Repository 'genebed_maf_to_fasta'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/genebed_maf_to_fasta

Changeset 0:f24a9ff28d3c (2020-08-21)
Next changeset 1:020c78e91cc5 (2020-11-10)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ commit 17e2194066ca843f6b2391a9632ea9de67d39351"
added:
genebed_maf_to_fasta.xml
images/maf_icons/stitchMaf.png
interval_maf_to_merged_fasta.py
macros.xml
test-data/local/interval2maf-in1-1.maf
test-data/local/interval2maf-in1-1.maf.index
test-data/local/interval2maf-in1-2.maf
test-data/local/interval2maf-in1-2.maf.index
test-data/local/maf_indexes.loc
test-data/maf_to_fasta-in1.bed
test-data/maf_to_fasta-in2.bed
test-data/maf_to_fasta-in2.maf
test-data/maf_to_fasta-out1.fasta
test-data/maf_to_fasta-out2.fasta
tool-data/maf_indexes.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test
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diff -r 000000000000 -r f24a9ff28d3c genebed_maf_to_fasta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genebed_maf_to_fasta.xml Fri Aug 21 15:10:13 2020 -0400
[
@@ -0,0 +1,73 @@
+<tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1">
+    <description>given a set of coding exon intervals</description>
+    <macros>
+          <import>macros.xml</import>
+    </macros>
+    <command>
+        <![CDATA[
+        #if $maf_source_type.maf_source == "cached"
+            #set $tab = '\t'
+            echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc &&
+        #end if
+
+        python '$__tool_directory__/interval_maf_to_merged_fasta.py' 
+            #if $maf_source_type.maf_source == "user"
+                --mafSource='$maf_source_type.maf_file' --mafIndex='$maf_source_type.maf_file.metadata.maf_index'
+            #else
+                --mafSource=$maf_source_type.mafType.fields.value
+            #end if
+            --geneBED
+            --dbkey=$dbkey 
+            --species=$maf_source_type.species 
+            --interval_file='$input1' 
+            --output_file='$out_file1' 
+            --mafSourceType=$maf_source_type.maf_source 
+            --mafIndexFileDir=.
+            --overwrite_with_gaps=$overwrite_with_gaps
+        ]]>
+    </command>
+    <inputs>
+        <param name="input1" type="data" format="bed" label="Gene BED File">
+            <validator type="unspecified_build" />
+            <!-- allow 12+ columns, not as strict as possible. TODO: only list bed files with 12+ columns -->
+            <validator type="expression" message="Input must be in BED12 format.">value.metadata.columns &gt;= 12</validator> 
+        </param>
+        <expand macro="maf_source" />
+        <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block.">
+            <option value="True" selected="true">No</option>
+            <option value="False">Yes</option>
+        </param>
+    </inputs>
+    <outputs>
+      <data format="fasta" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" dbkey="hg38" value="maf_to_fasta-in1.bed"/>
+            <param name="maf_source" value="cached"/>
+            <param name="maf_identifier" value="test"/>
+            <param name="species" value="hg38,eulFla1,mm10"/>
+            <param name="overwrite_with_gaps" value="True"/>
+            <output name="out_file1" file="maf_to_fasta-out1.fasta" />
+        </test>
+        <test>
+            <param name="input1" dbkey="hg38" value="maf_to_fasta-in2.bed"/>
+            <param name="maf_source" value="user"/>
+            <param name="maf_file" dbkey="hg38" value="maf_to_fasta-in2.maf"/>
+            <param name="species" value="hg38,eulFla1,mm10"/>
+            <param name="overwrite_with_gaps" value="True"/>
+            <output name="out_file1" file="maf_to_fasta-out2.fasta" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+The coding sequence of genes are usually composed of several coding exons. Each of these coding exons is an individual genomic region, which when concatenated with each other constitutes the coding sequence. A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of gene-based intervals, in the Gene BED format. For every interval it performs the following:
+
+  * finds all MAF blocks that overlap the coding regions;
+  * sorts MAF blocks by alignment score;
+  * stitches blocks together and resolves overlaps based on alignment score;
+  * outputs alignments in FASTA format.
+    </help>
+    <expand macro="citations" />
+</tool>
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diff -r 000000000000 -r f24a9ff28d3c images/maf_icons/stitchMaf.png
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Binary file images/maf_icons/stitchMaf.png has changed
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diff -r 000000000000 -r f24a9ff28d3c interval_maf_to_merged_fasta.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interval_maf_to_merged_fasta.py Fri Aug 21 15:10:13 2020 -0400
[
b'@@ -0,0 +1,205 @@\n+#!/usr/bin/env python\n+"""\n+Reads an interval or gene BED and a MAF Source.\n+Produces a FASTA file containing the aligned intervals/gene sequences, based upon the provided coordinates\n+\n+Alignment blocks are layered ontop of each other based upon score.\n+\n+usage: %prog maf_file [options]\n+   -d, --dbkey=d: Database key, ie hg17\n+   -c, --chromCol=c: Column of Chr\n+   -s, --startCol=s: Column of Start\n+   -e, --endCol=e: Column of End\n+   -S, --strandCol=S: Column of Strand\n+   -G, --geneBED: Input is a Gene BED file, process and join exons as one region\n+   -t, --mafSourceType=t: Type of MAF source to use\n+   -m, --mafSource=m: Path of source MAF file, if not using cached version\n+   -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version\n+   -i, --interval_file=i:       Input interval file\n+   -o, --output_file=o:      Output MAF file\n+   -p, --species=p: Species to include in output\n+   -O, --overwrite_with_gaps=O: Overwrite bases found in a lower-scoring block with gaps interior to the sequence for a species.\n+   -z, --mafIndexFileDir=z: Directory of local maf_index.loc file\n+\n+usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR\n+"""\n+# Dan Blankenberg\n+from __future__ import print_function\n+\n+import sys\n+\n+import bx.intervals.io\n+from bx.cookbook import doc_optparse\n+from galaxy.tools.util import maf_utilities\n+\n+\n+def stop_err(msg):\n+    sys.exit(msg)\n+\n+\n+def __main__():\n+    # Parse Command Line\n+    options, args = doc_optparse.parse(__doc__)\n+    mincols = 0\n+    strand_col = -1\n+\n+    if options.dbkey:\n+        primary_species = options.dbkey\n+    else:\n+        primary_species = None\n+    if primary_species in [None, "?", "None"]:\n+        stop_err("You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file.")\n+\n+    include_primary = True\n+    secondary_species = maf_utilities.parse_species_option(options.species)\n+    if secondary_species:\n+        species = list(secondary_species)  # make copy of species list\n+        if primary_species in secondary_species:\n+            secondary_species.remove(primary_species)\n+        else:\n+            include_primary = False\n+    else:\n+        species = None\n+\n+    if options.interval_file:\n+        interval_file = options.interval_file\n+    else:\n+        stop_err("Input interval file has not been specified.")\n+\n+    if options.output_file:\n+        output_file = options.output_file\n+    else:\n+        stop_err("Output file has not been specified.")\n+\n+    if not options.geneBED:\n+        if options.chromCol:\n+            chr_col = int(options.chromCol) - 1\n+        else:\n+            stop_err("Chromosome column not set, click the pencil icon in the history item to set the metadata attributes.")\n+\n+        if options.startCol:\n+            start_col = int(options.startCol) - 1\n+        else:\n+            stop_err("Start column not set, click the pencil icon in the history item to set the metadata attributes.")\n+\n+        if options.endCol:\n+            end_col = int(options.endCol) - 1\n+        else:\n+            stop_err("End column not set, click the pencil icon in the history item to set the metadata attributes.")\n+\n+        if options.strandCol:\n+            strand_col = int(options.strandCol) - 1\n+\n+    mafIndexFile = "%s/maf_indexes.loc" % options.mafIndexFileDir\n+\n+    overwrite_with_gaps = True\n+    if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == \'false\':\n+        overwrite_with_gaps = False\n+\n+    # Finish parsing command line\n+\n+    # get index for mafs based on type\n+    index = index_filename = None\n+    # using specified uid for locally cached\n+    if options.mafSourceType.lower() in ["cached"]:\n+        index = maf_utilities.maf_index_by_ui'..b'al_file, "r").readlines())\n+    else:\n+        region_enumerator = enumerate(bx.intervals.io.NiceReaderWrapper(\n+            open(interval_file, \'r\'), chrom_col=chr_col, start_col=start_col,\n+            end_col=end_col, strand_col=strand_col, fix_strand=True,\n+            return_header=False, return_comments=False))\n+\n+    # Step through intervals\n+    regions_extracted = 0\n+    line_count = 0\n+    for line_count, line in region_enumerator:\n+        try:\n+            if options.geneBED:  # Process as Gene BED\n+                try:\n+                    starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed(line)\n+                    # create spliced alignment object\n+                    alignment = maf_utilities.get_spliced_region_alignment(\n+                        index, primary_species, fields[0], starts, ends,\n+                        strand=\'+\', species=species, mincols=mincols,\n+                        overwrite_with_gaps=overwrite_with_gaps)\n+                except Exception as e:\n+                    print(e)\n+                try:\n+                    primary_name = secondary_name = fields[3]\n+                    alignment_strand = fields[5]\n+                except Exception as e:\n+                    print("Error loading exon positions from input line %i: %s" % (line_count, e))\n+                    continue\n+            else:  # Process as standard intervals\n+                try:\n+                    # create spliced alignment object\n+                    alignment = maf_utilities.get_region_alignment(\n+                        index, primary_species, line.chrom, line.start,\n+                        line.end, strand=\'+\', species=species, mincols=mincols,\n+                        overwrite_with_gaps=overwrite_with_gaps)\n+                    primary_name = "%s(%s):%s-%s" % (line.chrom, line.strand, line.start, line.end)\n+                    secondary_name = ""\n+                    alignment_strand = line.strand\n+                except Exception as e:\n+                    print("Error loading region positions from input line %i: %s" % (line_count, e.__dict__))\n+                    continue\n+\n+            # Write alignment to output file\n+            # Output primary species first, if requested\n+            if include_primary:\n+                output.write(">%s.%s\\n" % (primary_species, primary_name))\n+                if alignment_strand == "-":\n+                    output.write(alignment.get_sequence_reverse_complement(primary_species))\n+                else:\n+                    output.write(alignment.get_sequence(primary_species))\n+                output.write("\\n")\n+            # Output all remainging species\n+            for spec in secondary_species or alignment.get_species_names(skip=primary_species):\n+                if secondary_name:\n+                    output.write(">%s.%s\\n" % (spec, secondary_name))\n+                else:\n+                    output.write(">%s\\n" % (spec))\n+                if alignment_strand == "-":\n+                    output.write(alignment.get_sequence_reverse_complement(spec))\n+                else:\n+                    output.write(alignment.get_sequence(spec))\n+                output.write("\\n")\n+\n+            output.write("\\n")\n+            regions_extracted += 1\n+        except Exception as e:\n+            print("Unexpected error from input line %i: %s\\n%s" % (line_count, e, line))\n+            raise\n+\n+    # close output file\n+    output.close()\n+\n+    # remove index file if created during run\n+    maf_utilities.remove_temp_index_file(index_filename)\n+\n+    # Print message about success for user\n+    if regions_extracted > 0:\n+        print("%i regions were processed successfully." % (regions_extracted))\n+    else:\n+        print("No regions were processed successfully.")\n+        if line_count > 0 and options.geneBED:\n+            print("This tool requires your input file to conform to the 12 column BED standard.")\n+\n+\n+if __name__ == "__main__":\n+    __main__()\n'
b
diff -r 000000000000 -r f24a9ff28d3c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Aug 21 15:10:13 2020 -0400
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@@ -0,0 +1,51 @@
+<macros>
+    <xml name="requirements">
+        <requirement type="package" version="0.8.9">bx-python</requirement>
+        <yield />
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr398</citation>
+        </citations>
+    </xml>
+    <xml name="maf_source">
+        <conditional name="maf_source_type">
+            <param name="maf_source" type="select" label="MAF Source">
+                <option value="cached" selected="true">Locally Cached Alignments</option>
+                <option value="user">Alignments in Your History</option>
+            </param>
+            <when value="user">
+                <param format="maf" name="maf_file" label="Choose alignments" type="data">
+                    <options>
+                        <filter type="data_meta" ref="input1" key="dbkey" />
+                    </options>
+                    <validator type="dataset_ok_validator" />
+                </param>
+                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
+                    <options>
+                        <filter type="data_meta" ref="maf_file" key="species" />
+                    </options>
+                </param>
+            </when>
+            <when value="cached">
+                <param name="mafType" type="select" label="Choose alignments">
+                    <options from_data_table="maf_indexes">
+                        <column name="name" index="0"/>
+                        <column name="value" index="1"/>
+                        <column name="indexed_for" index="2"/>
+                        <column name="exists_in_maf" index="3" />
+                        <column name="path" index="4" />
+                        <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
+                        <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
+                    </options>
+                </param>
+                <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
+                    <options from_data_table="maf_indexes">
+                        <column name="value" index="3"/>
+                        <filter type="multiple_splitter" column="3" separator=","/>
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+</macros>
b
diff -r 000000000000 -r f24a9ff28d3c test-data/local/interval2maf-in1-1.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/local/interval2maf-in1-1.maf Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,1652 @@\n+##maf version=1\n+a score=5126687.0\n+s hg38.chr22             33698927 151 -  50818468 GGCCAGAGGGGGCTACGGTGCTCCGCCCTCCGCCCCTCCACCACCTCCGCCACCACC---TCAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGTGCTCATGGCTATGTCAACACCCTGGCTGTGGCCTCTCAGAATTGA \n+s eulFla1.LGHW01008773v1    48579 151 -     91162 GGCCAGAGCGGGTTACGGcgccccgccctccgccccgccgccacctccgcctccacc---tcAGGGAGGCTCCCAGCTGGGCCACTGCATCTCGGAGAACGAGGGGGGCGCCCACGGCTATGTCAACACTCTGGCGGTGGCCTCCCAGAATTGA \n+s mm10.chr6              29244363 148 - 149736546 GGCCAGAAGCAGCTATGGTGCTCCTCCCTCTGCCCCTCCCCCACCTCCACCACCACCACCTCAGGGAGGCTCCCAGCGGGGCCACT------TGGAAAATGAAGGGGGCCCTCATGGCTATGTCAACACTCTAGCTGTTGCCTCTCAGAATTGA \n+\n+a score=3181394.0\n+s hg38.chr22             33698828 99 -  50818468 CTCCATCTTCATGCTCAAGAACCTCTTCTTCCTCGGCTGCCGGGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCAATCGGGCCTCCCCGAGTCG \n+s eulFla1.LGHW01008773v1    48480 99 -     91162 CTCCGTCTTCATGCTCAAGAACCTCTTCTTCCTTGGCTGCCGCGGCCTGGAGGCCCTGGAGGGCTGCTGGGACCGGGGCGGCCGGGCCTCCCCTAGTCG \n+s mm10.chr6              29244264 99 - 149736546 GTCCATCTTTATGCTCAAGAATCTCTTTTTCCTTGGCTGCCGTGGCCTGGAGGCCTTGGAGGGCTGCTGGGACCGGGGGAGTTGGGTATCCCCAAGTCG \n+\n+a score=8321735.0\n+s hg38.chr22             33698587 241 -  50818468 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTTATCGCCGTCTACTTCCTCACCCTCGCCTCGCCGGTGCTCTGGCTCTACGAGCTCAACGCCGCGGCCGCAGCGGCTGCATCCTGGGGCCAGGCCTCCGGGCCTGGCAGCTGCAGCCGCCTTCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCTGCCTCCTGGTGGTCAGCTACCAGCAGCCCCT \n+s eulFla1.LGHW01008773v1    48254 226 -     91162 GCCGCGTGCCGCTGCCCGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACGCTCGCCTCGCCGGTGCTCTGGCTCTACGAACTCAACGCC---------------TCGTCCTGGGGCCAGGCCTCGGGGCCCGGCAGCTGCAGCCGCCTCCTGCGCCTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCCCTGCGCTGCCTCCTAGTGGTGAGCTACCAGCAGCCCCT \n+s mm10.chr6              29244026 238 - 149736546 GCCGCGTGCCGCTTCCGGCGCACCTGCGCTACCTGCTCATCGCCGTCTACTTCCTCACTCTTGCCTCCCCAGTGCTCTGGCTGTACGAGCTGAACACT---GCCACAGCAGCTCCGTCCTGGGGTCAGACCTCCGGGCCCGGAAGCTGCAGCCGCCTTTTACGTTTGCTGGGCGGCTGCCTGGTGGACGTGCCCTTGCTGGCGCTGCGCAGCCTCCTGGTCGTGAGCTACCAACAGCCGCT \n+\n+a score=3395583.0\n+s hg38.chr22             33698483 104 -  50818468 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCGGCCGGATGCTTCCTGGGCACGTGCTTGGACCTGCTCGACAGCTTCACGCTGGTGGAGCTGATGCTGGAGG \n+s eulFla1.LGHW01008773v1    48150 104 -     91162 ACCCCTGCTGCTGCAGCCCCAGCGGCACCGCGCCGCCGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTCGACAGCTTCACCCTGGTGGAGCTGACGCTGGAAG \n+s mm10.chr6              29243922 104 - 149736546 TCCCCTGCTCCTGCAGCCACAGCAGCATCGCGCCGCGGGCTGCTTCCTGGGCACGTGTCTGGACCTGCTGGACAGCTTTACACTGGTGGAGCTGATGCTGGACG \n+\n+a score=2062525.0\n+s hg38.chr22             33698413 70 -  50818468 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCGCCCCCGGGATCGGCAGG \n+s eulFla1.LGHW01008773v1    48080 70 -     91162 TGTCGGTGCCCCTGCTCTACAGCTTGGTGCGGGCCATCAGCGAGGCGGGCGCCCCGCCGGGCTCTGCGGG \n+s mm10.chr6              29243852 70 - 149736546 TGTCCGTGCCGCTGCTCTACAGCCTAGTGCGTGCCATTAGCGAGGCGGGCGCGCCCCCGGGCTCGGCGGG \n+\n+a score=4187755.0\n+s hg38.chr22             33698268 145 -  50818468 GAGTTCGCCTTCGCCTACCTGGCCTGGCTTATCTACTCCATCGCCTTCACTCCCAAGGTGGTGCTGATCCTGGGCACGTCCATCCTAGACCTCATCGAGCTACGCGCGCCCTTCGGCACCACGGGCTTCCGTCTCACCATGGCGC \n+s eulFla1.LGHW01008773v1    47935 145 -     91162 GAGTTCGCCTTCGCCTACCTGGCCTGGCTCATCTACTCCATCGCCTTCACGCCCAAGGTGGTGCTTATCCTGGGCACGTCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTCGGCACCACCGGCTTCCGCCTCACCATGGCGC \n+s mm10.chr6              29243707 145 - 149736546 GAGTTCGCTTTTGCGTACCTGGCCTGGCTCATCTACTCCATCGCTTTCACCCCTAAGGTGGTGCTCATCCTGGGCACATCCATCCTGGACCTCATCGAGCTGCGCGCGCCCTTTGGCACCACGGGCTTTCGCCTTACCATGGCGC \n+\n+a score=491529.0\n+s hg38.chr22             33698246 22 -  50818468 GGGGGCGGCCGCGGCAGCGGGC \n+s eulFla1.LGHW01008773v1    47913 22 -     91162 GGCGGCGGCCGGGGCAACCGGC \n+s mm10.chr6              29243685 22 - 149736546 GGGGACGACTGGGGCAGCGGGC \n+\n+a score=17457.0\n+s hg38.chr22             33698245 1 -  50818468 T \n+s eulFla1.LGHW01008773v1    47912 1 -     91162 T \n+s mm10.chr6              29243684 1 - 149736546 C \n+\n+a score=263332.0\n+s hg38.chr22  '..b'TTTGAGCTAGAACAGAACATCAAAGAACTTAACACCCTTGCGGACCAAGTTGACACCACTCACGAGTTGCTTACCAAGACCAGCCTGGTGGCCAGCTCTTCCGGGGCTGTTTCTGGGGTCATGAACATCCTGGGTTTGGCCCTAGCACCTGTGACAGCAGGAGGCAGTCTCATGCTCTCAGCAACTGGGACAGGGTTGGGGGCAGCAGCTG \n+s eulFla1.LGHW01001967v1   331301 239 +   548553 GTTTCTGTCCTATTTTCCCTTGAAGAAGTATCAGCTGGAAAAGAATATCCGAGAACTCAACACCATTGCAGACCAAGTTGATATGACCCACAGGAAGCTCACCAAGGCCAGCCTGGTGGCCAGCTCTTCGGGGGCTGTTTCTGGAGTCATGAGCATCCTGGGTTTTGCCCTGGCACCTGTGACAGTAGGAGGCAGTCTCGTGCTCTCAGCAGCTGGGGTGGGGTTGGGGGCAGCAGCTG \n+i eulFla1.LGHW01001967v1                         C 0 C 0                                                                                                                                                                                                                                         \n+\n+a score=372641.0\n+s hg38.chr22             35726609 13 + 50818468 CCATCACCAACAT \n+s eulFla1.LGHW01001967v1   331540 13 +   548553 CCATCACCAAGGT \n+i eulFla1.LGHW01001967v1                        C 0 C 0       \n+\n+a score=572286.0\n+s hg38.chr22             35726622 28 + 50818468 AGTAACAAATGTCTTAGAAAATAGAAGC \n+s eulFla1.LGHW01001967v1   331553 28 +   548553 TTTGACAAATGCCTTAGAAAATAGAAGC \n+i eulFla1.LGHW01001967v1                        C 0 C 0                      \n+\n+a score=904228.0\n+s hg38.chr22             35726650 36 + 50818468 AATTCAGCAGCAAGAGACAAAGCCAGCCGACTGGGG \n+s eulFla1.LGHW01001967v1   331581 36 +   548553 AATTCAGCAGCAAGAGACAAAGCTAGCAGACTGGTG \n+i eulFla1.LGHW01001967v1                        C 0 I 20                             \n+\n+a score=55358.0\n+s hg38.chr22 35726686 3 + 50818468 CCT \n+\n+a score=139942.0\n+s hg38.chr22 35726689 11 + 50818468 CTGACAACATC \n+\n+a score=1764916.0\n+s hg38.chr22             35726700 97 + 50818468 A-CATGAGGCTTTCGGAGGAATAAATTGGTCTGAAATCGAGGCTGCTGGCTTTTGTGTTAATAAGTGTGTAAAAGCTATCCAGGGCATCAAGGATCTT \n+s eulFla1.LGHW01001967v1   331637 88 +   548553 -GCATGAGGCTTTCGGAGGAATAAAGTTGCCTGAAGGTGAGGCTGCTGGCCAGTGTGTTGGTAAGTGTATAAGCATCATCAAGAGTCTT--------- \n+i eulFla1.LGHW01001967v1                        I 20 C 0                                                                                           \n+\n+a score=4155522.0\n+s hg38.chr22             35726797 189 + 50818468 CATGCCTACCAGATGGCCAAATCCAACTCTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCAAGAGACACATCCCTTTCTGGACGGCTAGAGGGGTGCAGAGAGCCTTTGAGGGCACAACTCTGGCCATGACCAATGGTGCCTGGGTGATGGGTGCTGCTGGGGCTGGCTTCTTACTTATGAAAGAC \n+s eulFla1.LGHW01001967v1   331725 189 +   548553 CGTGCCCACCAGATGGCCAAAGCTAACCTTGGCTTCATGGCTATGGTCAAGAATTTTGTGGCCACACACAACATCTCTTTCTGGAAGCCAGGAGAGGTGCAGACAATCTTTGTAGATGCAACTCTGGCGGTGACCAAGGGTGCCCAGGGGATGGGTGCTGCTGGGGCTGGCCTCTTTCTTATGCAAGAT \n+i eulFla1.LGHW01001967v1                         C 0 C 0                                                                                                                                                                                       \n+\n+a score=10960.0\n+s hg38.chr22             35726986 1 + 50818468 A       \n+s eulFla1.LGHW01001967v1   331914 1 +   548553 G       \n+i eulFla1.LGHW01001967v1                       C 0 C 0 \n+\n+a score=2757722.0\n+s hg38.chr22             35726987 103 + 50818468 TGAGCAGCTTCCTGCAGAGCTGGAAGCACCTGGAGGATGGGGCAAGGACGGAGACAGCAGAGGAACTGAGAGCACTTGCTAAGAAGCTGGAGCAGGAGCTGGA \n+s eulFla1.LGHW01001967v1   331915 103 +   548553 TGGGCAAACTTCTGCAGAACTGGAAGCACCTGGAGGAGGGGGCGAGGGCAGAGACAGCCAAGGAACTGAGGACACTTGCCAAGGAGCAGGAGCAGGAGCTGAG \n+i eulFla1.LGHW01001967v1                         C 0 C 0                                                                                                 \n+\n+a score=841012.0\n+s hg38.chr22             35727090 49 + 50818468 CCGGCTCACCCAGCACCACCGGCACCTGCCGCAGAAGGCGAGCCAGACC \n+s eulFla1.LGHW01001967v1   332018 49 +   548553 GCAGCTCGCCGAGCGCTACCAGGACCTGCAGCAGAAGGCGAGCCAGACC \n+i eulFla1.LGHW01001967v1                        C 0 I 915                                         \n+\n+a score=668337.0\n+s hg38.chr22 35727139 55 + 50818468 TGTTCCAGCTCCCGGGGCAGGGCTGTTCGAGGATCCCGTGTGGTTAAACCAGAAG \n+\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/local/interval2maf-in1-1.maf.index
b
Binary file test-data/local/interval2maf-in1-1.maf.index has changed
b
diff -r 000000000000 -r f24a9ff28d3c test-data/local/interval2maf-in1-2.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/local/interval2maf-in1-2.maf Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,2623 @@\n+##maf version=1\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=222067.0\n+s hg38.chr22 32358071 23 + 50818468 ATGAAAAGGTTGTCACTTGTCAC \n+\n+a score=28783.0\n+s hg38.chr22 32358094 6 + 50818468 AACTAA \n+\n+a score=94379.0\n+s hg38.chr22 32358100 18 + 50818468 CAGGCTTTCACCTCAAGG \n+\n+a score=12732.0\n+s hg38.chr22 32358118 2 + 50818468 AA \n+\n+a score=325051.0\n+s hg38.chr22 32358120 57 + 50818468 ATTTTCTTCCCTTGTGTACTTTTCCCCTGGCAGTGGACATGGCTGCACTCTTCCAAG \n+\n+a score=2523686.0\n+s hg38.chr22 32358177 267 + 50818468 AAGCAAGCAG'..b'GCTGGGCCTGGTGCTGCTCGTGGAGGCCGTGGCCGTGCTCATCGGACCGCCCTCCGCCG \n+s mm10.chr15             24791713 98 - 104043685 GCTCATGGCAACCGTGGGTGCACCCCGCTTCCCTAGTGCATTGGGCCTAGTGCTGCTCGTGGAGGCCGTGGCTGTGCTCATAGGACCGCCCTCTGCCG \n+\n+a score=1184954.0\n+s hg38.chr22             12737495 36 -  50818468 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s eulFla1.LGHW01006107v1   634009 36 +    657376 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s mm10.chr15             24791677 36 - 104043685 GTCCTACGGCATGGTGGGCGCACTGCAGTTTGAGGT \n+\n+a score=4109169.0\n+s hg38.chr22             12737373 122 -  50818468 CTGCGGCCGCACGTCCCGTATCTGTTCAGCCTGGCCCTGCTGGCCAATGGGCTCACAGACCTGAGCAGCGCACGCGCGCGCTCCTACGGCGCCCTCGTCGCCTTCTGCGTCGCCTTCGGCCT \n+s eulFla1.LGHW01006107v1   633887 122 +    657376 CTGCGACCGCGGGTGCCCTATCTCTTCAGCCTGGCCCTGCTGGCCAACGGGCTCACGGACCTGAGCAGTGCGCGCGCGCGCTCCTACGGAGCCCTCGTCGCCTTCTGCATCGCCTTCGGCCT \n+s mm10.chr15             24791555 122 - 104043685 CTGAGACCCCACGTCCCCTACCTCTTCAGCCTGGCCCTGTTGGCCAATGGGCTCACGGACCTGATTAGCGCGCGTGCGCGCTCCTACGGGACCCTCGTTGCTTTCTGCATTGCCTTCGGCCT \n+\n+a score=8150994.0\n+s hg38.chr22             12737111 262 -  50818468 GCAGCTGCGCGAGGCATCCCCCAGGGTCCGGCCC--CGCCGGCGCCTGCTGGACTTGGCAGTGTGCACCGACCGCGCCTTCGCCGTGTACGCCGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTCCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCCGACACCGACGCCGCCTTCCTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCGCGCCCGGCGTGCGGCGCCCTGGCGGGCCTGGCGCGT \n+s eulFla1.LGHW01006107v1   633625 262 +    657376 gcgcgtgcgcgaggcgCCCCCTGGCGGCCGCACC--CGCCGGCGGCTGCTGGACGTGGCTGTGTGTGCCGACCGCGCCTTCGTGGTGTACGCGGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTGCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGACGCCGCCTTCCTGTTATCCATCGTGGGCTTCGTAGACATCGTGGCGCGGCCAGCGTGCGGCGCCCTGGCGGGCCTGGCGCGC \n+s mm10.chr15             24791316 239 - 104043685 -------------------------GCCCGGCTCGCCGCCGGCGGCTGCTGGACGTGGCAGTGTGCACCGACCGTGCTTTCGTGGTGTACGTGGTCACCAAGTTCCTGATGGCACTCGGGCTCTTTGTGCCGGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGAGGCCGCCTTCTTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCACGACCGGCGTGCGGTGCTTTGGCGGGTCTGGGGCGC \n+\n+a score=373719.0\n+s hg38.chr22             12737090 21 -  50818468 GGAGGCTGACGGTGCGGGGCT \n+s eulFla1.LGHW01006107v1   633604 21 +    657376 ggaggcggagggcgaggggct \n+s mm10.chr15             24791310  6 - 104043685 --------ACGGTG------- \n+\n+a score=149374.0\n+s hg38.chr22             12737084 6 - 50818468 CGAGGC \n+s eulFla1.LGHW01006107v1   633592 6 +   657376 Agaggc \n+\n+a score=172154.0\n+s hg38.chr22             12737070 14 -  50818468 GGGGACGCTCCGGG \n+s eulFla1.LGHW01006107v1   633578 14 +    657376 ggggACTCTGCGGG \n+s mm10.chr15             24791305  5 - 104043685 ------GCCCC--- \n+\n+a score=5393236.0\n+s hg38.chr22             12736861 209 -  50818468 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGCGCTGTCGCCGCTCGGCCAGCAGCTGCTGGAGCGCTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCCTGCGGGGCTGTCATGAGGCCGCCGCCCGGGCCGGGCCCGCGACCG------CGCAGGGACAGCGCCGGCGACCGCGCC \n+s eulFla1.LGHW01006107v1   633363 215 +    657376 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGTGCTGTCGCCTCTCGGCCAGCAGCTGCTCGAGCACTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCGTGCGGAGCCGTCATGCggccgccgccggggccggggccggggccaccgccgcgcggggccggcgcccgggacctggcg \n+s mm10.chr15             24791115 190 - 104043685 TGGCCAACGGGCTGGCAGCGGCGGGCAGTCCCGTGTTTCTGTCCATGCTGTCGCCGCTCGGGCAGCTGCTGGGGGAGCGCTTCGGCTGGCGTGGCGGCTTCCTGCTGTTTGGCGGCCTCCTGCTGCACTGTTGCGCCTGTGGGGCAGTCATGCGTCCGCCCCCTGGACC---CCCG---CCG------CGCAGAGACCCCTC------------- \n+\n+a score=810987.0\n+s hg38.chr22             12736835 26 -  50818468 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s eulFla1.LGHW01006107v1   633337 26 +    657376 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s mm10.chr15             24791089 26 - 104043685 ACTCTACTTCGAGCGGCGACGGCCCC \n+\n+a score=2187734.0\n+s hg38.chr22             12736789 46 -  50818468 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s eulFla1.LGHW01006107v1   633291 46 +    657376 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s mm10.chr15             24791043 46 - 104043685 GCCTGGGCCTAGCTCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/local/interval2maf-in1-2.maf.index
b
Binary file test-data/local/interval2maf-in1-2.maf.index has changed
b
diff -r 000000000000 -r f24a9ff28d3c test-data/local/maf_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/local/maf_indexes.loc Fri Aug 21 15:10:13 2020 -0400
b
@@ -0,0 +1,7 @@
+#This is a sample file distributed with Galaxy that is used by some
+#alignment tools.  The maf_index.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<Display_name UID> <indexed_for:build1,build2,build3> <exists_in_maf:build1,build2,build3> <Comma_Separated_List_of_Full_Paths_To_Files>
+#
+Test TEST hg38,eulFla1,mm10 hg38,eulFla1,mm10 ${__HERE__}/interval2maf-in1-1.maf,${__HERE__}/interval2maf-in1-2.maf
b
diff -r 000000000000 -r f24a9ff28d3c test-data/maf_to_fasta-in1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-in1.bed Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,250 @@\n+chr22\t10736170\t10736283\tENST00000615943.1\t0\t-\t10736170\t10736170\t0\t1\t113,\t0,\n+chr22\t10939387\t10961338\tENST00000635667.1\t0\t-\t10939387\t10939387\t0\t9\t36,111,90,87,115,58,126,70,56,\t0,1209,2303,5579,7916,9824,10661,19679,21895,\n+chr22\t11066417\t11068174\tENST00000624155.2\t0\t+\t11066417\t11066417\t0\t2\t98,190,\t0,1567,\n+chr22\t11124336\t11125705\tENST00000422332.1\t0\t+\t11124336\t11124336\t0\t2\t43,1198,\t0,171,\n+chr22\t11249808\t11249959\tENST00000612732.1\t0\t-\t11249808\t11249808\t0\t1\t151,\t0,\n+chr22\t11474743\t11479643\tENST00000672261.1\t0\t+\t11474743\t11474743\t0\t3\t161,93,2466,\t0,402,2434,\n+chr22\t11827522\t11910358\tENST00000657566.1\t0\t+\t11827522\t11827522\t0\t17\t136,155,31,70,192,85,29,73,71,165,195,921,150,282,214,221,193,\t0,5238,39592,42306,44640,46318,48581,48701,54745,58878,60429,61787,64259,75338,76264,77814,82643,\n+chr22\t11883601\t11904000\tENST00000657645.1\t0\t+\t11883601\t11883601\t0\t7\t1027,165,195,921,150,282,214,\t0,2799,4350,5708,8180,19259,20185,\n+chr22\t12602465\t12626642\tENST00000634617.1\t0\t+\t12602465\t12602465\t0\t9\t62,70,126,58,119,101,90,112,36,\t0,2204,12943,13848,15705,18372,21776,22851,24141,\n+chr22\t15273854\t15273961\tENST00000613107.1\t0\t+\t15273854\t15273854\t0\t1\t107,\t0,\n+chr22\t15282556\t15288670\tENST00000623391.1\t0\t-\t15282556\t15282556\t0\t1\t6114,\t0,\n+chr22\t15290717\t15297196\tENST00000448473.1\t0\t+\t15290717\t15290717\t0\t5\t119,30,79,103,40,\t0,277,4614,5012,6439,\n+chr22\t15298377\t15304556\tENST00000623199.1\t0\t-\t15298377\t15298377\t0\t1\t6179,\t0,\n+chr22\t15326036\t15343065\tENST00000425869.1\t0\t-\t15326036\t15326036\t0\t3\t1720,67,121,\t0,16323,16908,\n+chr22\t15349466\t15350043\tENST00000441221.1\t0\t+\t15349466\t15349466\t0\t1\t577,\t0,\n+chr22\t15489989\t15492564\tENST00000429435.1\t0\t+\t15489989\t15489989\t0\t3\t142,76,79,\t0,882,2496,\n+chr22\t15541435\t15578006\tENST00000412729.1\t0\t+\t15541435\t15541435\t0\t4\t172,181,175,40,\t0,17010,34176,36531,\n+chr22\t15550903\t15553838\tENST00000443989.1\t0\t-\t15550903\t15550903\t0\t3\t1984,376,148,\t0,2307,2787,\n+chr22\t15557576\t15560694\tENST00000444162.1\t0\t-\t15557576\t15557576\t0\t3\t1015,109,170,\t0,2579,2948,\n+chr22\t15562016\t15564276\tENST00000417863.1\t0\t-\t15562016\t15562016\t0\t1\t2260,\t0,\n+chr22\t15572088\t15573265\tENST00000456143.1\t0\t-\t15572088\t15572088\t0\t1\t1177,\t0,\n+chr22\t15588360\t15588478\tENST00000447704.1\t0\t+\t15588360\t15588360\t0\t1\t118,\t0,\n+chr22\t15600907\t15604882\tENST00000428118.1\t0\t-\t15600907\t15600907\t0\t3\t1607,82,41,\t0,3144,3934,\n+chr22\t15611758\t15613096\tENST00000438441.1\t0\t-\t15611758\t15611758\t0\t1\t1338,\t0,\n+chr22\t15615401\t15615578\tENST00000440999.1\t0\t-\t15615401\t15615401\t0\t1\t177,\t0,\n+chr22\t15622600\t15632051\tENST00000426025.1\t0\t-\t15622600\t15622600\t0\t11\t112,85,136,139,430,79,67,205,154,109,133,\t0,1386,1938,2355,2871,4731,5049,5781,7137,8829,9318,\n+chr22\t15635179\t15644330\tENST00000435410.1\t0\t-\t15635179\t15635179\t0\t7\t132,57,169,66,79,192,127,\t0,831,1366,1620,2201,3672,9024,\n+chr22\t15690025\t15721631\tENST00000343518.11\t0\t+\t15690077\t15719777\t0\t11\t684,115,174,107,138,71,71,45,167,119,346,\t0,5345,5619,8636,10052,12660,17994,19756,20842,29634,31260,\n+chr22\t15690077\t15721631\tENST00000621704.4\t0\t+\t15690077\t15719777\t0\t12\t237,284,115,174,107,138,71,71,45,167,119,346,\t0,348,5293,5567,8584,10000,12608,17942,19704,20790,29582,31208,\n+chr22\t15690245\t15721522\tENST00000452800.1\t0\t+\t15690245\t15697532\t0\t12\t464,115,174,256,107,138,71,71,45,167,119,237,\t0,5125,5399,7128,8416,9832,12440,17774,19536,20622,29414,31040,\n+chr22\t15699360\t15703403\tENST00000422014.1\t0\t-\t15699360\t15699360\t0\t2\t2122,444,\t0,3599,\n+chr22\t15701458\t15701565\tENST00000390914.1\t0\t+\t15701458\t15701458\t0\t1\t107,\t0,\n+chr22\t15721485\t15722608\tENST00000417657.1\t0\t+\t15721485\t15721485\t0\t1\t1123,\t0,\n+chr22\t15746629\t15778297\tENST00000453395.5\t0\t+\t15746629\t15746629\t0\t3\t270,66,288,\t0,7758,31380,\n+chr22\t15749155\t15750825\tENST00000423297.1\t0\t-\t15749155\t15749155\t0\t2\t643,454,\t0,1216,\n+chr22\t15765686\t15778297\tENST00000438574.1\t0\t+\t15765686\t15765686\t0\t3\t94,137,288,\t0,9025,12323,\n+chr22\t15784958\t15827434\tENST00000413768.5\t0\t+\t15784958\t15784958\t0\t8\t99,111,115,112,138,143,91,1293,\t0,2213,3626,3861,5702,6051,30517,41183,\n+chr22\t15784962\t15827708\tENST'..b'5,36323,\n+chr22\t17739447\t17774770\tENST00000552886.1\t0\t-\t17739447\t17739447\t0\t3\t41,211,78,\t0,4355,35245,\n+chr22\t17740030\t17774495\tENST00000617586.1\t0\t-\t17740030\t17750116\t0\t4\t146,211,70,115,\t0,3772,10074,34350,\n+chr22\t17764179\t17764259\tENST00000583102.1\t0\t-\t17764179\t17764179\t0\t1\t80,\t0,\n+chr22\t17777321\t17779481\tENST00000600723.1\t0\t+\t17777321\t17777321\t0\t1\t2160,\t0,\n+chr22\t17787648\t18024561\tENST00000441493.7\t0\t-\t17790731\t17906812\t0\t32\t3268,74,100,94,111,95,1819,83,141,114,138,254,196,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,338,281,\t0,3349,3553,21195,23054,29041,29662,33778,34381,35298,39995,44205,54173,77250,78275,84188,98229,99521,99674,101385,103836,106159,107635,108597,109075,111799,113193,114229,114982,116983,118900,236632,\n+chr22\t17787648\t18024561\tENST00000672019.1\t0\t-\t17830068\t17906812\t0\t33\t3268,74,100,94,111,95,1819,83,141,114,138,88,254,196,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,338,281,\t0,3349,3553,21195,23054,29041,29662,33778,34381,35298,39995,42418,44205,54173,77250,78275,84188,98229,99521,99674,101385,103836,106159,107635,108597,109075,111799,113193,114229,114982,116983,118900,236632,\n+chr22\t17787651\t17811497\tENST00000476405.1\t0\t-\t17787651\t17787651\t0\t5\t3265,74,100,94,795,\t0,3346,3550,21192,23051,\n+chr22\t17790539\t17791667\tENST00000252134.11\t0\t-\t17790539\t17790539\t0\t3\t377,74,466,\t0,458,662,\n+chr22\t17790836\t17815669\tENST00000580469.1\t0\t-\t17790836\t17790836\t0\t6\t80,74,100,94,111,3163,\t0,161,365,18007,19866,21670,\n+chr22\t17790945\t17817489\tENST00000577821.5\t0\t-\t17790945\t17817489\t0\t8\t126,100,51,94,111,51,95,179,\t0,256,12865,17898,19757,21561,25744,26365,\n+chr22\t17791263\t17817425\tENST00000579997.5\t0\t-\t17791263\t17817425\t0\t6\t38,66,94,111,95,115,\t0,2465,17580,19439,25426,26047,\n+chr22\t17800721\t17802035\tENST00000657505.1\t0\t+\t17800721\t17800721\t0\t2\t415,576,\t0,738,\n+chr22\t17803553\t17810736\tENST00000584751.1\t0\t-\t17803571\t17810736\t0\t3\t308,94,34,\t0,5290,7149,\n+chr22\t17819021\t17832000\tENST00000498573.5\t0\t-\t17819021\t17832000\t0\t5\t108,83,141,114,147,\t0,2405,3008,3925,12832,\n+chr22\t17819035\t17831927\tENST00000578984.1\t0\t-\t17819035\t17831927\t0\t6\t94,83,141,114,63,74,\t0,2391,2994,3911,7418,12818,\n+chr22\t17834327\t17906835\tENST00000400561.6\t0\t-\t17834449\t17906812\t0\t20\t222,196,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,287,\t0,7494,30571,31596,37509,51550,52842,52995,54706,57157,59480,60956,61918,62396,65120,66514,67550,68303,70304,72221,\n+chr22\t17839591\t18001501\tENST00000495076.5\t0\t-\t17896820\t17906812\t0\t19\t2426,88,89,187,174,63,113,197,148,97,127,116,258,156,102,117,208,338,109,\t0,25307,26332,32245,46286,47578,47731,49442,51893,54216,55692,56654,57132,61250,62286,63039,65040,66957,161801,\n+chr22\t17839950\t17842482\tENST00000578905.1\t0\t-\t17839950\t17839950\t0\t1\t2532,\t0,\n+chr22\t17839950\t17906812\tENST00000414725.6\t0\t-\t17841775\t17906812\t0\t20\t2067,88,89,187,84,174,63,113,197,148,97,127,116,258,101,156,102,117,208,264,\t0,24948,25973,31886,44324,45927,47219,47372,49083,51534,53857,55333,56295,56773,59497,60891,61927,62680,64681,66598,\n+chr22\t17841674\t17906827\tENST00000383094.7\t0\t-\t17841775\t17906812\t0\t19\t343,88,89,187,174,63,113,197,148,97,127,116,258,101,156,102,117,208,279,\t0,23224,24249,30162,44203,45495,45648,47359,49810,52133,53609,54571,55049,57773,59167,60203,60956,62957,64874,\n+chr22\t17860162\t17895288\tENST00000461307.5\t0\t-\t17864653\t17895288\t0\t11\t4824,89,187,84,174,63,113,197,148,97,5,\t0,5761,11674,24112,25715,27007,27160,28871,31322,33645,35121,\n+chr22\t17864614\t17906874\tENST00000585038.1\t0\t-\t17864653\t17906812\t0\t22\t372,89,187,108,108,57,99,174,63,113,197,148,97,127,116,258,101,156,102,117,208,326,\t0,1309,7222,8132,10832,14731,16590,21263,22555,22708,24419,26870,29193,30669,31631,32109,34833,36227,37263,38016,40017,41934,\n+chr22\t17865923\t17876703\tENST00000462645.1\t0\t-\t17865923\t17865923\t0\t3\t89,187,296,\t0,5913,10484,\n+chr22\t17871929\t17876872\tENST00000465886.1\t0\t-\t17871929\t17871929\t0\t2\t94,465,\t0,4478,\n+chr22\t17871933\t17876739\tENST00000498345.1\t0\t-\t17871933\t17871933\t0\t3\t90,116,332,\t0,3277,4474,\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/maf_to_fasta-in2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-in2.bed Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,250 @@\n+chr22\t17904727\t18001180\tENST00000424046.1\t0\t-\t17904727\t17906812\t0\t3\t112,338,92,\t0,1821,96361,\n+chr22\t17980867\t17980961\tENST00000385046.1\t0\t-\t17980867\t17980867\t0\t1\t94,\t0,\n+chr22\t17983204\t17983619\tENST00000429618.1\t0\t-\t17983204\t17983204\t0\t2\t83,278,\t0,137,\n+chr22\t18004269\t18007308\tENST00000441167.1\t0\t-\t18004269\t18004269\t0\t2\t2346,147,\t0,2892,\n+chr22\t18019213\t18020200\tENST00000411920.1\t0\t+\t18019213\t18019213\t0\t3\t198,66,87,\t0,522,900,\n+chr22\t18029384\t18037968\tENST00000443243.1\t0\t+\t18029384\t18029384\t0\t2\t170,2209,\t0,6375,\n+chr22\t18076526\t18077797\tENST00000426483.1\t0\t-\t18076526\t18076526\t0\t2\t536,269,\t0,1002,\n+chr22\t18077185\t18078884\tENST00000607927.1\t0\t-\t18077185\t18077185\t0\t1\t1699,\t0,\n+chr22\t18077919\t18091019\tENST00000610387.4\t0\t+\t18078376\t18088075\t0\t5\t128,311,141,296,3048,\t0,376,1954,5517,10052,\n+chr22\t18077922\t18105396\tENST00000329627.11\t0\t+\t18078376\t18088075\t0\t6\t125,311,141,296,147,17425,\t0,373,1951,5514,7189,10049,\n+chr22\t18078007\t18088460\tENST00000399744.7\t0\t+\t18078376\t18088075\t0\t5\t599,141,296,147,489,\t0,1866,5429,7104,9964,\n+chr22\t18078014\t18131138\tENST00000474897.5\t0\t+\t18078376\t18121677\t0\t6\t592,141,223,149,681,296,\t0,1859,43464,46141,48339,52828,\n+chr22\t18078054\t18078775\tENST00000622035.1\t0\t-\t18078054\t18078054\t0\t1\t721,\t0,\n+chr22\t18078376\t18088119\tENST00000428061.2\t0\t+\t18078376\t18088075\t0\t4\t230,141,296,148,\t0,1497,5060,9595,\n+chr22\t18081465\t18081675\tENST00000427227.2\t0\t-\t18081465\t18081465\t0\t1\t210,\t0,\n+chr22\t18101611\t18101888\tENST00000450866.1\t0\t+\t18101611\t18101611\t0\t1\t277,\t0,\n+chr22\t18102456\t18103649\tENST00000446487.1\t0\t-\t18102456\t18102456\t0\t2\t338,193,\t0,1000,\n+chr22\t18110330\t18124268\tENST00000426208.5\t0\t+\t18121673\t18124268\t0\t3\t246,223,113,\t0,11148,13825,\n+chr22\t18110686\t18131154\tENST00000316027.10\t0\t+\t18121673\t18131136\t0\t5\t153,223,149,681,312,\t0,10792,13469,15667,20156,\n+chr22\t18110758\t18131154\tENST00000623543.1\t0\t-\t18110758\t18110758\t0\t1\t20396,\t0,\n+chr22\t18110808\t18131732\tENST00000330423.8\t0\t+\t18110865\t18131136\t0\t5\t60,223,149,681,890,\t0,10670,13347,15545,20034,\n+chr22\t18121106\t18131117\tENST00000416740.1\t0\t+\t18121403\t18131117\t0\t4\t595,149,681,275,\t0,3049,5247,9736,\n+chr22\t18126706\t18146554\tENST00000608634.1\t0\t+\t18126706\t18145989\t0\t3\t328,164,899,\t0,4136,18949,\n+chr22\t18150169\t18177397\tENST00000215794.8\t0\t+\t18157663\t18176817\t0\t11\t53,263,97,146,80,147,96,168,132,50,626,\t0,7388,10002,11620,17085,17720,19674,20583,22980,23623,26602,\n+chr22\t18178037\t18205915\tENST00000434390.1\t0\t-\t18178037\t18178037\t0\t9\t428,957,34,62,66,87,25,59,141,\t0,5072,10585,11084,13145,18119,21152,21645,27737,\n+chr22\t18340144\t18345899\tENST00000617623.1\t0\t+\t18340144\t18340144\t0\t7\t172,137,188,127,113,114,147,\t0,695,4347,4767,4996,5190,5608,\n+chr22\t18361819\t18386597\tENST00000619172.5\t0\t-\t18361819\t18361819\t0\t12\t438,155,41,73,2323,34,62,66,87,25,59,212,\t0,5081,5698,5965,6571,11103,11602,13664,18636,21667,22160,24566,\n+chr22\t18361829\t18386526\tENST00000618517.4\t0\t-\t18361829\t18361829\t0\t9\t428,957,34,62,66,87,25,59,141,\t0,5071,11093,11592,13654,18626,21657,22150,24556,\n+chr22\t18370584\t18386480\tENST00000613790.4\t0\t-\t18370584\t18370584\t0\t8\t129,34,62,66,87,25,59,95,\t0,2338,2837,4899,9871,12902,13395,15801,\n+chr22\t18370665\t18391105\tENST00000615974.1\t0\t-\t18370665\t18370665\t0\t9\t48,34,62,66,87,25,59,59,287,\t0,2257,2756,4818,9790,12821,13314,19243,20153,\n+chr22\t18374105\t18375689\tENST00000622906.1\t0\t+\t18374105\t18374105\t0\t2\t116,259,\t0,1325,\n+chr22\t18400406\t18404206\tENST00000612861.1\t0\t-\t18400406\t18400406\t0\t1\t3800,\t0,\n+chr22\t18422243\t18500594\tENST00000624459.2\t0\t+\t18422243\t18422243\t0\t12\t104,59,25,87,66,62,34,2041,73,41,155,439,\t0,2733,3260,6231,64895,66961,67488,69742,72316,72615,73118,77912,\n+chr22\t18424976\t18490146\tENST00000624001.2\t0\t+\t18424976\t18424976\t0\t6\t59,25,87,66,62,415,\t0,527,3498,62162,64228,64755,\n+chr22\t18486998\t18488582\tENST00000614584.1\t0\t-\t18486998\t18486998\t0\t2\t259,116,\t0,1468,\n+chr22\t18487125\t18489905\tENST00000615181.4\t0\t+\t18487125\t18487125\t0\t3\t79,62,174,\t0,2079,2606,\n+chr22\t18487868\t18491247\tENST00000620909.1\t0\t-\t18487868\t18487868\t0\t2\t715,105,\t0,3274,\n+c'..b'3,6965,7147,7562,\n+chr22\t19717219\t19724216\tENST00000455843.5\t0\t+\t19718737\t19722484\t0\t12\t1599,97,87,124,135,118,102,97,136,103,1152,363,\t0,2382,2586,2895,3100,3329,3548,4420,4602,5017,5208,6634,\n+chr22\t19717269\t19721720\tENST00000431124.5\t0\t+\t19717277\t19721720\t0\t8\t176,97,87,124,135,118,102,81,\t0,2332,2536,2845,3050,3279,3498,4370,\n+chr22\t19718158\t19719055\tENST00000490204.1\t0\t+\t19718158\t19718158\t0\t2\t660,114,\t0,783,\n+chr22\t19718431\t19722629\tENST00000383045.7\t0\t+\t19718737\t19722484\t0\t11\t387,97,87,124,135,118,102,97,136,103,202,\t0,1170,1374,1683,1888,2117,2336,3208,3390,3805,3996,\n+chr22\t19718457\t19723319\tENST00000438754.6\t0\t+\t19718737\t19722311\t0\t11\t361,97,87,124,135,118,102,97,125,103,892,\t0,1144,1348,1657,1862,2091,2310,3182,3375,3779,3970,\n+chr22\t19718468\t19724772\tENST00000431044.5\t0\t+\t19719688\t19722484\t0\t12\t103,97,87,124,135,118,102,97,136,103,1152,919,\t0,1133,1337,1646,1851,2080,2299,3171,3353,3768,3959,5385,\n+chr22\t19719434\t19720833\tENST00000395109.6\t0\t+\t19719688\t19720833\t0\t6\t264,87,124,135,118,66,\t0,371,680,885,1114,1333,\n+chr22\t19719529\t19720213\tENST00000477238.1\t0\t+\t19719529\t19719529\t0\t2\t169,408,\t0,276,\n+chr22\t19720187\t19720874\tENST00000413258.1\t0\t+\t19720187\t19720874\t0\t4\t51,135,25,107,\t0,132,454,580,\n+chr22\t19720341\t19721869\tENST00000480423.5\t0\t+\t19720341\t19720341\t0\t4\t113,118,102,230,\t0,207,426,1298,\n+chr22\t19720553\t19724224\tENST00000470814.1\t0\t+\t19720553\t19720553\t0\t6\t113,102,97,518,1152,371,\t0,214,1086,1268,1874,3300,\n+chr22\t19722944\t19724771\tENST00000366425.3\t0\t+\t19723569\t19724464\t0\t2\t635,918,\t0,909,\n+chr22\t19756702\t19767334\tENST00000332710.8\t0\t+\t19759643\t19766867\t0\t9\t43,120,376,102,172,156,68,101,946,\t0,2855,4202,6538,7452,8255,9055,9199,9686,\n+chr22\t19756702\t19779546\tENST00000329705.11\t0\t+\t19759643\t19779407\t0\t9\t43,120,376,102,172,156,68,101,327,\t0,2855,4202,6538,7452,8255,9055,9199,22517,\n+chr22\t19756702\t19783593\tENST00000359500.7\t0\t+\t19759643\t19783022\t0\t10\t43,120,376,102,172,156,68,101,120,280,\t0,2855,4202,6538,7452,8255,9055,9199,26210,26611,\n+chr22\t19760820\t19767332\tENST00000649276.1\t0\t+\t19760843\t19766867\t0\t7\t460,102,172,156,68,101,944,\t0,2420,3334,4137,4937,5081,5568,\n+chr22\t19761196\t19763702\tENST00000475303.1\t0\t+\t19761196\t19761196\t0\t2\t84,462,\t0,2044,\n+chr22\t19765078\t19766327\tENST00000484336.1\t0\t+\t19765078\t19765078\t0\t3\t35,68,426,\t0,679,823,\n+chr22\t19783222\t19854874\tENST00000329517.11\t0\t-\t19788708\t19821355\t0\t8\t5738,216,99,163,126,148,97,55,\t0,18778,23436,29062,37375,38005,71220,71597,\n+chr22\t19788414\t19854843\tENST00000403325.5\t0\t-\t19788708\t19821355\t0\t7\t546,216,99,163,126,148,401,\t0,13586,18244,23870,32183,32813,66028,\n+chr22\t19788417\t19854939\tENST00000405009.5\t0\t-\t19788617\t19821355\t0\t8\t209,114,99,163,126,148,97,120,\t0,13685,18241,23867,32180,32810,66025,66402,\n+chr22\t19788463\t19854806\tENST00000460402.5\t0\t-\t19788463\t19788463\t0\t6\t497,216,99,163,97,125,\t0,13537,18195,23821,65979,66218,\n+chr22\t19792293\t19793094\tENST00000424559.2\t0\t+\t19792293\t19792293\t0\t1\t801,\t0,\n+chr22\t19801998\t19854816\tENST00000481086.1\t0\t-\t19801998\t19801998\t0\t4\t218,99,163,374,\t0,4660,10286,52444,\n+chr22\t19812294\t19854843\tENST00000453108.1\t0\t-\t19812294\t19821355\t0\t3\t153,148,401,\t0,8933,42148,\n+chr22\t19846137\t19854896\tENST00000407472.5\t0\t-\t19851166\t19852261\t0\t3\t6349,97,77,\t0,8305,8682,\n+chr22\t19846145\t19854863\tENST00000484072.5\t0\t-\t19846145\t19846145\t0\t3\t1244,97,44,\t0,8297,8674,\n+chr22\t19846145\t19854874\tENST00000328554.9\t0\t-\t19851166\t19852261\t0\t3\t6341,97,215,\t0,8297,8514,\n+chr22\t19846145\t19854886\tENST00000405640.1\t0\t-\t19851166\t19852261\t0\t2\t6341,444,\t0,8297,\n+chr22\t19851988\t19854816\tENST00000416337.1\t0\t-\t19851988\t19852261\t0\t3\t498,97,135,\t0,2454,2693,\n+chr22\t19875516\t19932553\tENST00000400518.5\t0\t-\t19877104\t19932369\t0\t18\t291,195,98,72,93,96,137,175,92,20,71,63,79,75,145,57,69,197,\t0,1523,2573,2849,4662,5105,7808,19890,22522,23532,35860,39697,40248,42626,43343,44026,55513,56840,\n+chr22\t19875517\t19916366\tENST00000494454.5\t0\t-\t19875517\t19875517\t0\t13\t290,195,98,72,93,96,137,175,92,20,71,63,602,\t0,1522,2572,2848,4661,5104,7807,19889,22521,23531,35859,39696,40247,\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/maf_to_fasta-in2.maf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-in2.maf Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,2623 @@\n+##maf version=1\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=196573.0\n+s hg38.chr22 18627690 7 - 50818468 CAAATAA \n+\n+a score=6623803.0\n+s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n+\n+a score=222067.0\n+s hg38.chr22 32358071 23 + 50818468 ATGAAAAGGTTGTCACTTGTCAC \n+\n+a score=28783.0\n+s hg38.chr22 32358094 6 + 50818468 AACTAA \n+\n+a score=94379.0\n+s hg38.chr22 32358100 18 + 50818468 CAGGCTTTCACCTCAAGG \n+\n+a score=12732.0\n+s hg38.chr22 32358118 2 + 50818468 AA \n+\n+a score=325051.0\n+s hg38.chr22 32358120 57 + 50818468 ATTTTCTTCCCTTGTGTACTTTTCCCCTGGCAGTGGACATGGCTGCACTCTTCCAAG \n+\n+a score=2523686.0\n+s hg38.chr22 32358177 267 + 50818468 AAGCAAGCAG'..b'GCTGGGCCTGGTGCTGCTCGTGGAGGCCGTGGCCGTGCTCATCGGACCGCCCTCCGCCG \n+s mm10.chr15             24791713 98 - 104043685 GCTCATGGCAACCGTGGGTGCACCCCGCTTCCCTAGTGCATTGGGCCTAGTGCTGCTCGTGGAGGCCGTGGCTGTGCTCATAGGACCGCCCTCTGCCG \n+\n+a score=1184954.0\n+s hg38.chr22             12737495 36 -  50818468 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s eulFla1.LGHW01006107v1   634009 36 +    657376 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s mm10.chr15             24791677 36 - 104043685 GTCCTACGGCATGGTGGGCGCACTGCAGTTTGAGGT \n+\n+a score=4109169.0\n+s hg38.chr22             12737373 122 -  50818468 CTGCGGCCGCACGTCCCGTATCTGTTCAGCCTGGCCCTGCTGGCCAATGGGCTCACAGACCTGAGCAGCGCACGCGCGCGCTCCTACGGCGCCCTCGTCGCCTTCTGCGTCGCCTTCGGCCT \n+s eulFla1.LGHW01006107v1   633887 122 +    657376 CTGCGACCGCGGGTGCCCTATCTCTTCAGCCTGGCCCTGCTGGCCAACGGGCTCACGGACCTGAGCAGTGCGCGCGCGCGCTCCTACGGAGCCCTCGTCGCCTTCTGCATCGCCTTCGGCCT \n+s mm10.chr15             24791555 122 - 104043685 CTGAGACCCCACGTCCCCTACCTCTTCAGCCTGGCCCTGTTGGCCAATGGGCTCACGGACCTGATTAGCGCGCGTGCGCGCTCCTACGGGACCCTCGTTGCTTTCTGCATTGCCTTCGGCCT \n+\n+a score=8150994.0\n+s hg38.chr22             12737111 262 -  50818468 GCAGCTGCGCGAGGCATCCCCCAGGGTCCGGCCC--CGCCGGCGCCTGCTGGACTTGGCAGTGTGCACCGACCGCGCCTTCGCCGTGTACGCCGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTCCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCCGACACCGACGCCGCCTTCCTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCGCGCCCGGCGTGCGGCGCCCTGGCGGGCCTGGCGCGT \n+s eulFla1.LGHW01006107v1   633625 262 +    657376 gcgcgtgcgcgaggcgCCCCCTGGCGGCCGCACC--CGCCGGCGGCTGCTGGACGTGGCTGTGTGTGCCGACCGCGCCTTCGTGGTGTACGCGGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTGCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGACGCCGCCTTCCTGTTATCCATCGTGGGCTTCGTAGACATCGTGGCGCGGCCAGCGTGCGGCGCCCTGGCGGGCCTGGCGCGC \n+s mm10.chr15             24791316 239 - 104043685 -------------------------GCCCGGCTCGCCGCCGGCGGCTGCTGGACGTGGCAGTGTGCACCGACCGTGCTTTCGTGGTGTACGTGGTCACCAAGTTCCTGATGGCACTCGGGCTCTTTGTGCCGGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGAGGCCGCCTTCTTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCACGACCGGCGTGCGGTGCTTTGGCGGGTCTGGGGCGC \n+\n+a score=373719.0\n+s hg38.chr22             12737090 21 -  50818468 GGAGGCTGACGGTGCGGGGCT \n+s eulFla1.LGHW01006107v1   633604 21 +    657376 ggaggcggagggcgaggggct \n+s mm10.chr15             24791310  6 - 104043685 --------ACGGTG------- \n+\n+a score=149374.0\n+s hg38.chr22             12737084 6 - 50818468 CGAGGC \n+s eulFla1.LGHW01006107v1   633592 6 +   657376 Agaggc \n+\n+a score=172154.0\n+s hg38.chr22             12737070 14 -  50818468 GGGGACGCTCCGGG \n+s eulFla1.LGHW01006107v1   633578 14 +    657376 ggggACTCTGCGGG \n+s mm10.chr15             24791305  5 - 104043685 ------GCCCC--- \n+\n+a score=5393236.0\n+s hg38.chr22             12736861 209 -  50818468 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGCGCTGTCGCCGCTCGGCCAGCAGCTGCTGGAGCGCTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCCTGCGGGGCTGTCATGAGGCCGCCGCCCGGGCCGGGCCCGCGACCG------CGCAGGGACAGCGCCGGCGACCGCGCC \n+s eulFla1.LGHW01006107v1   633363 215 +    657376 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGTGCTGTCGCCTCTCGGCCAGCAGCTGCTCGAGCACTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCGTGCGGAGCCGTCATGCggccgccgccggggccggggccggggccaccgccgcgcggggccggcgcccgggacctggcg \n+s mm10.chr15             24791115 190 - 104043685 TGGCCAACGGGCTGGCAGCGGCGGGCAGTCCCGTGTTTCTGTCCATGCTGTCGCCGCTCGGGCAGCTGCTGGGGGAGCGCTTCGGCTGGCGTGGCGGCTTCCTGCTGTTTGGCGGCCTCCTGCTGCACTGTTGCGCCTGTGGGGCAGTCATGCGTCCGCCCCCTGGACC---CCCG---CCG------CGCAGAGACCCCTC------------- \n+\n+a score=810987.0\n+s hg38.chr22             12736835 26 -  50818468 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s eulFla1.LGHW01006107v1   633337 26 +    657376 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s mm10.chr15             24791089 26 - 104043685 ACTCTACTTCGAGCGGCGACGGCCCC \n+\n+a score=2187734.0\n+s hg38.chr22             12736789 46 -  50818468 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s eulFla1.LGHW01006107v1   633291 46 +    657376 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s mm10.chr15             24791043 46 - 104043685 GCCTGGGCCTAGCTCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/maf_to_fasta-out1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-out1.fasta Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,1750 @@\n+>hg38.ENST00000615943.1\n+\n+>eulFla1.ENST00000615943.1\n+\n+>mm10.ENST00000615943.1\n+\n+\n+>hg38.ENST00000635667.1\n+\n+>eulFla1.ENST00000635667.1\n+\n+>mm10.ENST00000635667.1\n+\n+\n+>hg38.ENST00000624155.2\n+\n+>eulFla1.ENST00000624155.2\n+\n+>mm10.ENST00000624155.2\n+\n+\n+>hg38.ENST00000422332.1\n+\n+>eulFla1.ENST00000422332.1\n+\n+>mm10.ENST00000422332.1\n+\n+\n+>hg38.ENST00000612732.1\n+\n+>eulFla1.ENST00000612732.1\n+\n+>mm10.ENST00000612732.1\n+\n+\n+>hg38.ENST00000672261.1\n+\n+>eulFla1.ENST00000672261.1\n+\n+>mm10.ENST00000672261.1\n+\n+\n+>hg38.ENST00000657566.1\n+\n+>eulFla1.ENST00000657566.1\n+\n+>mm10.ENST00000657566.1\n+\n+\n+>hg38.ENST00000657645.1\n+\n+>eulFla1.ENST00000657645.1\n+\n+>mm10.ENST00000657645.1\n+\n+\n+>hg38.ENST00000634617.1\n+\n+>eulFla1.ENST00000634617.1\n+\n+>mm10.ENST00000634617.1\n+\n+\n+>hg38.ENST00000613107.1\n+\n+>eulFla1.ENST00000613107.1\n+\n+>mm10.ENST00000613107.1\n+\n+\n+>hg38.ENST00000623391.1\n+\n+>eulFla1.ENST00000623391.1\n+\n+>mm10.ENST00000623391.1\n+\n+\n+>hg38.ENST00000448473.1\n+\n+>eulFla1.ENST00000448473.1\n+\n+>mm10.ENST00000448473.1\n+\n+\n+>hg38.ENST00000623199.1\n+\n+>eulFla1.ENST00000623199.1\n+\n+>mm10.ENST00000623199.1\n+\n+\n+>hg38.ENST00000425869.1\n+\n+>eulFla1.ENST00000425869.1\n+\n+>mm10.ENST00000425869.1\n+\n+\n+>hg38.ENST00000441221.1\n+\n+>eulFla1.ENST00000441221.1\n+\n+>mm10.ENST00000441221.1\n+\n+\n+>hg38.ENST00000429435.1\n+\n+>eulFla1.ENST00000429435.1\n+\n+>mm10.ENST00000429435.1\n+\n+\n+>hg38.ENST00000412729.1\n+\n+>eulFla1.ENST00000412729.1\n+\n+>mm10.ENST00000412729.1\n+\n+\n+>hg38.ENST00000443989.1\n+\n+>eulFla1.ENST00000443989.1\n+\n+>mm10.ENST00000443989.1\n+\n+\n+>hg38.ENST00000444162.1\n+\n+>eulFla1.ENST00000444162.1\n+\n+>mm10.ENST00000444162.1\n+\n+\n+>hg38.ENST00000417863.1\n+\n+>eulFla1.ENST00000417863.1\n+\n+>mm10.ENST00000417863.1\n+\n+\n+>hg38.ENST00000456143.1\n+\n+>eulFla1.ENST00000456143.1\n+\n+>mm10.ENST00000456143.1\n+\n+\n+>hg38.ENST00000447704.1\n+\n+>eulFla1.ENST00000447704.1\n+\n+>mm10.ENST00000447704.1\n+\n+\n+>hg38.ENST00000428118.1\n+\n+>eulFla1.ENST00000428118.1\n+\n+>mm10.ENST00000428118.1\n+\n+\n+>hg38.ENST00000438441.1\n+\n+>eulFla1.ENST00000438441.1\n+\n+>mm10.ENST00000438441.1\n+\n+\n+>hg38.ENST00000440999.1\n+\n+>eulFla1.ENST00000440999.1\n+\n+>mm10.ENST00000440999.1\n+\n+\n+>hg38.ENST00000426025.1\n+\n+>eulFla1.ENST00000426025.1\n+\n+>mm10.ENST00000426025.1\n+\n+\n+>hg38.ENST00000435410.1\n+\n+>eulFla1.ENST00000435410.1\n+\n+>mm10.ENST00000435410.1\n+\n+\n+>hg38.ENST00000343518.11\n+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'..b'---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>mm10.ENST00000585038.1\n+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+\n+>hg38.ENST00000462645.1\n+\n+>eulFla1.ENST00000462645.1\n+\n+>mm10.ENST00000462645.1\n+\n+\n+>hg38.ENST00000465886.1\n+\n+>eulFla1.ENST00000465886.1\n+\n+>mm10.ENST00000465886.1\n+\n+\n+>hg38.ENST00000498345.1\n+\n+>eulFla1.ENST00000498345.1\n+\n+>mm10.ENST00000498345.1\n+\n+\n'
b
diff -r 000000000000 -r f24a9ff28d3c test-data/maf_to_fasta-out2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-out2.fasta Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,1750 @@\n+>hg38.ENST00000424046.1\n+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>eulFla1.ENST00000424046.1\n+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>mm10.ENST00000424046.1\n+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+\n+>hg38.ENST00000385046.1\n+\n+>eulFla1.ENST00000385046.1\n+\n+>mm10.ENST00000385046.1\n+\n+\n+>hg38.ENST00000429618.1\n+\n+>eulFla1.ENST00000429618.1\n+\n+>mm10.ENST00000429618.1\n+\n+\n+>hg38.ENST00000441167.1\n+\n+>eulFla1.ENST00000441167.1\n+\n+>mm10.ENST00000441167.1\n+\n+\n+>hg38.ENST00000411920.1\n+\n+>eulFla1.ENST00000411920.1\n+\n+>mm10.ENST00000411920.1\n+\n+\n+>hg38.ENST00000443243.1\n+\n+>eulFla1.ENST00000443243.1\n+\n+>mm10.ENST00000443243.1\n+\n+\n+>hg38.ENST00000426483.1\n+\n+>eulFla1.ENST00000426483.1\n+\n+>mm10.ENST00000426483.1\n+\n+\n+>hg38.ENST00000607927.1\n+\n+>eulFla1.ENST00000607927.1\n+\n+>mm10.ENST00000607927.1\n+\n+\n+>hg38.ENST00000610387.4\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>eulFla1.ENST00000610387.4\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>mm10.ENST00000610387.4\n+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'..b'-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>eulFla1.ENST00000400518.5\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>mm10.ENST00000400518.5\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+\n+>hg38.ENST00000494454.5\n+\n+>eulFla1.ENST00000494454.5\n+\n+>mm10.ENST00000494454.5\n+\n+\n'
b
diff -r 000000000000 -r f24a9ff28d3c tool-data/maf_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/maf_indexes.loc.sample Fri Aug 21 15:10:13 2020 -0400
b
b'@@ -0,0 +1,17 @@\n+#This is a sample file distributed with Galaxy that is used by some\n+#alignment tools.  The maf_index.loc file has this format (white space \n+#characters are TAB characters):\n+#\n+#<Display_name UID>\t<indexed_for:build1,build2,build3>\t<exists_in_maf:build1,build2,build3>\t<Comma_Separated_List_of_Full_Paths_To_Files>\n+#\n+#ENCODE TBA (hg17)\tENCODE_TBA_hg17\tarmadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2\tarmadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2\t/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr3'..b'data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo\n+#8-way multiZ (ponAbe2)\t8_WAY_MULTIZ_ponAbe2\tponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1\tponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1\t/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo\n'
b
diff -r 000000000000 -r f24a9ff28d3c tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Aug 21 15:10:13 2020 -0400
b
@@ -0,0 +1,8 @@
+<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini -->
+<tables>
+    <!-- Locations of MAF files that have been indexed with bx-python -->
+    <table name="maf_indexes">
+        <columns>name, value, indexed_for, exists_in_maf, path</columns>
+        <file path="maf_indexes.loc" />
+    </table>
+</tables>
b
diff -r 000000000000 -r f24a9ff28d3c tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Aug 21 15:10:13 2020 -0400
b
@@ -0,0 +1,8 @@
+<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini -->
+<tables>
+    <!-- Locations of MAF files that have been indexed with bx-python -->
+    <table name="maf_indexes">
+        <columns>name, value, indexed_for, exists_in_maf, path</columns>
+        <file path="${__HERE__}/test-data/local/maf_indexes.loc" />
+    </table>
+</tables>