGGCAGGGCCATCAGGCACCA
-AAGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGA
-CACGCTGTTGGCCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCAT
-TGCTGCTGTGTGGAAGTTCACTCCTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGA
-GATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGA
-CAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGG
-TGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTGT
-GGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGG
-GGAATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCC
-TCTGTGGAATCCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGC
-CTCTGCAGGAGGCTGCCATTTGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCC
-ATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCCCTGGACTATTCACCCCCTA
-GTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCTGGGGGCTTGTCACCTCC
-CCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACAGCCTTGC
-CTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCC
-TCTCAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAA
-GGGCCATTAGGCTCTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTT
-TTTTGTGGGAGACTATTCCTCCCATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTC
-CTCCCTCTCATCCCAGAGAAACAGGTCAGCTGGGAGCTTCTGCCCCCACTGCCTAGGGAC
-CAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGAT
-CCTTTATTAAAAGCACACTGTTGGTTTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTT
-TCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGA
-GCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCT
-TGAAGCTGGTCTCCACACAGTGCTGGTTCCGTCACCCCCTCCCAAGGAAGTAGGTCTGAG
-CAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAACGGCCCAAGTCTGGGTCTGGGGGGGAA
-GGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCTCGTCCTCCTCTGCCTGTGGCTGCT
-GCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCT
-CACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTT
-GGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGG
-ACAGAATTACAAGGTGCTGGCCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCT
-CATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCAC
-TGCAACGGGAAAGCCACAGACTGGGGTGAAGAGTTCAGTCACATGCGACCGGTGACTCCC
-TGTCCCCACCCCCATGACACTCCCCAGCCCTCCAAGGCCACTGTGTTTCCCAGTTAGCTC
-AGAGCCTCAGTCGATCCCTGACCCAGCACCGGGCACTGATGAGACAGCGGCTGTTTGAGG
-AGCCACCTCCCAGCCACCTCGGGGCCAGGGCCAGGGTGTGCAGCAccactgtacaatggg
-gaaactggcccagagaggtgaggcagcttgcctggggtcacagagcaaggcaaaagcagc
-gctgggtacaagctcaAAACCATAGTGCCCAGGGCACTGCCGCTGCAGGCGCAGGCATCG
-CATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGT
-CCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCATTGCCTTGGACCGCTCTT
-GGCAGTCGAAGAAGATTCTCCTGTCAGTTTGAGCTGGGTGAGCTTAGAGAGGAAAGCTCC
-ACTATGGCTCCCAAACCAGGAAGGAGCCATAGCCCAGGCAGGAGGGCTGAGGACCTCTGG
-TGGCGGCCCAGGGCTTCCAGCATGTGCCCTAGGGGAAGCAGGGGCCAGCTGGCAAGAGCA
-GGGGGTGGGCAGAAAGCACCCGGTGGACTCAGGGCTGGAGGGGAGGAGGCGATCTTGCCC
-AAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTGCT
-GCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTT
-GGCGGATGGACTCTAGCAGAGTGGCCAGCCACCGGAGGGGTCAACCACTTCCCTGGGAGC
-TCCCTGGACTGGAGCCGGGAGGTGGGGAACAGGGCAAGGAGGAAAGGCTGCTCAGGCAGG
-GCTGGGGAAGCTTACTGTGTCCAAGAGCCTGCTGGGAGGGAAGTCACCTCCCCTCAAACG
-AGGAGCCCTGCGCTGGGGAGGCCGGACCTTTGGAGACTGTGTGTGGGGGCCTGGGCACTG
-ACTTCTGCAACCACCTGAGCGCGGGCATCCTGTGTGCAGATACTCCCTGCTTCCTCTCTA
-GCCCCCACCCTGCAGAGCTGGACCCCTGAGCTAGCCATGCTCTGACAGTCTCAGTTGCAC
-ACACGAGCCAGCAGAGGGGTTTTGTGCCACTTCTGGATGCTAGGGTTACACTGGGAGACA
-CAGCAGTGAAGCTGAAATGAAAAATGTGTTGCTGTAGTTTGTTATTAGACCCCTTCTTTC
-CATTGGTTTAATTAGGAATGGGGAACCCAGAGCCTCACTTGTTCAGGCTCCCTCTGCCCT
-AGAAGTGAGAAGTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAA
-CAAGATATTTGAAATGGAAACTATTCAAAAAATTGAGAATTTCTGACCACTTAACAAACC
-CACAGAAAATCCACCCGAGTGCACTGAGCACGCCAGAAATCAGGTGGCCTCAAAGAGCTG
-CTCCCACCTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTGCCTGGCGCCTTGGCCTACA
-GGGGCCGCGGTTGAGGGTGGGAGTGGGGGTGCACTGGCCAGCACCTCAGGAGCtgggggt
-ggtggtgggggcggtgggggtggtgttagtACCCCATCTTGTAGGTCTGAAACACAAAGT
-GTGGGGTGTCTAGGGAAGAAGGTGTGTGACCAGGGAGGTCCCCGGCCCAGCTCCCATCCC
-AGAACCCAGCTCACCTACCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCAGTTC
-TGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCAATGTACATGAG
-GTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG
-GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCAGGGACATGT
-GAGAGGTGACAGGGACCTGCAGGGGCAGCCAACAAGACCTTGTGTGCACCTCCCATGGGT
-GGAATAAGGGGCCCAACAGCCTTGACTGGAGAGGAGCTCTGGCAAGGCCCTGGGCCACTG
-CACCTGTCTCCACCTCTGTCCCACCCCTCCCACCTGCTGTTCCAGCTGCTCTCTCTTGCT
-GATGGACAAGGGGGCATCAAACAGCTTCTCCTCTGTCTCTGCCCCCAGCATCACATGGGT
-CTTTGTTACAGCACCAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCG
-ACATGGGGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCACATCA
-TCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCC
-CCTGGCTCCTGGCCTATGTGCTGTACCTGTGTCTGATGCCCTGGGTCCCCACTAAGCCAG
-GCCGGGCCTCCCGCCCACACCCCTCGGCCCTGCCCTCTGGCCATACAGGTTCTCGGTGGT
-GTTGAAGAGCAGCAAGGAGCTGACAGAGCTGATGTTGCTGGGAAGACCCCCAAGTCCCTC
-TTCTGCATCGTCCTCGGGCTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTT
-CTCCTGAGAGGGCCAGGATGGCCAAGGGATGGTGAATATTTGGTGCTGGGCCTAATCAGC
-TGCCATCCCATCCCAGTCAGCCTCCTCTGGGGGACAGAACCCTATGGTGGCCCCGGCTCC
-TCCCCAGTATCCAGTCCTCCTGGTGTGTGACAGGCTATATGCGCGGCCAGCAGACCTGCA
-GGGCCCGCTCGTCCAGGGGGCGGTGCTTGCTCTGGATCCTGTGGCGGGGGCGTCTCTGCA
-GGCCAGGGTCCTGGGCGCCCGTGAAGATGGAGCCATATTCCTGCAGGCGCCCTGGAGCAG
-GGTACTTGGCACTGGAGAACACCTGTGGACACAGGGACAAGTCTGAGGGGGCCCCAAGAG
-GCTCAGAGGGCTAGGATTGCTTGGCAGGAGAGGGTGGAGTTGGAAGCCTGGGCGAGAAGA
-AAGCTCAAGGTACAGGTGGGCAGCAGGGCAGAGACTGGGCAGCCTCAGAGGCACGGGGAA
-ATGGAGGGACTGCCCAGTAGCCTCAGGACACAGGGGTATGGGGACTACCTTGATGGCCTT
-CTTGCTGCCCTTGATCTTCTCAATCTTGGCCTGGGCCAAGGAGACCTTCTCTCCAATGGC
-CTGCACCTGGCTCCGGCTCTGCTCTACCTGCTGGGAGATCCTGCCATGGAGAAGATCACA
-GAGGCTGGGCTGCTCCCCACCCTCTGCACACCTCCTGCTTCTAACAGCAGAGCTGCCAGG
-CCAGGCCCTCAGGCAAGGGCTCTGAAGTCAGGGTCACCTACTTGCCAGGGCCGATCTTGG
-TGCCATCCAGGGGGCCTCTACAAGGATAATCTGACCTGCAGGGTCGAGGAGTTGACGGTG
-CTGAGTTCCCTGCACTCTCAGTAGGGACAGGCCCTATGCTGCCACCTGTACATGCTATCT
-GAAGGACAGCCTCCAGGGCACACAGAGGATGGTATTTACACATGCACACATGGCTACTGA
-TGGGGCAAGCACTTCACAACCCCTCATGATCACGTGCAGCAGACAATGTGGCCTCTGCAG
-AGGGGGAACGGAGACCGGAGGCTGAGACTGGCAAGGCTGGACCTGAGTGTCGTCACCTAA
-ATTCAGACGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAGTCC
-CGACCACCGCCTCAGTGTGGTCTAGCTcctcacctgcttccatcctccctggtgcggggt
-gggcccagtgatatcagctgcctgctgttccccagatgtgccaagtgcattcttgtgtgc
-ttgcatctcatggaacgccatttccccagacatccctgtggctggctccTGATGCCCGAG
-GCCCAAGTGTCTGATGCTTTAAGGCACATCACCCCACTCATGCTTTTCCATGTTCTTTGG
-CCGCAGCAAGGCCGCTCTCACTGCAAAGTTAACTCTGATGCGTGTGTAACACAACATCCT
-CCTCCCAGTCGCCCCTGTAGCTCCCCTACCTCCAAGAGCCCAGCCCTTGCCCACAGGGCC
-ACACTCCACGTGCAGAGCAGCCTCAGCACTCACCGGGCACGAGCGAGCCTGTGTGGTGCG
-CAGGGAtgagaaggcagaggcgcgactggggttcatgaggaagggcaggaggagggtgtg
-ggatggtggaggggtttgagaaggcagaggcgcgactggggttcatgaggaaagggaggg
-ggaggatgtgggatggtggaggggCTGCAGACTCTGGGCTAGGGAAAGCTGGGATGTCTC
-TAAAGGTTGGAATGAATGGCCTAGAATCCGACCCAATAAGCCAAAGCCACTTCCACCAAC
-GTTAGAAGGCCTTGGCCCCCAGAGAGCCAATTTCACAATCCAGAAGTCCCCGTGCCCTAA
-AGGGTCTGCCCTGATTACTCCTGGCTCCTTGTGTGCAGGGGGCTCAGGCATGGCAGGGCT
-GGGAGTACCAGCAGGCACTCAAGCGGCTTAAGTGTTCCATGACAGACTGGTATGAAGGTG
-GCCACAATTCAGAAAGAAAAAAGAAGAGCACCATCTCCTTCCAGTGAGGAAGCGGGACCA
-CCACCCAGCGTGTGCTCCATCTTTTCTGGCTGGGGAGAGGCCTTCATCTGCTGTAAAGGG
-TCCTCCAGCACAAGCTGTCTTAATTGACCCTAGTTCCCAGGGCAGCCTCGTTCTGCCTTG
-GGTGCTGACACGACCTTCGGTAGGTGCATAAGCTCTGCATTCGAGGTCCACAGGGGCAGT
-GGGAGGGAACTGagactggggagggacaaaggctgctctgt

tests/test_create_dag_image/input_files/chr1-10000-20000.gtf

-#!genome-build GRCh38.p13
-#!genome-version GRCh38
-#!genome-date 2013-12
-#!genome-build-accession NCBI:GCA_000001405.28
-#!genebuild-last-updated 2019-08
-1-10000-20000	havana	gene	1870	4410	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
-1-10000-20000	havana	transcript	1870	4410	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
-1-10000-20000	havana	exon	1870	2228	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000	havana	exon	2614	2722	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000	havana	exon	3222	4410	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
-1-10000-20000	havana	transcript	2011	3671	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	2011	2058	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	2180	2228	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	2614	2698	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	2976	3053	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	3222	3375	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	3454	3671	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	gene	4405	8367	.	-	.	gene_id	"ENSG00000227232"; gene_version	"5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
-1-10000-20000	havana	transcript	4405	8367	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name	"WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	8269	8367	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	7916	8062	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	7607	7743	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	7234	7369	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	6859	7056	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	6608	6766	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	5797	5948	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	5006	5039	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000	havana	exon	4405	4502	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";

tests/test_create_dag_image/input_files/chr1-10000-20000.transcripts.fa

->ENST00000456328 gene=DDX11L1
-GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
-GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA
-GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG
-TGGAGAGGAGCCATGCCTAGAGTGGGATGGGCCATTGTTCATCTTCTGGCCCCTGTTGTCTGCATGTAAC
-TTAATACCACAACCAGGCATAGGGGAAAGATTGGAGGAAAGATGAGTGAGAGCATCAACTTCTCTCACAA
-CCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCTCCAGAGCTGCAGAAGACG
-ACGGCCGACTTGGATCACACTCTTGTGAGTGTCCCCAGTGTTGCAGAGGCAGGGCCATCAGGCACCAAAG
-GGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGGCC
-TGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAAGTTCACTC
-CTGCCTTTTCCTTTCCCTAGAGCCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAG
-TTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCT
-CTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGG
-AGAGTGTGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGA
-ATCCCGAAGAAATGGTGGGTCCTGGCCATCCGTGAGATCTTCCCAGGGCAGCTCCCCTCTGTGGAATCCA
-ATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGT
-CCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGT
-TAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGCCACAGGGCCCCTGCCT
-GGGGGCTTGTCACCTCCCCCACCTTCTTCCTGAGTCATTCCTGCAGCCTTGCTCCCTAACCTGCCCCACA
-GCCTTGCCTGGATTTCTATCTCCCTGGCTTGGTGCCAGTTCCTCCAAGTCGATGGCACCTCCCTCCCTCT
-CAACCACTTGAGCAAACTCCAAGACATCTTCTACCCCAACACCAGCAATTGTGCCAAGGGCCATTAGGCT
-CTCAGCATGACTATTTTTAGAGACCCCGTGTCTGTCACTGAAACCTTTTTTGTGGGAGACTATTCCTCCC
-ATCTGCAACAGCTGCCCCTGCTGACTGCCCTTCTCTCCTCCCTCTCATCCCAGAGAAACAGGTCAGCTGG
-GAGCTTCTGCCCCCACTGCCTAGGGACCAACAGGGGCAGGAGGCAGTCACTGACCCCGAGACGTTTGCAT
-CCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGTTGGTTTCTG
->ENST00000450305 gene=DDX11L1
-GTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGTTGGAGGAAAGATGAGTGAGAG
-CATCAACTTCTCTCACAACCTAGGCCAGTGTGTGGTGATGCCAGGCATGCCCTTCCCCAGCATCAGGTCT
-CCAGAGCTGCAGAAGACGACGGCCGACTTGGATCACACTCTTCTCAGAGCCCAGGCCAGGGGCCCCCAAG
-AAAGGCTCTGGTGGAGAACCTGTGCATGAAGGCTGTCAACCAGTCCATAGGCAGGGCCATCAGGCACCAA
-AGGGATTCTGCCAGCATAGTGCTCCTGGACCAGTGATACACCCGGCACCCTGTCCTGGACACGCTGTTGG
-CCTGGATCTGAGCCCTGGTGGAGGTCAAAGCCACCTTTGGTTCTGCCATTGCTGCTGTGTGGAATTTCAC
-CAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCC
-GCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCAGGAGAGTG
-TGGAGTCCAGAGTGTTGCCAGGACCCAGGCACAGGCATTAGTGCCCGTTGGAGAAAACAGGGGAATCCCG
-AA
->ENST00000488147 gene=WASH7P
-GTAGAGCAGAGCCGGAGCCAGGTGCAGGCCATTGGAGAGAAGGTCTCCTTGGCCCAGGCCAAGATTGAGA
-AGATCAAGGGCAGCAAGAAGGCCATCAAGGTGTTCTCCAGTGCCAAGTACCCTGCTCCAGGGCGCCTGCA
-GGAATATGGCTCCATCTTCACGGGCGCCCAGGACCCTGGCCTGCAGAGACGCCCCCGCCACAGGATCCAG
-AGCAAGCACCGCCCCCTGGACGAGCGGGCCCTGCAGGAGAAGCTGAAGGACTTTCCTGTGTGCGTGAGCA
-CCAAGCCGGAGCCCGAGGACGATGCAGAAGAGGGACTTGGGGGTCTTCCCAGCAACATCAGCTCTGTCAG
-CTCCTTGCTGCTCTTCAACACCACCGAGAACCTGTAGAAGAAGTATGTCTTCCTGGACCCCCTGGCTGGT
-GCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGCTGTTTGATGCCCCCTTGTCCA
-TCAGCAAGAGAGAGCAGCTGGAACAGCAGGTCCCAGAGAACTACTTCTATGTGCCAGACCTGGGCCAGGT
-GCCTGAGATTGATGTTCCATCCTACCTGCCTGACCTGCCCGGCATTGCCAACGACCTCATGTACATTGCC
-GACCTGGGCCCCGGCATTGCCCCCTCTGCCCCTGGCACCATTCCAGAACTGCCCACCTTCCACACTGAGG
-TAGCCGAGCCTCTCAAGACCTACAAGATGGGGTactaacaccacccccaccgcccccaccaccaccccca
-GCTCCTGAGGTGCTGGCCAGTGCACCCCCACTCCCACCCTCAACCGCGGCCCCTGTAGGCCAAGGCGCCA
-GGCAGGACGACAGCAGCAGCAGCGCGTCTCCTTCAGTCCAGGGAGCTCCCAGGGAAGTGGTTGACCCCTC
-CGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCA
-TGAAGGAGCGAAAGCTGGAGAAGCAGCAGCAGAAGGAGCAGGAGCAAGTGAGAGCCACGAGCCAAGGTGG
-GCACTTGATGTCGCTCCATGGGGGGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCA
-GAGAAAACGGCACACCAATCAATAAAGAACTGAGCAGAAA