Skip to content

Commit

Permalink
fix test
Browse files Browse the repository at this point in the history
  • Loading branch information
@bgruening
bgruening committed Aug 27, 2024
1 parent e5089a1 commit c04516d
Show file tree
Hide file tree
Showing 5 changed files with 225 additions and 30 deletions.
13 changes: 6 additions & 7 deletions tools/rgrnastar/rg_rnaStar.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -572,23 +572,23 @@ with Cufflinks if your sequences come from an unstranded library preparation.">
</data>
<expand macro="outWigOutputs"/>
</outputs>

<tests>
<test expect_num_outputs="3">
<conditional name="singlePaired">
<param name="sPaired" value="single" />
<param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
<param name="sPaired" value="paired" />
<param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
<param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
</conditional>
<conditional name="refGenomeSource">
<param name="geneSource" value="history" />
<param name="genomeFastaFiles" value="tophat_test.fa.gz" />
<param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
<param name="genomeSAindexNbases" value="5" />
</conditional>
<section name="oformat">
<param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
<conditional name="wasp_conditional">
<param name="waspOutputMode" value="wasp_mode"/>
<param name="varVCFfile" value="rnastar_test_mapped_reads.vcf" ftype="vcf" />
<param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
</conditional>
</section>
<section name="algo">
Expand All @@ -597,8 +597,7 @@ with Cufflinks if your sequences come from an unstranded library preparation.">
</conditional>
</section>
<output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
<output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
<output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
<output name="splice_junctions" file="rnastar_test_splicejunctions_wasp.bed"/>
</test>
<!-- test with cached genome index -->
<test expect_num_outputs="3">
Expand Down
4 changes: 2 additions & 2 deletions tools/rgrnastar/rg_rnaStarSolo.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -523,7 +523,7 @@
<param name="quantModeGene" value="true" />
<conditional name="wasp_conditional">
<param name="waspOutputMode" value="wasp_mode"/>
<param name="varVCFfile" value="rnastar_test_varVCFfile.vcf.vcf" ftype="vcf" />
<param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
</conditional>
</section>
<output name="output_barcodes" >
Expand Down Expand Up @@ -554,7 +554,7 @@
<has_line_matching expression="\s+yesUMIs\s+8" />
</assert_contents>
</output>
<output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
<output name="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/>
<output name="reads_per_gene" >
<assert_contents>
<has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
Expand Down
Binary file added tools/rgrnastar/test-data/filtered4.bam
View file
Binary file not shown.
45 changes: 24 additions & 21 deletions tools/rgrnastar/test-data/rnastar_test.log
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,32 +3,35 @@
Finished on | .*
Mapping speed, Million of reads per hour | .*

Number of input reads | 100
Average input read length | 75
Number of input reads | 15447
Average input read length | 119
UNIQUE READS:
Uniquely mapped reads number | 99
Uniquely mapped reads % | 99.00%
Average mapped length | 74.65
Number of splices: Total | 52
Uniquely mapped reads number | 150
Uniquely mapped reads % | 0.97%
Average mapped length | 105.11
Number of splices: Total | 131
Number of splices: Annotated (sjdb) | 0
Number of splices: GT/AG | 52
Number of splices: GC/AG | 0
Number of splices: AT/AC | 0
Number of splices: Non-canonical | 0
Mismatch rate per base, % | 2.00%
Deletion rate per base | 0.00%
Deletion average length | 0.00
Insertion rate per base | 0.00%
Insertion average length | 0.00
Number of splices: GT/AG | 100
Number of splices: GC/AG | 6
Number of splices: AT/AC | 1
Number of splices: Non-canonical | 24
Mismatch rate per base, % | 6.68%
Deletion rate per base | 0.04%
Deletion average length | 1.17
Insertion rate per base | 0.04%
Insertion average length | 1.50
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 1
% of reads mapped to multiple loci | 1.00%
Number of reads mapped to too many loci | 0
% of reads mapped to too many loci | 0.00%
Number of reads mapped to multiple loci | 451
% of reads mapped to multiple loci | 2.92%
Number of reads mapped to too many loci | 58
% of reads mapped to too many loci | 0.38%
UNMAPPED READS:
Number of reads unmapped: too many mismatches | 0
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 0.00%
% of reads unmapped: other | 0.00%
Number of reads unmapped: too short | 7912
% of reads unmapped: too short | 51.22%
Number of reads unmapped: other | 6876
% of reads unmapped: other | 44.51%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
193 changes: 193 additions & 0 deletions tools/rgrnastar/test-data/rnastar_test_splicejunctions_wasp.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,193 @@
21 13873 52149 1 1 0 0 1 12
21 13882 20712 2 2 0 0 3 28
21 13882 29808 2 2 0 0 1 28
21 13882 35980 2 2 0 0 1 26
21 13882 50180 2 2 0 0 1 19
21 13887 27728 1 1 0 0 1 21
21 13887 35985 1 1 0 0 1 15
21 13887 51866 1 1 0 0 4 40
21 13887 62408 1 1 0 0 2 24
21 13887 88031 1 1 0 0 2 40
21 13887 152470 1 1 0 2 2 40
21 13894 50193 1 1 0 0 1 24
21 13907 27883 2 2 0 0 2 45
21 13976 19932 2 2 0 0 4 41
21 13976 88119 2 2 0 0 2 33
21 13976 108267 2 2 0 0 2 33
21 13991 30873 2 2 0 0 1 18
21 13991 52131 2 2 0 0 1 18
21 15394 46773 1 1 0 0 1 39
21 18885 50205 2 4 0 0 1 35
21 18949 28120 1 1 0 0 1 26
21 18953 27816 2 2 0 0 1 16
21 18953 37719 2 2 0 1 0 34
21 19001 46120 2 2 0 0 1 17
21 19001 52299 2 2 0 0 1 17
21 19001 63039 2 2 0 0 1 17
21 19533 60698 2 2 0 1 0 44
21 19658 51267 1 1 0 0 1 45
21 19737 28120 1 1 0 0 1 16
21 19826 51848 1 1 0 1 1 36
21 19830 37617 1 1 0 0 2 12
21 19842 20715 1 1 0 0 1 23
21 19842 51866 1 1 0 1 0 22
21 19842 62903 1 1 0 0 1 18
21 19842 88031 1 1 0 0 2 37
21 20671 27816 2 2 0 0 1 20
21 20671 52116 2 2 0 0 2 25
21 20671 62856 2 2 0 0 3 23
21 20704 30891 1 1 0 0 3 38
21 20704 37617 1 1 0 0 2 12
21 20704 52149 1 1 0 0 5 22
21 20704 120492 1 1 0 0 2 38
21 20765 51916 2 2 0 0 1 14
21 20819 30873 2 2 0 0 1 18
21 20819 52131 2 2 0 0 1 18
21 25471 61751 2 2 0 0 1 12
21 26064 51210 2 2 0 0 1 13
21 27406 35153 1 1 0 0 1 28
21 27406 51199 1 1 0 1 0 26
21 27494 38948 2 2 0 0 1 33
21 27494 46813 2 2 0 1 1 44
21 27494 75795 2 2 0 0 1 39
21 27684 52116 2 2 0 0 1 16
21 27713 51848 1 1 0 0 1 40
21 27846 29795 1 1 0 1 0 16
21 27859 29808 2 2 0 0 1 20
21 27864 35985 1 1 0 0 1 24
21 27864 45984 1 1 0 0 1 24
21 27864 51866 1 1 0 1 1 32
21 27864 62408 1 1 0 0 2 41
21 27864 74425 1 1 0 0 1 24
21 27864 88031 1 1 0 1 1 36
21 27935 30198 1 1 0 0 1 33
21 27935 62479 1 1 0 0 1 27
21 27951 88119 2 2 0 0 2 31
21 28186 46133 1 1 0 0 2 18
21 28186 63052 1 1 0 1 1 25
21 29614 31023 1 1 0 0 1 12
21 29614 63020 1 1 0 0 2 24
21 29901 37719 2 2 0 1 6 28
21 29901 88119 2 2 0 0 5 36
21 29901 91677 2 2 0 0 3 24
21 29901 108267 2 2 0 0 5 36
21 29916 30873 2 2 0 0 1 18
21 29916 52131 2 2 0 0 1 18
21 29949 52299 2 2 0 0 2 18
21 30122 62898 2 2 0 0 1 19
21 30127 37629 1 1 0 0 1 24
21 30127 51866 1 1 0 0 2 15
21 30127 88031 1 1 0 1 4 28
21 30901 62898 2 2 0 0 1 31
21 30906 51866 1 1 0 0 1 36
21 30906 62408 1 1 0 0 1 14
21 35204 75757 1 1 0 1 0 43
21 35246 51292 1 1 0 0 1 33
21 35288 38995 1 1 0 0 1 22
21 35986 45984 1 1 0 0 2 17
21 35986 88031 1 1 0 0 3 32
21 35994 50193 1 1 0 0 2 25
21 35994 51874 1 1 0 0 3 24
21 35994 74433 1 1 0 0 2 23
21 36035 51916 2 2 0 0 1 14
21 36066 37411 1 1 0 0 1 37
21 36074 46072 2 4 0 0 1 33
21 37630 51866 1 1 0 0 1 37
21 37630 62903 1 1 0 0 3 12
21 37630 81353 1 1 0 0 1 44
21 37679 51916 2 2 0 0 1 14
21 38899 46764 1 1 0 0 1 20
21 38954 51292 1 1 0 0 1 43
21 38981 75826 1 1 0 0 1 34
21 38996 60894 1 1 0 0 1 22
21 45985 88031 1 1 0 0 1 38
21 46057 62479 1 1 0 0 1 14
21 46065 143522 1 1 0 0 2 45
21 46069 88115 1 1 0 1 2 41
21 46073 88119 2 2 0 0 1 29
21 46814 70282 2 2 0 0 1 32
21 46870 51210 2 2 0 1 0 21
21 50168 62885 1 1 0 0 1 18
21 50168 81335 1 1 0 0 1 34
21 50244 137072 2 2 0 0 2 35
21 50274 88119 2 2 0 0 1 39
21 50274 91677 2 2 0 0 1 13
21 50658 51848 1 1 0 1 0 42
21 51216 75722 2 2 0 0 2 21
21 51280 56626 2 2 0 0 1 19
21 51288 75795 2 2 0 0 1 22
21 51288 149429 2 2 0 0 2 41
21 51293 60852 1 1 0 1 1 29
21 51293 117556 1 1 0 0 2 44
21 51302 60411 2 2 0 0 1 33
21 51302 60861 2 2 0 0 2 42
21 51320 75826 1 1 0 0 1 34
21 51849 62390 1 1 0 0 1 37
21 51849 62885 1 1 0 1 0 18
21 51853 52149 1 1 0 0 1 12
21 51899 52192 1 1 0 0 1 22
21 51899 120538 1 1 0 1 4 32
21 51955 206521 2 2 0 1 2 27
21 52117 62856 2 2 0 0 3 18
21 52162 62903 1 1 0 1 0 14
21 52162 81353 1 1 0 0 1 44
21 52162 88031 1 1 0 1 5 44
21 52162 98665 1 1 0 0 1 36
21 52162 152470 1 1 0 0 3 44
21 52162 289491 1 1 0 1 10 36
21 52182 62923 2 4 0 0 1 13
21 52252 62856 2 2 0 1 0 21
21 52252 88119 2 2 0 0 1 30
21 52329 63068 1 1 0 0 1 28
21 57410 60698 2 2 0 0 1 29
21 57410 75645 2 2 0 0 2 38
21 57475 60763 2 2 0 0 1 36
21 60286 60730 2 4 0 1 0 40
21 60390 60840 2 2 0 0 1 24
21 60699 75645 2 2 0 0 2 27
21 62480 98737 1 1 0 0 2 12
21 62496 108267 2 2 0 0 1 43
21 62544 63039 2 2 0 0 2 40
21 62557 63052 1 1 0 0 1 15
21 62890 120492 1 1 0 0 2 42
21 62899 81348 2 2 0 0 1 24
21 62899 108178 2 2 0 0 2 20
21 62904 88031 1 1 0 1 4 44
21 62936 120538 1 1 0 0 4 38
21 62976 80498 1 1 0 1 0 24
21 62976 137268 1 1 0 0 2 33
21 63053 81502 1 1 0 0 1 32
21 63053 88180 1 1 0 0 1 43
21 70140 75651 2 2 0 0 1 31
21 70283 75795 2 2 0 0 1 15
21 70283 149429 2 2 0 2 1 45
21 74506 143522 1 1 0 0 3 45
21 74510 88115 1 1 0 0 2 35
21 75799 117556 1 1 0 1 0 37
21 75818 117576 2 2 0 0 1 15
21 76355 87984 2 2 0 0 1 16
21 76378 91540 1 1 0 0 1 24
21 81349 115881 2 2 0 0 1 37
21 81354 115886 1 1 0 0 1 33
21 81438 88115 1 1 0 0 1 36
21 88064 120538 1 1 0 1 5 32
21 88120 91677 2 2 0 0 1 26
21 91565 115886 1 1 0 0 2 33
21 91597 120538 1 1 0 0 1 25
21 98666 143455 1 1 0 1 0 18
21 98750 138516 1 1 0 0 1 14
21 108179 115881 2 2 0 0 1 38
21 108223 152509 2 2 0 0 1 25
21 112412 138384 2 2 0 0 1 16
21 115887 152470 1 1 0 0 1 22
21 115919 120538 1 1 0 0 7 43
21 126053 137131 1 1 0 0 1 26
21 131927 138384 2 2 0 0 1 21
21 136828 136968 2 2 0 0 2 26
21 137014 289491 1 1 0 0 6 25
21 137087 137268 1 1 0 0 1 14
21 137346 138586 1 1 0 0 1 19
21 138427 152465 2 2 0 1 6 40
21 138432 152470 1 1 0 0 2 31
21 138513 143522 1 1 0 0 2 45
21 682607 689282 2 2 0 1 0 36

0 comments on commit c04516d

Please sign in to comment.