# HG changeset patch # User iuc # Date 1430275591 14400 # Node ID 5b3e360ae7f7dc4b655a0fb6d4f55336f5d4f0c3 # Parent 33ded39275c3f722248f0ff9c7bf9ad737fde430 Uploaded diff -r 33ded39275c3 -r 5b3e360ae7f7 macros.xml --- a/macros.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - - - - seqtk - - - - 1.0-r75-dirty - - - - - - - - - - - - - - - - - `_, developed by Heng Li at the Broad Institute - ]]> - - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_comp.xml --- a/seqtk_comp.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - - - get the nucleotide composition of FASTA/Q - - macros.xml - - - - $default]]> - - - - - - - - - - - - - test0 - ACTGACTGAA - >ambig_ref - ACGTCGTGTTVHDBN - -The seqtk tool will report: - -:: - - #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts - test0 11 4 2 2 2 0 0 1 0 0 0 0 - ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 - - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_cutN.xml --- a/seqtk_cutN.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - - - cut sequence at long N - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - test - AACTGATCGATCGATCGNNNNNNNNNNNACATG - -This will be split into the component sequences without the ambiguity. - -:: - - >test:1-17 - AACTGATCGATCGATCG - >test:29-33 - ACATG - - -@ATTRIBUTION@ - ]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_dropse.xml --- a/seqtk_dropse.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ - - - drop unpaired from interleaved Paired End FASTA/Q - - macros.xml - - - - $default]]> - - - - - - - - - - - - >F - @test-6/2 - TGCGAAGACC - + - >2?A?A@@7? - @test-4/1 - CTTGACGCTG - + - I@>3EFCG@C - @test-2/1 - AGACCAAAAT - + - ??><6E?IFC - @test-2/2 - CTGGCGAATT - + - ?=?*?A?>F - @test-6/2 - TGCGAAGACC - + - >2?A?A@@7? - @test-2/1 - AGACCAAAAT - + - ??><6E?IFC - @test-2/2 - CTGGCGAATT - + - ?=?*?A? - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_fqchk.xml --- a/seqtk_fqchk.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ - - - fastq QC (base/quality summary) - - macros.xml - - - - $default]]> - - - - - - - - - - - - - >>>>>CCCCCCC65 - -each based is examined individually and information reported: - -:: - - #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values - #POS #bases %A %C %G %T %N avgQ errQ %low %high - #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3 - 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0 - 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 - 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0 - 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 - 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0 - 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 - 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 - 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 - 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0 - 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_hety.xml --- a/seqtk_hety.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ - - - regional heterozygosity - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - het_region - ACTTTACATCGAGCMMMMMMMACAGTACTG - -As can be seen in the following output: - -:: - - #chr start end A B num_het - het_region 0 8 0.00 8 0 - het_region 8 9 0.00 8 0 - het_region 9 10 0.00 8 0 - het_region 10 11 0.00 8 0 - het_region 11 12 0.00 8 0 - het_region 12 13 0.00 8 0 - het_region 13 14 0.00 8 0 - het_region 14 15 1.00 8 1 - het_region 15 16 2.00 8 2 - het_region 16 17 3.00 8 3 - het_region 17 18 4.00 8 4 - het_region 18 19 5.00 8 5 - het_region 19 20 6.00 8 6 - het_region 20 21 7.00 8 7 - het_region 21 22 7.00 8 7 - het_region 22 23 6.00 8 6 - het_region 23 24 5.00 8 5 - het_region 24 25 4.00 8 4 - het_region 25 26 3.00 8 3 - het_region 26 27 2.00 8 2 - het_region 27 28 1.00 8 1 - het_region 28 29 0.00 8 0 - het_region 29 30 0.00 1 0 - -If you know what A and B are measures of, please `submit an issue `__ and it will be corrected - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_listhet.xml --- a/seqtk_listhet.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - - - extract the position of each het - - macros.xml - - - - $default]]> - - - - - - - - - - - - ambig - ACGTMRWSYKVHDBN - -The seqtk suite recognises MRWSYK: - -:: - - #chr position base - ambig 5 M - ambig 6 R - ambig 7 W - ambig 8 S - ambig 9 Y - ambig 10 K - - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_mergefa.xml --- a/seqtk_mergefa.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ - - - merge two FASTA/Q files - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - - - - - - - - - - test0 - ACTGACTGAAA - - # seq2.fa - >test0 - ACTGAMTGCGN - -In the following the `-m` option has been set to highlight seqtk-mergefa's features. - -:: - - >test0 - ACTGACTGxxa - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_mergepe.xml --- a/seqtk_mergepe.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ - - - interleave two unpaired FASTA/Q files for a paired-end file - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - >F - - # r2.fq - @test-6/2 - TGCGAAGACC - + - >2?A?A@@7? - -will produce the following paired file: - -:: - - @test-6/1 - AGCTTGACGC - + - ?.HCF@C>>F - @test-6/2 - TGCGAAGACC - + - >2?A?A@@7? - -While this may not have been an illuminating example, it is important to note -that this tool will properly interleave data. For example if you have the ids: - -:: - - @r-1/1 - @r-2/1 - @r-3/1 - @r-4/1 - -and - -:: - - @r-1/2 - @r-2/2 - @r-3/2 - @r-4/2 - -These will be interleaved as - -:: - - @r-1/1 - @r-1/2 - @r-2/1 - @r-2/2 - @r-3/1 - @r-3/2 - @r-4/1 - @r-4/2 - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_mutfa.xml --- a/seqtk_mutfa.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ - - - point mutate FASTA at specified positions - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - test0 - ACTGACTGAA - - # Input SNP file - test0 1 . G - test0 4 . A - -This will effect the desired mutations in the output file - -:: - - # Output result - >test0 - GCTAACTGAA - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_randbase.xml --- a/seqtk_randbase.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ - - - choose a random base from hets - - macros.xml - - - - $default]]> - - - - - - - - - - - - ambig - ACGTMRWSYK - -results in - -:: - - # Output result - >ambig - ACGTCGTGTT - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_sample.xml --- a/seqtk_sample.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - random subsample of fasta or fastq sequences - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - `__. - -The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset. - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_seq.xml --- a/seqtk_seq.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ - - - common transformation of FASTA/Q - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_subseq.xml --- a/seqtk_subseq.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ - - - extract subsequences from FASTA/Q files - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - seq1 - ACGTMRWSYK - >seq2 - RWSYKACGTM - -results in - -:: - - # Output result - >seq1 - ACGTMRWSYK - -@ATTRIBUTION@ -]]> - diff -r 33ded39275c3 -r 5b3e360ae7f7 seqtk_trimfq.xml --- a/seqtk_trimfq.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ - - - trim FASTQ using the Phred algorithm - - macros.xml - - - - $default]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/paired_dat.fq --- a/test-data/paired_dat.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -@test-6/1 -AGCTTGACGC -+ -?.HCF@C>>F -@test-6/2 -TGCGAAGACC -+ ->2?A?A@@7? -@test-4/1 -CTTGACGCTG -+ -I@>3EFCG@C -@test-4/2 -TGCGAAGACC -+ -A?A@@B@<6E?IFC -@test-2/2 -CTGGCGAATT -+ -?=?*?A?>F -@test-4/1 -CTTGACGCTG -+ -I@>3EFCG@C -@test-2/1 -AGACCAAAAT -+ -??><6E?IFC diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/paired_dat2.fq --- a/test-data/paired_dat2.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -@test-6/2 -TGCGAAGACC -+ ->2?A?A@@7? -@test-4/2 -TGCGAAGACC -+ -A?A@@B@test0 -ACTGACTGAA ->ambig_ref -ACGTCGTGTTVHDBN - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_comp.out --- a/test-data/seqtk_comp.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -#chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts -test0 10 4 2 2 2 0 0 0 0 0 0 0 -ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_cutn.fa --- a/test-data/seqtk_cutn.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->test -AACTGATCGATCGATCGNNNNNNNNNNNACATG - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_cutn.out --- a/test-data/seqtk_cutn.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->test:1-17 -AACTGATCGATCGATCG ->test:29-33 -ACATG diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_dropse.fq --- a/test-data/seqtk_dropse.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -@test-6/1 -AGCTTGACGC -+ -?.HCF@C>>F -@test-6/2 -TGCGAAGACC -+ ->2?A?A@@7? -@test-4/2 -TGCGAAGACC -+ -A?A@@B@<6E?IFC -@test-2/2 -CTGGCGAATT -+ -?=?*?A?>F -@test-6/2 -TGCGAAGACC -+ ->2?A?A@@7? -@test-2/1 -AGACCAAAAT -+ -??><6E?IFC -@test-2/2 -CTGGCGAATT -+ -?=?*?A?>>>>>CCCCCCC65 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_fqchk.out --- a/test-data/seqtk_fqchk.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -#min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values -#POS #bases %A %C %G %T %N avgQ errQ %low %high -#ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3 -1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0 -2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 -3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0 -4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 -5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0 -6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 -7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 -8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 -9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0 -10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 -11 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 -12 1 0.0 100.0 0.0 0.0 0.0 10.0 10.0 100.0 0.0 -13 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0 -14 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0 -15 1 100.0 0.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0 -16 1 0.0 0.0 100.0 0.0 0.0 4.0 4.0 100.0 0.0 -17 1 0.0 100.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0 -18 1 100.0 0.0 0.0 0.0 0.0 10.0 10.0 100.0 0.0 -19 1 0.0 0.0 100.0 0.0 0.0 10.0 10.0 100.0 0.0 -20 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0 -21 1 100.0 0.0 0.0 0.0 0.0 7.0 7.0 100.0 0.0 -22 1 0.0 0.0 0.0 100.0 0.0 4.0 4.0 100.0 0.0 -23 1 0.0 100.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0 -24 1 0.0 0.0 100.0 0.0 0.0 4.0 4.0 100.0 0.0 -25 1 100.0 0.0 0.0 0.0 0.0 4.0 4.0 100.0 0.0 -26 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0 -27 1 0.0 100.0 0.0 0.0 0.0 13.0 13.0 100.0 0.0 -28 1 100.0 0.0 0.0 0.0 0.0 16.0 16.0 100.0 0.0 -29 1 100.0 0.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0 -30 1 100.0 0.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0 -31 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 -32 1 100.0 0.0 0.0 0.0 0.0 12.0 12.0 100.0 0.0 -33 1 0.0 0.0 100.0 0.0 0.0 10.0 10.0 100.0 0.0 -34 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 -35 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 -36 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 -37 1 100.0 0.0 0.0 0.0 0.0 8.0 8.0 100.0 0.0 -38 1 0.0 0.0 0.0 100.0 0.0 8.0 8.0 100.0 0.0 -39 1 0.0 100.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0 -40 1 0.0 100.0 0.0 0.0 0.0 9.0 9.0 100.0 0.0 -41 1 100.0 0.0 0.0 0.0 0.0 20.0 20.0 0.0 100.0 -42 1 0.0 0.0 0.0 100.0 0.0 20.0 20.0 0.0 100.0 -43 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0 -44 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0 -45 1 0.0 0.0 100.0 0.0 0.0 37.0 37.0 0.0 100.0 -46 1 0.0 0.0 0.0 100.0 0.0 29.0 29.0 0.0 100.0 -47 1 0.0 0.0 0.0 100.0 0.0 29.0 29.0 0.0 100.0 -48 1 0.0 100.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0 -49 1 100.0 0.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0 -50 1 100.0 0.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0 -51 1 0.0 100.0 0.0 0.0 0.0 29.0 29.0 0.0 100.0 -52 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0 -53 1 0.0 100.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0 -54 1 100.0 0.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0 -55 1 0.0 100.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0 -56 1 100.0 0.0 0.0 0.0 0.0 34.0 34.0 0.0 100.0 -57 1 0.0 0.0 100.0 0.0 0.0 34.0 34.0 0.0 100.0 -58 1 0.0 0.0 0.0 100.0 0.0 34.0 34.0 0.0 100.0 -59 1 0.0 0.0 0.0 100.0 0.0 21.0 21.0 0.0 100.0 -60 1 0.0 0.0 0.0 100.0 0.0 20.0 20.0 0.0 100.0 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_hety.fa --- a/test-data/seqtk_hety.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->het_region -ACTTTACATCGAGCMMMMMMMACAGTACTG - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_hety.out --- a/test-data/seqtk_hety.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -#chr start end A B num_het -het_region 0 8 0.00 8 0 -het_region 8 9 0.00 8 0 -het_region 9 10 0.00 8 0 -het_region 10 11 0.00 8 0 -het_region 11 12 0.00 8 0 -het_region 12 13 0.00 8 0 -het_region 13 14 0.00 8 0 -het_region 14 15 1.00 8 1 -het_region 15 16 2.00 8 2 -het_region 16 17 3.00 8 3 -het_region 17 18 4.00 8 4 -het_region 18 19 5.00 8 5 -het_region 19 20 6.00 8 6 -het_region 20 21 7.00 8 7 -het_region 21 22 7.00 8 7 -het_region 22 23 6.00 8 6 -het_region 23 24 5.00 8 5 -het_region 24 25 4.00 8 4 -het_region 25 26 3.00 8 3 -het_region 26 27 2.00 8 2 -het_region 27 28 1.00 8 1 -het_region 28 29 0.00 8 0 -het_region 29 30 0.00 1 0 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_listhet.fa --- a/test-data/seqtk_listhet.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->ambig -ACGTMRWSYKVHDBN - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_listhet.out --- a/test-data/seqtk_listhet.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -#chr position base -ambig 5 M -ambig 6 R -ambig 7 W -ambig 8 S -ambig 9 Y -ambig 10 K diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mergefa.out --- a/test-data/seqtk_mergefa.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -ACTGAMTGMRN diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mergefa1.fa --- a/test-data/seqtk_mergefa1.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -ACTGACTGAAA diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mergefa2.fa --- a/test-data/seqtk_mergefa2.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -ACTGAMTGCGN diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mergefa2.out --- a/test-data/seqtk_mergefa2.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -ACTGACTGxxa diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mutfa.fa --- a/test-data/seqtk_mutfa.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -ACTGACTGAA diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mutfa.out --- a/test-data/seqtk_mutfa.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test0 -GCTAACTGAA diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_mutfa.snp --- a/test-data/seqtk_mutfa.snp Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -test0 1 . G -test0 4 . A diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_randbase.fa --- a/test-data/seqtk_randbase.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->ambig -ACGTMRWSYK diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_randbase.out --- a/test-data/seqtk_randbase.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->ambig -ACGTCGTGTT diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_sample.fa --- a/test-data/seqtk_sample.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ ->seq0 -AAAAAAAAAA -AAAAAAAAAA ->seq1 -TTTTTTTTTT -TTTTTTTTTT ->seq2 -CCCCCCCCCC -CCCCCCCCCC ->seq3 -GGGGGGGGGG -GGGGGGGGGG ->seq4 -AAAAAAAAAA -TTTTTTTTTT ->seq5 -AAAAAAAAAA -CCCCCCCCCC ->seq6 -AAAAAAAAAA -GGGGGGGGGG ->seq7 -TTTTTTTTTT -CCCCCCCCCC ->seq8 -TTTTTTTTTT -GGGGGGGGGG diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_sample.out --- a/test-data/seqtk_sample.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->seq7 -TTTTTTTTTTCCCCCCCCCC ->seq1 -TTTTTTTTTTTTTTTTTTTT ->seq4 -AAAAAAAAAATTTTTTTTTT ->seq3 -GGGGGGGGGGGGGGGGGGGG diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_seq.fa --- a/test-data/seqtk_seq.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->test -AACTGATCGATCGATCGNNNNNNNNNNNACATG - diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_seq_revcom.fa --- a/test-data/seqtk_seq_revcom.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test -CATGTNNNNNNNNNNNCGATCGATCGATCAGTT diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_subseq.fa --- a/test-data/seqtk_subseq.fa Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->seq1 -ACGTMRWSYK ->seq2 -RWSYKACGTM diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_subseq.out --- a/test-data/seqtk_subseq.out Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->seq1 -ACGTMRWSYK diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_subseq_list.txt --- a/test-data/seqtk_subseq_list.txt Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -seq1 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_trimfq.fq --- a/test-data/seqtk_trimfq.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@SEQ_ID1 -GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT -+ -!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_trimfq_be.fq --- a/test-data/seqtk_trimfq_be.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@SEQ_ID1 -GGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCAC -+ -(((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCC diff -r 33ded39275c3 -r 5b3e360ae7f7 test-data/seqtk_trimfq_default.fq --- a/test-data/seqtk_trimfq_default.fq Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@SEQ_ID1 -TAGTAAATCCATTTGTTCAACTCACAGTTT -+ -*-+*''))**55CCF>>>>>>CCCCCCC65 diff -r 33ded39275c3 -r 5b3e360ae7f7 tool_dependencies.xml --- a/tool_dependencies.xml Wed Feb 18 10:52:53 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - - diff -r 33ded39275c3 -r 5b3e360ae7f7 tool_test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.json Tue Apr 28 22:46:31 2015 -0400 @@ -0,0 +1,1 @@ +{"tests": [{"data": {"status": "success", "inputs": {"in_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "job": {"inputs": {"in_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-02-18T11:43:38.160465", "tool_id": "seqtk_comp", "outputs": {"default": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "seqtk comp /tmp/tmpjaBvNBfiles/000/dataset_1.dat | awk 'BEGIN{print 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/tmp/tmpjaBvNBfiles/000/dataset_27.dat 4 > /tmp/tmpjaBvNBfiles/000/dataset_28.dat", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T11:47:24.088424", "params": {"s": "\"4\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "subsample_size": "\"4\"", "dbkey": "\"hg17\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "1679", "id": "adba32ec9811aba7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_seqtk_sample.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"r": "True", "M": "", "in_file": {"src": "hda", "id": "073082a17e1b2f0b"}, "n": ""}, "job": {"inputs": {"in_file": {"src": "hda", "id": "073082a17e1b2f0b"}}, "update_time": "2015-02-18T11:47:47.706460", "tool_id": "seqtk_seq", "outputs": {"default": {"src": "hda", "id": "a908e285532ac9b0"}}, "stdout": "", "command_line": "seqtk seq -q 0 -X 255 -l 0 -Q 33 -s 11 -f 1.0 -L 0 -r 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