| Previous changeset 1:9af3f57e50b9 (2016-01-20) Next changeset 3:b71579ad576c (2016-12-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31 |
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modified:
extract_genomic_dna.py extract_genomic_dna.xml extract_genomic_dna_utils.py test-data/extract_genomic_dna_out1.fasta test-data/extract_genomic_dna_out2.fasta test-data/extract_genomic_dna_out4.gff |
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added:
test-data/extract_genomic_dna_out3.gff test-data/mm9.fasta test-data/mm9_input1.gff |
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removed:
test-data/1.bed test-data/cufflinks_out1.gtf test-data/droPer1.bed test-data/extract_genomic_dna_out3.interval test-data/extract_genomic_dna_out5.fasta test-data/extract_genomic_dna_out6.fasta test-data/extract_genomic_dna_out7.fasta test-data/gff_filter_by_attribute_out1.gff test-data/tophat_in1.fasta |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 extract_genomic_dna.py --- a/extract_genomic_dna.py Wed Jan 20 09:49:37 2016 -0500 +++ b/extract_genomic_dna.py Wed Mar 09 05:07:21 2016 -0500 |
| [ |
| @@ -17,6 +17,8 @@ parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file") parser.add_argument('--output_format', dest='output_format', help="Output format") +parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format") +parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter") parser.add_argument('--output', dest='output', help="Output dataset") args = parser.parse_args() @@ -158,12 +160,21 @@ c = 0 if input_is_gff: start, end = egdu.convert_bed_coords_to_gff([start, end]) - fields = [args.genome, str(chrom), str(start), str(end), strand] - meta_data = "_".join(fields) - if name.strip(): - out.write(">%s %s\n" % (meta_data, name)) + if args.fasta_header_type == "bedtools_getfasta_default": + out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom), + str(start), + str(end), + strand, + includes_strand_col)) else: - out.write(">%s\n" % meta_data) + # args.fasta_header_type == "char_delimited": + fields = [args.genome, str(chrom), str(start), str(end), strand] + field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter) + meta_data = field_delimiter.join(fields) + if name.strip(): + out.write(">%s %s\n" % (meta_data, name)) + else: + out.write(">%s\n" % meta_data) while c < l: b = min(c + 50, l) out.write("%s\n" % str(sequence[c:b])) @@ -181,7 +192,7 @@ ".", egdu.gff_attributes_to_str(feature.attributes, "GTF")]) else: - # Where is fields being set here? + # Here fields was set up around line 73. meta_data = "\t".join(fields) if input_is_gff: format_str = "%s seq \"%s\";\n" |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 extract_genomic_dna.xml --- a/extract_genomic_dna.xml Wed Jan 20 09:49:37 2016 -0500 +++ b/extract_genomic_dna.xml Wed Mar 09 05:07:21 2016 -0500 |
| [ |
| b'@@ -1,8 +1,10 @@\n-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.1">\n+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.2">\n <description>using coordinates from assembled/unassembled genomes</description>\n <requirements>\n+ <requirement type="package" version="35x1">faToTwoBit</requirement>\n <requirement type="package" version="0.7.1">bx-python</requirement>\n- <requirement type="package" version="35x1">faToTwoBit</requirement>\n+ <!-- conda dependencies -->\n+ <requirement type="package" version="324">ucsc-fatotwobit</requirement>\n </requirements>\n <command>\n <![CDATA[\n@@ -26,7 +28,13 @@\n #else:\n --reference_genome $reference_genome_cond.reference_genome\n #end if\n- --output_format $output_format\n+ --output_format $output_format_cond.output_format\n+ #if str($output_format_cond.output_format) == "fasta":\n+ --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type\n+ #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":\n+ --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter\n+ #end if\n+ #end if\n --output $output\n ]]>\n </command>\n@@ -60,71 +68,74 @@\n </param>\n </when>\n </conditional>\n- <param name="output_format" type="select" label="Select output format">\n- <option value="fasta" selected="True">fasta</option>\n- <option value="interval">interval</option>\n- </param>\n+ <conditional name="output_format_cond">\n+ <param name="output_format" type="select" label="Select output format">\n+ <option value="fasta" selected="True">fasta</option>\n+ <option value="interval">interval</option>\n+ </param>\n+ <when value="fasta">\n+ <conditional name="fasta_header_type_cond">\n+ <param name="fasta_header_type" type="select" label="Select fasta header format">\n+ <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>\n+ <option value="char_delimited">character delimited field values</option>\n+ </param>\n+ <when value="bedtools_getfasta_default"/>\n+ <when value="char_delimited">\n+ <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">\n+ <option value="underscore" selected="True">underscore (_)</option>\n+ <option value="semicolon">semicolon (;)</option>\n+ <option value="comma">comma (,)</option>\n+ <option value="tilde">tilde (~)</option>\n+ <option value="vertical_bar">vertical bar (|)</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="interval"/>\n+ </conditional>\n </inputs>\n <outputs>\n <data format_source="input" name="output" metadata_source="input">\n <change_format>\n- <when input="output_format" value="fasta" format="fasta" />\n+ <when input="output_format_cond.output_format" value="fasta" format="fasta" />\n </change_format>\n </data>\n </outputs>\n <tests>\n <test>\n- <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />\n- <param name="interpret_features" value="yes"/>\n- <param name="index_source" value="cached"/>\n- <param name="out_format" value="fasta"/>\n- <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare='..b'e="cached"/>\n- <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />\n- </test>\n- <!-- Test custom sequences support and GFF feature interpretation. -->\n- <test>\n- <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />\n- <param name="interpret_features" value="no"/>\n- <param name="index_source" value="history"/>\n- <param name="ref_file" value="tophat_in1.fasta"/>\n- <param name="out_format" value="fasta"/>\n- <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />\n+ <param name="reference_genome_source" value="history"/>\n+ <param name="reference_genome" value="mm9.fasta"/>\n+ <param name="output_format" value="interval"/>\n+ <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />\n </test>\n <test>\n- <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />\n+ <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />\n <param name="interpret_features" value="yes"/>\n- <param name="index_source" value="history"/>\n- <param name="ref_file" value="tophat_in1.fasta"/>\n- <param name="out_format" value="fasta"/>\n- <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" />\n+ <param name="reference_genome_source" value="history"/>\n+ <param name="reference_genome" value="mm9.fasta"/>\n+ <param name="output_format" value="interval"/>\n+ <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />\n </test>\n </tests>\n <help>\n@@ -145,16 +156,33 @@\n - Chromosome, start or end coordinates that are invalid for the specified build.\n - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).\n \n-.. class:: infomark\n-\n- **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools. \n-\n -----\n \n **What it does**\n \n This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.\n \n+If the output format is FASTA, the header format can be specified. Selecting the **bedtools getfasta default**\n+option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and\n+the "force strandedness" option is assumed. If the input data includes a strand column and the strand is \'+\'\n+or \'-\', it is included in the header. If the input data includes a strand column and the value is anything but\n+\'+\' or \'-\', a \'.\' is included in the header. If the input data does not include a strand column, a \'.\' is included\n+in the header.\n+\n+An example FASTA header produced by selecting this option is:\n+\n+ >chr7:127475281-127475310(+)\n+\n+Selecing the **character delimited field values** option allows selection of a character delimiter that is used\n+when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the\n+selected character. For example, selecting an underscore will produce a FASTA header like this:\n+\n+ >mm9_53_550_+ test_chromosome\n+\n+while selecting a vertical bar will produce a FASTA header like this:\n+\n+ >mm9|53|550|+ test_chromosome\n+\n If strand is not defined, the default value is "+".\n \n -----\n@@ -167,7 +195,7 @@\n chr7 127485994 127486166 NM_000230 0 +\n chr7 127486011 127486166 D49487 0 +\n \n-Extracting sequences with **FASTA** output data type returns::\n+Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::\n \n >hg17_chr7_127475281_127475310_+ NM_000230\n GTAGGAATCGCAGCGCCAGCGGTTGCAAG\n' |
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| diff -r 9af3f57e50b9 -r 702970e4a134 extract_genomic_dna_utils.py --- a/extract_genomic_dna_utils.py Wed Jan 20 09:49:37 2016 -0500 +++ b/extract_genomic_dna_utils.py Wed Mar 09 05:07:21 2016 -0500 |
| [ |
| @@ -292,6 +292,39 @@ stop_err('Error running faToTwoBit. ' + str(e)) +def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col): + """ + Return a fasta header that is the default produced by the bedtools + getfasta tool, assuming "force strandedness". This will produce a + header with this format: <chrom>:<start>-<end>(strand). If the input + data includes a strand column and the strand is '+' or '-', then use it. + If the input data includes a strand column and the value of strand is + anything but '+' or '-', set strand to '.' in the header. If the input + data does not include a strand column, set strand to '.' in the header. + """ + if includes_strand_col and strand in ['+', '-']: + strand_val = strand + else: + strand_val = '.' + return '%s:%s-%s(%s)' % (chrom, start, end, strand_val) + + +def get_fasta_header_delimiter(delimiter): + # Return a specified fasta header delimiter. + if delimiter == 'underscore': + return '_' + if delimiter == 'semicolon': + return ';' + if delimiter == 'comma': + return ',' + if delimiter == 'tilde': + return '~' + if delimiter == 'vertical_bar': + return '|' + # Set the default to underscore. + return '_' + + def get_lines(feature): # Get feature's line(s). if isinstance(feature, GFFFeature): |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/1.bed --- a/test-data/1.bed Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,65 +0,0 @@ -chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - -chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + -chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - -chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + -chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - -chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - -chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + -chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - -chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + -chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - -chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + -chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - -chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - -chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + -chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - -chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + -chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + -chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - -chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + -chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - -chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - -chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + -chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - -chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + -chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + -chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - -chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + -chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - -chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + -chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - -chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + -chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - -chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - -chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + -chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - -chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + -chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + -chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - -chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + -chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - -chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + -chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - -chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + -chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - -chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + -chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - -chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + -chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - -chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - -chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + -chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - -chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + -chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + -chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - -chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + -chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - -chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - -chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + -chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - -chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + -chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - -chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + -chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - -chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + -chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/cufflinks_out1.gtf --- a/test-data/cufflinks_out1.gtf Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; -test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; -test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; -test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/droPer1.bed --- a/test-data/droPer1.bed Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -super_1 139823 139913 AK028861 0 - 139823 139913 0 1 90, 0, -super_1 156750 156844 BC126698 0 - 156750 156844 0 1 94, 0, |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out1.fasta --- a/test-data/extract_genomic_dna_out1.fasta Wed Jan 20 09:49:37 2016 -0500 +++ b/test-data/extract_genomic_dna_out1.fasta Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -1,88 +1,20 @@ ->hg17_chr1_147962192_147962580_- -ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG -GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT -GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT -CCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGG -ACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATT -CGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGC -CTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTG -GGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA ->hg17_chr1_147984545_147984630_+ -ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTT -TGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG ->hg17_chr1_148078400_148078582_- -GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAA -GAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGA -GCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACG -GCTTCCAGTACCTCACCAACGGCATCATGTGA ->hg17_chr1_148185136_148185276_+ -ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGC -CCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATC -CGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA ->hg17_chr10_55251623_55253124_- -TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCT -CAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACT -ATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAA -ACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAA -GTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAAT -TCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAAT -ACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGC -TGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCA -AATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAA -AGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCA -ATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATA -AGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCT -CTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCA -CTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTC -ATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTG -TGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTAC -CTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAAC -ATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctcc -ttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctc -ctttttctcttttttgtcctcctccctctcctccttctatccctcttcct -cttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCC -AACAccacctcttctacctccatttccaactcctcttcctccaccacctc -cttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAG -TGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGA -GAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAA -CAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTA -GCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAA -CTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAG -TAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAAT -ATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTA -A ->hg17_chr11_116124407_116124501_- -ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGG -CAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA ->hg17_chr11_116206508_116206563_+ -ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTC -TGCCC ->hg17_chr11_116211733_116212337_- -CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGC -TGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAA -AAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGT -GAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGG -AGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTC -CAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCC -ACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGC -GCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCG -CGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCA -CGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCG -CGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAG -GTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCA -GTGA ->hg17_chr11_1812377_1812407_+ -ATGCTCCACCTGCATGGCTGGCAAACCATG ->hg17_chr12_38440094_38440321_- -GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATC -TATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATC -ACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAG -GGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCT -GACAATGATGCTTCTGATGTGGAATAA ->hg17_chr13_112381694_112381953_+ -ATGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTA -CCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGA -AGATGGACCCGGCAGGTCTGGAGGGAGGCCCCCGTGATGAATCCCGTGAT -GAGCCGCCGATCCGAGCTCAGGCTGCGTCATGGGACCAGCCACAAGGTTG -CCTGACCTATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTAC -AGCTGCCAG +>mm9~test_chromosome~53~550~+ +TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC +GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC +TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT +TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +>mm9~test_chromosome~53~250~+ +TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC +GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +>mm9~test_chromosome~351~400~+ +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +>mm9~test_chromosome~501~550~+ +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out2.fasta --- a/test-data/extract_genomic_dna_out2.fasta Wed Jan 20 09:49:37 2016 -0500 +++ b/test-data/extract_genomic_dna_out2.fasta Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -1,6 +1,17 @@ ->droPer1_super_1_139823_139913_- AK028861 -CGTCGGCTTCTGCTTCTGCTGATGATGGTCGTTCTTCTTCCTTTACTTCT -TCCTATTTTTCTTCCTTCCCTTACACTATATCTTCCTTTA ->droPer1_super_1_156750_156844_- BC126698 -CCGGGCTGCGGCAAGGGATTCACCTGCTCCAAACAGCTCAAGGTGCACTC -CCGCACGCACACGGGCGAGAAGCCCTATCACTGCGACATCTGCT +>test_chromosome:53-550(+) +TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC +GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC +TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT +TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTA +CTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTA +CGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG +ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGT +ATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTA +TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTT +CTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out3.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extract_genomic_dna_out3.gff Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; seq "TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC"; |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out3.interval --- a/test-data/extract_genomic_dna_out3.interval Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTGGACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGTGATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGTCCCTGTTCGTGAGGTCTGTCCAGTGACCCATCGTCCAGCCCTATACCGGGACCCTGTTACAGACATACCCTATGCCACTGCTCGAGCCTTCAAGATCATTCGTGAGGCTTACAAGAAGTACATTACTGCCCATGGACTGCCGCCCACTGCCTCAGCCCTGGGCCCCGGCCCGCCACCTCCTGAGCCCCTCCCTGGCTCTGGGCCCCGAGCCTTGCGCCAGAAAATTGTCATTAAATGA -chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG -chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - GTTCTCAGCTTCCTTGCTTCCATGGCTCCAGCACCATTCGAAACCTCAAAGAGAGGTTCCACATGAGCATGACTGAGGAGCAGCTGCAGCTGCTGGTGGAGCAGATGGTGGATGGCAGTATGCGGTCTATCACCACCAAACTCTATGACGGCTTCCAGTACCTCACCAACGGCATCATGTGA -chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + ATGGAAGCGTTTTTGGGGTCGCGGTCCGGACTTTGGGCGGGGGGTCCGGCCCCAGGACAGTTTTACCGCATTCCGTCCACTCCCGATTCCTTCATGGATCCGGCGTCTGCACTTTACAGAGGTCCAATCACGCGGACCCA -chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAGAGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAACATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAGATTTTGTAGACCCATTTTCACCCAAAATACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAGGCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATCTGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTGGAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTTCCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTTCAAGGCCTTGTGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTTACCTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAACATCTCTCCTTCTGCCTGtccccttccccctcctcctcctatttctcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctcttttttgtcctcctccctctcctccttctatccctcttcctcttcctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCCAACAccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCATTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCTGCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGACAGTGTGTAAAACAGACCCTCAGAGAGAACCAAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGAAAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTATGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGAACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA -chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - ATCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTTGCCTACAAATGGAGTGTTGAGGATATGTAA -chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + ATGCAGCCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC -chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTGTGACCCAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCACGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGCGACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGCCCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAGCTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTACACTAAGAAGCTCAACACCCAGTGA -chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + ATGCTCCACCTGCATGGCTGGCAAACCATG -chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATCTATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGGAAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATAA |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out4.gff --- a/test-data/extract_genomic_dna_out4.gff Wed Jan 20 09:49:37 2016 -0500 +++ b/test-data/extract_genomic_dna_out4.gff Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -1,10 +1,1 @@ -chr10 Cufflinks transcript 62044837 62045189 1000 . . gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; seq "AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACTTTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTTTTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTCTGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCGGGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTTCTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCCTCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTCGCT"; -chr10 Cufflinks transcript 75372919 75373002 1000 . . gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; seq "GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCACCAGCACCTCAGGCTGTGACGCATTCTCATGGATC"; -chr10 Cufflinks transcript 80362428 80363292 1000 - . gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; seq "ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTTGGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGGCGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCCTCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCCGGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGTGTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCCATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTACAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGCCTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGTGTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATCGAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTGAGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCTCAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTCACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGGTATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAGCATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAAGCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctgaccttaactctgaat"; -chr11 Cufflinks transcript 7904565 7904642 1000 . . gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; seq "CATCTTCTATTTGAGCCTCCATCCAGGCACCTCTGAAACAAAGGTGCACTCACTGCATGTCCACTTGTCACAGGAGCC"; -chr11 Cufflinks exon 78140156 78140259 1000 . . gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; seq "CTGCTTGCTAATTTTCTCTCTTGGGATCAGGGGGACGTGAACTCCAGCCCTGACTCGTGCTCCTTATGCTCTGAGTACATAGCAAATAAATGAGAGCAAAACAC"; -chr11 Cufflinks exon 105616462 105616737 1000 . . gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; seq "TAGGTGTAATAGTGGAAAACAATAGTTTTTAAACTTCAGAGTCCAGGGCTGTAACTCAGTAGTAACAGTGTTCTCTAAGTATGTTATTCTTCCTCTACATGCTGAAATTTTTCATATTTGGAGCATTCACTGTTCCATGTATCAGTAAATTATATTGTGAGCTGTCATCATATCTAAGCACCATATTGAATATTTTTCATGATTAAAATTTGTTGAAACAACAATTCTATGACCGAAAAAAGCAAGGCTTTGTAAATAACATGTTTGTTACTAGTA"; -chr12 Cufflinks exon 30701762 30702509 1000 . . gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; seq "TGTGGAGTGTACTTATATGATCCCTATGCTGATAGGATTACCTTCCTAGACATAGCTAGACGCAAAGCCACATGTGTAAGGCTGCTGAGCAAAGACAGCATCCCAGCATGGGTGTGTTCACGGTGGATTCACCACGTTGCATATGTAAAGTGGTCCCCTTGGCTTACCCTTCACTTTGCTCATGAGATTCAGAAGCTGGTGGTCCAGCAGGGGTGAGCATTTGTGAAATAGTAAGCTGAACTTAGTGGTGAGATTTCAGAACAGACTTCTGTGAAGTAAGAGATGTAACCATGCATCTAAAATCAGATGGCCGTGTAACTGCTCGGGCATAGAAATGGTGGGAGAACCTGTCCTGGGTACCTGGCATTTCACATGAGCCCAGGGATATGTCTTGTGCCAAGGCACACAAGTGTCCATGGACTTGGACAGGTGCCAAGGGTTTTTGTCTCTGTTCCTATGTGGGAGGCTGGCTGTGATTTACATTAATTTCTGTATTTCAAACGAAGATGTCTGCAGATCTCCATTTTGATGTTACAGCCTCATTGCCCAGGCAGTGGGCAGTGCCCAGACACCCTTTCTGACTAGCCACTGCATTGGGCTTCTGTGATTCAAAGTAGTGTATATATTTATTTACTTCTCTGACTGTGGCCAACAGCCAAATGCCATTTTATGTTCCTTGTATTCAGTCCATTACCAAAGAGGTGTTTGCACTTTGTAATGATACCTTTCAGTTCAAATAAAAGGACCA"; -chr13 Cufflinks exon 49159496 49159569 1000 . . gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; seq "ttttcttttggattacttgatttttttttatttgatcttatttatgatgattttgagtacatttttgaacagtt"; -chr13 Cufflinks transcript 100200304 100200330 1000 . . gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; seq "TCTCATATGAATAGCCACCCTCTTCTG"; -chr14 Cufflinks transcript 31949103 31949152 1000 . . gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; seq "GGATGCTATCCGCGATGTGCATGTAAAGGGCCTCATGTACCAGTGGATCG"; +test_chromosome galaxy_extract_genomic_dna interval 52 550 1000 + . frac "1.000000" ; cov "145.770185" ; conf_lo "8543307.525072" ; FPKM "10679134.4063403048" ; transcript_id "CUFF.1.1" ; gene_id "CUFF.1" ; conf_hi "12814961.287608" seq "TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC"; |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out5.fasta --- a/test-data/extract_genomic_dna_out5.fasta Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,31 +0,0 @@ ->mm9_chr10_62044837_62045189_+ -AATTACAAGATCGACACACCAAGATAGGCAGATCCATGGTTGGTTTTACT -TTGTAAATCTAAAAGTATGTTGGAAAACGATGCAATGAATTCTTATCCTT -TTTCAAAATGAAGAATTTGTGATGGTTAGTGGACAGTTCAGAAGCCTCTC -TGCAAGAAAGGGGGCGCTGAGAAGTGGTAAAAAAAGGAAGGAAGCACTCG -GGCTTTGTCAGCAGGGTGGACCCTGGGGTCCACAGTGGGAACAGTCCCTT -CTGGCCTCTACTCACTGACCAAACGCTTTACTAAAACTCCGCTTCTGGCC -TCTGTTGCCACCTCCTGGTCGCTGTCCTCGGAAGTTTCTACTTCCTCCTC -GCT ->mm9_chr10_75372919_75373002_+ -GCGTCTCGCAGCTTCTGCCCGTCGATCTCCATGTCGAGCCGGATGGGCAC -CAGCACCTCAGGCTGTGACGCATTCTCATGGATC ->mm9_chr10_80362428_80363292_- -ATGACGGACAAGTGTTTCCGGAAGTGCATCGGGAAGCCCGGGGGCTCCTT -GGATAACTCGGAGCAGGTGAGACATCTCGGGAACCCGGGGTGGTGAGGGG -CGCGGGGTCAGGAGCGTCTAGGAGGTTGAGAGATGTGCGCGTGCGCGGCC -TCTAGCCTTAGCTACTGAGGAAGTTGTGCGCGTGCGCGGGGTGAGGACCC -GGCTTCTGTGCCTAGATCGGTGCAGCCTTCATGGGTGATCCTCGGGTCGT -GTGACCGTCAGTCAGGGATCCCCCTCCACGCTTTGCAGAAATGCATCGCC -ATGTGCATGGACCGCTACATGGACGCCTGGAATACCGTGTCCCGCGCCTA -CAACTCTCGACTGCAGCGGGAACGAGCCAACATGTGACCGGGACCTGTGC -CTCGGGACACCGTGCTTATGGTCTGAACTGTTTTCCCTGCCAGTTAGGGT -GTCTCCTCCTAGCCGCCCTGAAGTCTGGCAGCATGGAGGGCTTGGGGATC -GAGGCCTCTCCCCTGGGTTGCTGCGTCCAGCTCAATCTCAGAAGAGAGTG -AGGACCCGACAGAGCACAGGGATCTGGCTGGCCCCACTGACCTGTGACCT -CAGGAGAGCAGGCCAATAAATCGCTGCTGGGGCAGTAAAGCAGGCGTGTC -ACCTCACTGCTTCAGGTCCCTTCCCCTGAGTAGGCCCAGACCTCCCAGGG -TATCTTTCCCCTTGGGGTCAGTGGGCTGCTGGCTCTCAGGGAATTCGGAG -CATGATCTCAGGTGTTTGGTCATCCCGGGGAGACCAGCCGAGGTTAAGAA -GCAAGGCTTCATGTagccttcacctatcatgcatgaggcccagggtgctg -accttaactctgaat |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out6.fasta --- a/test-data/extract_genomic_dna_out6.fasta Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ ->mm9_test_chromosome_53_550_+ -TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG -CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC -GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC -TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT -TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC ->mm9_test_chromosome_53_250_+ -TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG -CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC -GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC ->mm9_test_chromosome_351_400_+ -ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT ->mm9_test_chromosome_501_550_+ -TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/extract_genomic_dna_out7.fasta --- a/test-data/extract_genomic_dna_out7.fasta Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,17 +0,0 @@ ->mm9_test_chromosome_53_550_+ -TACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAC -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAG -CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTAC -GTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCGT -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC -TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTGT -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTT -TTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGCTA -CTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTA -CGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG -ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGT -ATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTA -TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTT -CTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/gff_filter_by_attribute_out1.gff --- a/test-data/gff_filter_by_attribute_out1.gff Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ -chr10 Cufflinks transcript 62044837 62045189 1000 . . gene_id "CUFF.23531"; transcript_id "CUFF.23531.1"; FPKM "19.5178121606"; frac "1.000000"; conf_lo "9.264456"; conf_hi "29.771168"; cov "1.108611"; -chr10 Cufflinks transcript 75372919 75373002 1000 . . gene_id "CUFF.24985"; transcript_id "CUFF.24985.1"; FPKM "124.4970510798"; frac "1.000000"; conf_lo "71.411330"; conf_hi "177.582772"; cov "7.071429"; -chr10 Cufflinks transcript 80362428 80363292 1000 - . gene_id "CUFF.26065"; transcript_id "CUFF.26065.1"; FPKM "43.6170921216"; frac "1.000000"; conf_lo "32.260169"; conf_hi "54.974016"; cov "2.477449"; -chr11 Cufflinks transcript 7904565 7904642 1000 . . gene_id "CUFF.33508"; transcript_id "CUFF.33508.1"; FPKM "61.6484988869"; frac "1.000000"; conf_lo "22.882428"; conf_hi "100.414569"; cov "3.501633"; -chr11 Cufflinks exon 78140156 78140259 1000 . . gene_id "CUFF.43148"; transcript_id "CUFF.43148.1"; exon_number "1"; FPKM "54.8483511750"; frac "1.000000"; conf_lo "23.181641"; conf_hi "86.515061"; cov "3.115385"; -chr11 Cufflinks exon 105616462 105616737 1000 . . gene_id "CUFF.48385"; transcript_id "CUFF.48385.1"; exon_number "1"; FPKM "18.9452034252"; frac "1.000000"; conf_lo "7.520816"; conf_hi "30.369591"; cov "1.076087"; -chr12 Cufflinks exon 30701762 30702509 1000 . . gene_id "CUFF.53897"; transcript_id "CUFF.53897.1"; exon_number "1"; FPKM "48.9333329111"; frac "1.000000"; conf_lo "37.780391"; conf_hi "60.086275"; cov "2.779412"; -chr13 Cufflinks exon 49159496 49159569 1000 . . gene_id "CUFF.67788"; transcript_id "CUFF.67788.1"; exon_number "1"; FPKM "44.9657653777"; frac "1.000000"; conf_lo "10.974842"; conf_hi "78.956689"; cov "2.554054"; -chr13 Cufflinks transcript 100200304 100200330 1000 . . gene_id "CUFF.73108"; transcript_id "CUFF.73108.1"; FPKM "123.2395051093"; frac "1.000000"; conf_lo "30.079196"; conf_hi "216.399814"; cov "7.000000"; -chr14 Cufflinks transcript 31949103 31949152 1000 . . gene_id "CUFF.77316"; transcript_id "CUFF.77316.1"; FPKM "85.5634278330"; frac "1.000000"; conf_lo "28.521143"; conf_hi "142.605713"; cov "4.860000"; -chr14 Cufflinks exon 67604227 67604668 1000 . . gene_id "CUFF.81446"; transcript_id "CUFF.81446.1"; exon_number "1"; FPKM "123.6776546104"; frac "1.000000"; conf_lo "100.611653"; conf_hi "146.743656"; cov "7.024887"; -chr14 Cufflinks exon 75165582 75165744 1000 . . gene_id "CUFF.82088"; transcript_id "CUFF.82088.1"; exon_number "1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; -chr16 Cufflinks transcript 57154027 57154067 1000 . . gene_id "CUFF.103364"; transcript_id "CUFF.103364.1"; FPKM "162.3154457537"; frac "1.000000"; conf_lo "75.554191"; conf_hi "249.076701"; cov "9.219512"; -chr16 Cufflinks exon 74862302 74862560 1000 . . gene_id "CUFF.105450"; transcript_id "CUFF.105450.1"; exon_number "1"; FPKM "11.0120241741"; frac "1.000000"; conf_lo "2.020744"; conf_hi "20.003304"; cov "0.625483"; -chr16 Cufflinks transcript 98168779 98168914 1000 . . gene_id "CUFF.107834"; transcript_id "CUFF.107834.1"; FPKM "24.4666664555"; frac "1.000000"; conf_lo "5.971605"; conf_hi "42.961728"; cov "1.389706"; -chr17 Cufflinks exon 8483212 8483268 1000 . . gene_id "CUFF.108498"; transcript_id "CUFF.108498.1"; exon_number "1"; FPKM "50.0370923000"; frac "1.000000"; conf_lo "9.181978"; conf_hi "90.892207"; cov "2.842105"; -chr17 Cufflinks exon 30355791 30355913 1000 . . gene_id "CUFF.111759"; transcript_id "CUFF.111759.1"; exon_number "1"; FPKM "19.3232673516"; frac "1.000000"; conf_lo "2.040012"; conf_hi "36.606523"; cov "1.097561"; -chr18 Cufflinks transcript 39571718 39571880 1000 . . gene_id "CUFF.123569"; transcript_id "CUFF.123569.1"; FPKM "20.4139057543"; frac "1.000000"; conf_lo "4.982443"; conf_hi "35.845368"; cov "1.159509"; -chr19 Cufflinks exon 17633088 17633203 1000 . . gene_id "CUFF.131333"; transcript_id "CUFF.131333.1"; exon_number "1"; FPKM "20.4893265884"; frac "1.000000"; conf_lo "2.163116"; conf_hi "38.815537"; cov "1.163793"; -chr19 Cufflinks transcript 41997624 41997859 1000 . . gene_id "CUFF.133569"; transcript_id "CUFF.133569.1"; FPKM "28.1988698132"; frac "1.000000"; conf_lo "13.125940"; conf_hi "43.271800"; cov "1.601695"; |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/mm9.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9.fasta Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/mm9_input1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_input1.gff Wed Mar 09 05:07:21 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; |
| b |
| diff -r 9af3f57e50b9 -r 702970e4a134 test-data/tophat_in1.fasta --- a/test-data/tophat_in1.fasta Wed Jan 20 09:49:37 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ ->test_chromosome -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC -AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT -ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |