| Next changeset 1:0c84cce7b030 (2020-11-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a" |
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added:
maf_stats.py maf_stats.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_stats-in1.bed test-data/maf_stats-in2.bed test-data/maf_stats-out1.dat test-data/maf_stats-out2.dat 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 5a92f4c476b5 maf_stats.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maf_stats.py Thu Aug 13 09:30:47 2020 -0400 |
| [ |
| @@ -0,0 +1,114 @@ +#!/usr/bin/env python +# Dan Blankenberg +""" +Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended. +""" +from __future__ import print_function + +import sys + +import bx.intervals.io +from bx.bitset import BitSet +from galaxy.tools.util import maf_utilities + + +def __main__(): + maf_source_type = sys.argv.pop(1) + input_maf_filename = sys.argv[1].strip() + input_interval_filename = sys.argv[2].strip() + output_filename = sys.argv[3].strip() + dbkey = sys.argv[4].strip() + try: + chr_col = int(sys.argv[5].strip()) - 1 + start_col = int(sys.argv[6].strip()) - 1 + end_col = int(sys.argv[7].strip()) - 1 + except Exception: + print("You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file.", file=sys.stderr) + sys.exit() + summary = sys.argv[8].strip() + if summary.lower() == "true": + summary = True + else: + summary = False + + mafIndexFile = "%s/maf_index.loc" % sys.argv[9] + try: + maf_index_filename = sys.argv[10].strip() + except Exception: + maf_index_filename = None + index = index_filename = None + if maf_source_type == "user": + # index maf for use here + index, index_filename = maf_utilities.open_or_build_maf_index(input_maf_filename, maf_index_filename, species=[dbkey]) + if index is None: + print("Your MAF file appears to be malformed.", file=sys.stderr) + sys.exit() + elif maf_source_type == "cached": + # access existing indexes + index = maf_utilities.maf_index_by_uid(input_maf_filename, mafIndexFile) + if index is None: + print("The MAF source specified (%s) appears to be invalid." % (input_maf_filename), file=sys.stderr) + sys.exit() + else: + print('Invalid source type specified: %s' % maf_source_type, file=sys.stdout) + sys.exit() + + out = open(output_filename, 'w') + + num_region = None + num_bad_region = 0 + species_summary = {} + total_length = 0 + # loop through interval file + for num_region, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(input_interval_filename, 'r'), chrom_col=chr_col, start_col=start_col, end_col=end_col, fix_strand=True, return_header=False, return_comments=False)): + src = "%s.%s" % (dbkey, region.chrom) + region_length = region.end - region.start + if region_length < 1: + num_bad_region += 1 + continue + total_length += region_length + coverage = {dbkey: BitSet(region_length)} + + for block in index.get_as_iterator(src, region.start, region.end): + for spec in maf_utilities.get_species_in_block(block): + if spec not in coverage: + coverage[spec] = BitSet(region_length) + for block in maf_utilities.iter_blocks_split_by_species(block): + if maf_utilities.component_overlaps_region(block.get_component_by_src(src), region): + # need to chop and orient the block + block = maf_utilities.orient_block_by_region(maf_utilities.chop_block_by_region(block, src, region), src, region, force_strand='+') + start_offset, alignment = maf_utilities.reduce_block_by_primary_genome(block, dbkey, region.chrom, region.start) + for i in range(len(alignment[dbkey])): + for spec, text in alignment.items(): + if text[i] != '-': + coverage[spec].set(start_offset + i) + if summary: + # record summary + for key in coverage.keys(): + if key not in species_summary: + species_summary[key] = 0 + species_summary[key] = species_summary[key] + coverage[key].count_range() + else: + # print coverage for interval + coverage_sum = coverage[dbkey].count_range() + out.write("%s\t%s\t%s\t%s\n" % ("\t".join(region.fields), dbkey, coverage_sum, region_length - coverage_sum)) + keys = list(coverage.keys()) + keys.remove(dbkey) + keys.sort() + for key in keys: + coverage_sum = coverage[key].count_range() + out.write("%s\t%s\t%s\t%s\n" % ("\t".join(region.fields), key, coverage_sum, region_length - coverage_sum)) + if summary: + out.write("#species\tnucleotides\tcoverage\n") + for spec in species_summary: + out.write("%s\t%s\t%.4f\n" % (spec, species_summary[spec], float(species_summary[spec]) / total_length)) + out.close() + if num_region is not None: + print("%i regions were processed with a total length of %i." % (num_region + 1, total_length)) + if num_bad_region: + print("%i regions were invalid." % (num_bad_region)) + maf_utilities.remove_temp_index_file(index_filename) + + +if __name__ == "__main__": + __main__() |
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| diff -r 000000000000 -r 5a92f4c476b5 maf_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maf_stats.xml Thu Aug 13 09:30:47 2020 -0400 |
| [ |
| @@ -0,0 +1,130 @@ +<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"> + <description>Alignment coverage information</description> + <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_index.loc && + #end if + python '$__tool_directory__/maf_stats.py' $maf_source_type.maf_source + #if $maf_source_type.maf_source == 'user': + '$input2' + #else: + $maf_source_type.mafType.fields.value + #end if + '$input1' '$out_file1' $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary '.' + #if $maf_source_type.maf_source == 'user': + '$input2.metadata.maf_index' + #end if + ]]> + </command> + <inputs> + <param format="interval" name="input1" label="Interval File" type="data"> + <validator type="unspecified_build" /> + </param> + <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="input2" 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="input2" 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> + <param name="summary" type="select" label="Type of Output"> + <option value="false" selected="true">Coverage by Region</option> + <option value="true">Summarize Coverage</option> + </param> + </inputs> + <outputs> + <data format="interval" name="out_file1" metadata_source="input1"> + <change_format> + <when input="summary" value="true" format="tabular" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="maf_stats-in1.bed" dbkey="hg38" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="TEST"/> + <output name="out_file1" file="maf_stats-out1.dat"/> + <param name="summary" value="false"/> + </test> + <test> + <param name="input1" value="maf_stats-in2.bed" dbkey="hg38" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="TEST"/> + <output name="out_file1" file="maf_stats-out2.dat"/> + <param name="summary" value="true"/> + </test> + </tests> + <help> + **What it does** + + This tool takes a MAF file and an interval file and relates coverage information by interval for each species. + If a column does not exist in the reference genome, it is not included in the output. + + Consider the interval: "chrX 1000 1100 myInterval" + Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: + + chrX 1000 1100 myInterval H XXX YYY + + chrX 1000 1100 myInterval M XXX YYY + + chrX 1000 1100 myInterval R XXX YYY + + + where XXX and YYY are: + + XXX = number of nucleotides + + YYY = number of gaps + + ---- + + Alternatively, you can request only summary information for a set of intervals: + + ======== =========== ======== + #species nucleotides coverage + ======== =========== ======== + hg18 30639 0.2372 + rheMac2 7524 0.0582 + panTro2 30390 0.2353 + ======== =========== ======== + + where **coverage** is the number of nucleotides divided by the total length of the provided intervals. + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr398</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 5a92f4c476b5 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 Thu Aug 13 09:30:47 2020 -0400 |
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| 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' |
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| diff -r 000000000000 -r 5a92f4c476b5 test-data/local/interval2maf-in1-1.maf.index |
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| Binary file test-data/local/interval2maf-in1-1.maf.index has changed |
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| diff -r 000000000000 -r 5a92f4c476b5 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 Thu Aug 13 09:30:47 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 5a92f4c476b5 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 5a92f4c476b5 test-data/local/maf_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/local/maf_indexes.loc Thu Aug 13 09:30:47 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 5a92f4c476b5 test-data/maf_stats-in1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_stats-in1.bed Thu Aug 13 09:30:47 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 5a92f4c476b5 test-data/maf_stats-in2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_stats-in2.bed Thu Aug 13 09:30:47 2020 -0400 |
| b |
| @@ -0,0 +1,51 @@ +chr22 17119390 17121127 XM_011546124.2_cds_1_0_chr22_17119391_r 0 - +chr22 17817310 17819129 NM_015241.3_cds_6_0_chr22_17817311_r 0 - +chr22 18846931 18848320 XM_017029167.2_cds_0_0_chr22_18846932_f 0 + +chr22 18918315 18918491 NM_016335.5_cds_3_0_chr22_18918316_r 0 - +chr22 18918315 18918491 NM_001195226.2_cds_3_0_chr22_18918316_r 0 - +chr22 21030830 21031812 NM_004173.3_cds_3_0_chr22_21030831_r 0 - +chr22 21634684 21635644 NM_001331066.1_cds_3_0_chr22_21634685_f 0 + +chr22 21634684 21635266 NM_152612.3_cds_3_0_chr22_21634685_f 0 + +chr22 22514001 22515630 NM_080740.5_cds_0_0_chr22_22514002_r 0 - +chr22 22646311 22646521 XM_005261818.2_cds_1_0_chr22_22646312_f 0 + +chr22 22646311 22646521 XM_005261815.3_cds_1_0_chr22_22646312_f 0 + +chr22 23394179 23394792 XM_017029168.1_cds_3_0_chr22_23394180_f 0 + +chr22 23394222 23394792 XM_017029169.1_cds_2_0_chr22_23394223_f 0 + +chr22 23573265 23573585 NM_001369906.1_cds_0_0_chr22_23573266_r 0 - +chr22 23573265 23573585 NM_020070.4_cds_0_0_chr22_23573266_r 0 - +chr22 26026444 26027678 XM_011530458.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029014.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029015.1_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029016.1_cds_31_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029013.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 NM_032608.7_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029012.1_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530465.2_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530464.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530461.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530460.2_cds_42_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_011530459.2_cds_43_0_chr22_26026445_f 0 + +chr22 26026444 26027678 XM_017029017.1_cds_41_0_chr22_26026445_f 0 + +chr22 26026444 26027678 NM_001318245.2_cds_42_0_chr22_26026445_f 0 + +chr22 27796762 27800543 NM_002430.3_cds_1_0_chr22_27796763_r 0 - +chr22 27982220 27983851 XM_005261405.2_cds_0_0_chr22_27982221_r 0 - +chr22 27982220 27983851 NM_001145418.1_cds_0_0_chr22_27982221_r 0 - +chr22 29441541 29442122 NM_021026.2_cds_1_0_chr22_29441542_f 0 + +chr22 29488848 29490703 NM_021076.4_cds_3_0_chr22_29488849_f 0 + +chr22 31712082 31717291 NM_173566.3_cds_5_0_chr22_31712083_r 0 - +chr22 32190771 32191352 NM_001364983.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529832.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001159545.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529828.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001159546.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364986.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001098527.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529826.2_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364985.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364982.1_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 XM_011529827.3_cds_0_0_chr22_32190772_r 0 - +chr22 32190771 32191352 NM_001364984.1_cds_0_0_chr22_32190772_r 0 - +chr22 32358071 32358444 NM_001098535.1_cds_0_0_chr22_32358072_f 0 + +chr22 32358153 32358611 XM_017028534.1_cds_1_0_chr22_32358154_f 0 + +chr22 32358158 32358444 NM_006604.2_cds_1_0_chr22_32358159_f 0 + +chr22 35726210 35727194 NM_030642.1_cds_2_0_chr22_35726211_f 0 + |
| b |
| diff -r 000000000000 -r 5a92f4c476b5 test-data/maf_stats-out1.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_stats-out1.dat Thu Aug 13 09:30:47 2020 -0400 |
| b |
| b'@@ -0,0 +1,266 @@\n+chr22\t10736170\t10736283\tENST00000615943.1\t0\t-\t10736170\t10736170\t0\t1\t113,\t0,\thg38\t0\t113\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,\thg38\t0\t21951\n+chr22\t11066417\t11068174\tENST00000624155.2\t0\t+\t11066417\t11066417\t0\t2\t98,190,\t0,1567,\thg38\t0\t1757\n+chr22\t11124336\t11125705\tENST00000422332.1\t0\t+\t11124336\t11124336\t0\t2\t43,1198,\t0,171,\thg38\t0\t1369\n+chr22\t11249808\t11249959\tENST00000612732.1\t0\t-\t11249808\t11249808\t0\t1\t151,\t0,\thg38\t0\t151\n+chr22\t11474743\t11479643\tENST00000672261.1\t0\t+\t11474743\t11474743\t0\t3\t161,93,2466,\t0,402,2434,\thg38\t0\t4900\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,\thg38\t0\t82836\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,\thg38\t0\t20399\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,\thg38\t0\t24177\n+chr22\t15273854\t15273961\tENST00000613107.1\t0\t+\t15273854\t15273854\t0\t1\t107,\t0,\thg38\t0\t107\n+chr22\t15282556\t15288670\tENST00000623391.1\t0\t-\t15282556\t15282556\t0\t1\t6114,\t0,\thg38\t0\t6114\n+chr22\t15290717\t15297196\tENST00000448473.1\t0\t+\t15290717\t15290717\t0\t5\t119,30,79,103,40,\t0,277,4614,5012,6439,\thg38\t0\t6479\n+chr22\t15298377\t15304556\tENST00000623199.1\t0\t-\t15298377\t15298377\t0\t1\t6179,\t0,\thg38\t0\t6179\n+chr22\t15326036\t15343065\tENST00000425869.1\t0\t-\t15326036\t15326036\t0\t3\t1720,67,121,\t0,16323,16908,\thg38\t0\t17029\n+chr22\t15349466\t15350043\tENST00000441221.1\t0\t+\t15349466\t15349466\t0\t1\t577,\t0,\thg38\t0\t577\n+chr22\t15489989\t15492564\tENST00000429435.1\t0\t+\t15489989\t15489989\t0\t3\t142,76,79,\t0,882,2496,\thg38\t0\t2575\n+chr22\t15541435\t15578006\tENST00000412729.1\t0\t+\t15541435\t15541435\t0\t4\t172,181,175,40,\t0,17010,34176,36531,\thg38\t0\t36571\n+chr22\t15550903\t15553838\tENST00000443989.1\t0\t-\t15550903\t15550903\t0\t3\t1984,376,148,\t0,2307,2787,\thg38\t0\t2935\n+chr22\t15557576\t15560694\tENST00000444162.1\t0\t-\t15557576\t15557576\t0\t3\t1015,109,170,\t0,2579,2948,\thg38\t0\t3118\n+chr22\t15562016\t15564276\tENST00000417863.1\t0\t-\t15562016\t15562016\t0\t1\t2260,\t0,\thg38\t0\t2260\n+chr22\t15572088\t15573265\tENST00000456143.1\t0\t-\t15572088\t15572088\t0\t1\t1177,\t0,\thg38\t0\t1177\n+chr22\t15588360\t15588478\tENST00000447704.1\t0\t+\t15588360\t15588360\t0\t1\t118,\t0,\thg38\t0\t118\n+chr22\t15600907\t15604882\tENST00000428118.1\t0\t-\t15600907\t15600907\t0\t3\t1607,82,41,\t0,3144,3934,\thg38\t0\t3975\n+chr22\t15611758\t15613096\tENST00000438441.1\t0\t-\t15611758\t15611758\t0\t1\t1338,\t0,\thg38\t0\t1338\n+chr22\t15615401\t15615578\tENST00000440999.1\t0\t-\t15615401\t15615401\t0\t1\t177,\t0,\thg38\t0\t177\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,\thg38\t0\t9451\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,\thg38\t0\t9151\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,\thg38\t0\t31606\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,\thg38\t0\t31554\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,\thg38\t0\t31277\n+chr22\t15699360\t15703403\tENST00000422014.1\t0\t-\t15699360\t15699360\t0\t2\t2122,444,\t0,3599,\thg38\t0\t4043\n+chr22\t15701458\t15701565\tENST00000390914.1\t0\t+\t15701458\t15701458\t0\t1\t107,\t0,\thg38\t0\t107\n+chr22\t15721485\t15722608\tENST00000417657.1\t0\t+\t15721485\t15721485\t0\t1\t1123,\t0,\thg38\t0\t1123\n+chr22\t15746629\t15778297\tENST00000453395.5\t0\t+\t1'..b'458,662,\thg38\t0\t1128\n+chr22\t17790836\t17815669\tENST00000580469.1\t0\t-\t17790836\t17790836\t0\t6\t80,74,100,94,111,3163,\t0,161,365,18007,19866,21670,\thg38\t0\t24833\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,\thg38\t179\t26365\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,\teulFla1\t179\t26365\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,\tmm10\t179\t26365\n+chr22\t17791263\t17817425\tENST00000579997.5\t0\t-\t17791263\t17817425\t0\t6\t38,66,94,111,95,115,\t0,2465,17580,19439,25426,26047,\thg38\t115\t26047\n+chr22\t17791263\t17817425\tENST00000579997.5\t0\t-\t17791263\t17817425\t0\t6\t38,66,94,111,95,115,\t0,2465,17580,19439,25426,26047,\teulFla1\t115\t26047\n+chr22\t17791263\t17817425\tENST00000579997.5\t0\t-\t17791263\t17817425\t0\t6\t38,66,94,111,95,115,\t0,2465,17580,19439,25426,26047,\tmm10\t115\t26047\n+chr22\t17800721\t17802035\tENST00000657505.1\t0\t+\t17800721\t17800721\t0\t2\t415,576,\t0,738,\thg38\t0\t1314\n+chr22\t17803553\t17810736\tENST00000584751.1\t0\t-\t17803571\t17810736\t0\t3\t308,94,34,\t0,5290,7149,\thg38\t0\t7183\n+chr22\t17819021\t17832000\tENST00000498573.5\t0\t-\t17819021\t17832000\t0\t5\t108,83,141,114,147,\t0,2405,3008,3925,12832,\thg38\t108\t12871\n+chr22\t17819021\t17832000\tENST00000498573.5\t0\t-\t17819021\t17832000\t0\t5\t108,83,141,114,147,\t0,2405,3008,3925,12832,\teulFla1\t108\t12871\n+chr22\t17819021\t17832000\tENST00000498573.5\t0\t-\t17819021\t17832000\t0\t5\t108,83,141,114,147,\t0,2405,3008,3925,12832,\tmm10\t99\t12880\n+chr22\t17819035\t17831927\tENST00000578984.1\t0\t-\t17819035\t17831927\t0\t6\t94,83,141,114,63,74,\t0,2391,2994,3911,7418,12818,\thg38\t94\t12798\n+chr22\t17819035\t17831927\tENST00000578984.1\t0\t-\t17819035\t17831927\t0\t6\t94,83,141,114,63,74,\t0,2391,2994,3911,7418,12818,\teulFla1\t94\t12798\n+chr22\t17819035\t17831927\tENST00000578984.1\t0\t-\t17819035\t17831927\t0\t6\t94,83,141,114,63,74,\t0,2391,2994,3911,7418,12818,\tmm10\t85\t12807\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,\thg38\t0\t72508\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,\thg38\t0\t161910\n+chr22\t17839950\t17842482\tENST00000578905.1\t0\t-\t17839950\t17839950\t0\t1\t2532,\t0,\thg38\t0\t2532\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,\thg38\t0\t66862\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,\thg38\t0\t65153\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,\thg38\t0\t35126\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,\thg38\t0\t42260\n+chr22\t17865923\t17876703\tENST00000462645.1\t0\t-\t17865923\t17865923\t0\t3\t89,187,296,\t0,5913,10484,\thg38\t0\t10780\n+chr22\t17871929\t17876872\tENST00000465886.1\t0\t-\t17871929\t17871929\t0\t2\t94,465,\t0,4478,\thg38\t0\t4943\n+chr22\t17871933\t17876739\tENST00000498345.1\t0\t-\t17871933\t17871933\t0\t3\t90,116,332,\t0,3277,4474,\thg38\t0\t4806\n' |
| b |
| diff -r 000000000000 -r 5a92f4c476b5 test-data/maf_stats-out2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_stats-out2.dat Thu Aug 13 09:30:47 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#species nucleotides coverage +hg38 52730 1.0000 +eulFla1 35593 0.6750 +mm10 37813 0.7171 |
| b |
| diff -r 000000000000 -r 5a92f4c476b5 tool-data/maf_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/maf_indexes.loc.sample Thu Aug 13 09:30:47 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 5a92f4c476b5 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Aug 13 09:30:47 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 5a92f4c476b5 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Aug 13 09:30:47 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> |