From 45d8f994932171f95201decf1e74f9ad1dac5a05 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 1 Feb 2011 13:27:02 +0000 Subject: [PATCH] added kmer_freq biopiece and tests git-svn-id: http://biopieces.googlecode.com/svn/trunk@1243 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/kmer_freq | 65 +++ bp_test/in/kmer_freq.in | 6 + bp_test/out/kmer_freq.out.1 | 518 +++++++++++++++++++++++ bp_test/out/kmer_freq.out.2 | 38 ++ bp_test/out/kmer_freq.out.3 | 38 ++ bp_test/out/kmer_freq.out.4 | 806 ++++++++++++++++++++++++++++++++++++ bp_test/test/test_kmer_freq | 19 + 7 files changed, 1490 insertions(+) create mode 100755 bp_bin/kmer_freq create mode 100644 bp_test/in/kmer_freq.in create mode 100644 bp_test/out/kmer_freq.out.1 create mode 100644 bp_test/out/kmer_freq.out.2 create mode 100644 bp_test/out/kmer_freq.out.3 create mode 100644 bp_test/out/kmer_freq.out.4 create mode 100755 bp_test/test/test_kmer_freq diff --git a/bp_bin/kmer_freq b/bp_bin/kmer_freq new file mode 100755 index 0000000..733eed3 --- /dev/null +++ b/bp_bin/kmer_freq @@ -0,0 +1,65 @@ +#!/usr/bin/env ruby + +# Copyright (C) 2007-2011 Martin A. Hansen. + +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# http://www.gnu.org/copyleft/gpl.html + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# This program is part of the Biopieces framework (www.biopieces.org). + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Determine the frequencies for k-mers in sequences in the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +require 'biopieces' +require 'seq' +require 'pp' + +casts = [] +casts << {:long=>'size', :short=>'s', :type=>'uint', :mandatory=>false, :default=>4, :allowed=>nil, :disallowed=>'0'} +casts << {:long=>'type', :short=>'t', :type=>'string', :mandatory=>false, :default=>"dna", :allowed=>"dna,rna,protein", :disallowed=>nil} + +bp = Biopieces.new + +options = bp.parse(ARGV, casts) + +oligos = Seq.generate_oligos(options[:size], options[:type]) + +bp.each_record do |record| + if record.has_key? :SEQ + kmers = {} + oligos.each { |oligo| kmers[oligo.upcase] = 0 } + + (0 ... record[:SEQ].length - options[:size]).each do |i| + kmer = record[:SEQ][i .. i + options[:size] - 1].upcase + kmers[kmer] += 1 if kmers[kmer] + end + + record.merge! kmers + end + + bp.puts record +end + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ diff --git a/bp_test/in/kmer_freq.in b/bp_test/in/kmer_freq.in new file mode 100644 index 0000000..32f2412 --- /dev/null +++ b/bp_test/in/kmer_freq.in @@ -0,0 +1,6 @@ +DUMMY: nothing +--- +SEQ: atcgatcgatcg +--- +SEQ: atcgatcgatcgATCGATCGATCG +--- diff --git a/bp_test/out/kmer_freq.out.1 b/bp_test/out/kmer_freq.out.1 new file mode 100644 index 0000000..cbb552a --- /dev/null +++ b/bp_test/out/kmer_freq.out.1 @@ -0,0 +1,518 @@ +DUMMY: nothing +--- +SEQ: atcgatcgatcg +AAAA: 0 +AAAT: 0 +AAAC: 0 +AAAG: 0 +AATA: 0 +AATT: 0 +AATC: 0 +AATG: 0 +AACA: 0 +AACT: 0 +AACC: 0 +AACG: 0 +AAGA: 0 +AAGT: 0 +AAGC: 0 +AAGG: 0 +ATAA: 0 +ATAT: 0 +ATAC: 0 +ATAG: 0 +ATTA: 0 +ATTT: 0 +ATTC: 0 +ATTG: 0 +ATCA: 0 +ATCT: 0 +ATCC: 0 +ATCG: 2 +ATGA: 0 +ATGT: 0 +ATGC: 0 +ATGG: 0 +ACAA: 0 +ACAT: 0 +ACAC: 0 +ACAG: 0 +ACTA: 0 +ACTT: 0 +ACTC: 0 +ACTG: 0 +ACCA: 0 +ACCT: 0 +ACCC: 0 +ACCG: 0 +ACGA: 0 +ACGT: 0 +ACGC: 0 +ACGG: 0 +AGAA: 0 +AGAT: 0 +AGAC: 0 +AGAG: 0 +AGTA: 0 +AGTT: 0 +AGTC: 0 +AGTG: 0 +AGCA: 0 +AGCT: 0 +AGCC: 0 +AGCG: 0 +AGGA: 0 +AGGT: 0 +AGGC: 0 +AGGG: 0 +TAAA: 0 +TAAT: 0 +TAAC: 0 +TAAG: 0 +TATA: 0 +TATT: 0 +TATC: 0 +TATG: 0 +TACA: 0 +TACT: 0 +TACC: 0 +TACG: 0 +TAGA: 0 +TAGT: 0 +TAGC: 0 +TAGG: 0 +TTAA: 0 +TTAT: 0 +TTAC: 0 +TTAG: 0 +TTTA: 0 +TTTT: 0 +TTTC: 0 +TTTG: 0 +TTCA: 0 +TTCT: 0 +TTCC: 0 +TTCG: 0 +TTGA: 0 +TTGT: 0 +TTGC: 0 +TTGG: 0 +TCAA: 0 +TCAT: 0 +TCAC: 0 +TCAG: 0 +TCTA: 0 +TCTT: 0 +TCTC: 0 +TCTG: 0 +TCCA: 0 +TCCT: 0 +TCCC: 0 +TCCG: 0 +TCGA: 2 +TCGT: 0 +TCGC: 0 +TCGG: 0 +TGAA: 0 +TGAT: 0 +TGAC: 0 +TGAG: 0 +TGTA: 0 +TGTT: 0 +TGTC: 0 +TGTG: 0 +TGCA: 0 +TGCT: 0 +TGCC: 0 +TGCG: 0 +TGGA: 0 +TGGT: 0 +TGGC: 0 +TGGG: 0 +CAAA: 0 +CAAT: 0 +CAAC: 0 +CAAG: 0 +CATA: 0 +CATT: 0 +CATC: 0 +CATG: 0 +CACA: 0 +CACT: 0 +CACC: 0 +CACG: 0 +CAGA: 0 +CAGT: 0 +CAGC: 0 +CAGG: 0 +CTAA: 0 +CTAT: 0 +CTAC: 0 +CTAG: 0 +CTTA: 0 +CTTT: 0 +CTTC: 0 +CTTG: 0 +CTCA: 0 +CTCT: 0 +CTCC: 0 +CTCG: 0 +CTGA: 0 +CTGT: 0 +CTGC: 0 +CTGG: 0 +CCAA: 0 +CCAT: 0 +CCAC: 0 +CCAG: 0 +CCTA: 0 +CCTT: 0 +CCTC: 0 +CCTG: 0 +CCCA: 0 +CCCT: 0 +CCCC: 0 +CCCG: 0 +CCGA: 0 +CCGT: 0 +CCGC: 0 +CCGG: 0 +CGAA: 0 +CGAT: 2 +CGAC: 0 +CGAG: 0 +CGTA: 0 +CGTT: 0 +CGTC: 0 +CGTG: 0 +CGCA: 0 +CGCT: 0 +CGCC: 0 +CGCG: 0 +CGGA: 0 +CGGT: 0 +CGGC: 0 +CGGG: 0 +GAAA: 0 +GAAT: 0 +GAAC: 0 +GAAG: 0 +GATA: 0 +GATT: 0 +GATC: 2 +GATG: 0 +GACA: 0 +GACT: 0 +GACC: 0 +GACG: 0 +GAGA: 0 +GAGT: 0 +GAGC: 0 +GAGG: 0 +GTAA: 0 +GTAT: 0 +GTAC: 0 +GTAG: 0 +GTTA: 0 +GTTT: 0 +GTTC: 0 +GTTG: 0 +GTCA: 0 +GTCT: 0 +GTCC: 0 +GTCG: 0 +GTGA: 0 +GTGT: 0 +GTGC: 0 +GTGG: 0 +GCAA: 0 +GCAT: 0 +GCAC: 0 +GCAG: 0 +GCTA: 0 +GCTT: 0 +GCTC: 0 +GCTG: 0 +GCCA: 0 +GCCT: 0 +GCCC: 0 +GCCG: 0 +GCGA: 0 +GCGT: 0 +GCGC: 0 +GCGG: 0 +GGAA: 0 +GGAT: 0 +GGAC: 0 +GGAG: 0 +GGTA: 0 +GGTT: 0 +GGTC: 0 +GGTG: 0 +GGCA: 0 +GGCT: 0 +GGCC: 0 +GGCG: 0 +GGGA: 0 +GGGT: 0 +GGGC: 0 +GGGG: 0 +--- +SEQ: atcgatcgatcgATCGATCGATCG +AAAA: 0 +AAAT: 0 +AAAC: 0 +AAAG: 0 +AATA: 0 +AATT: 0 +AATC: 0 +AATG: 0 +AACA: 0 +AACT: 0 +AACC: 0 +AACG: 0 +AAGA: 0 +AAGT: 0 +AAGC: 0 +AAGG: 0 +ATAA: 0 +ATAT: 0 +ATAC: 0 +ATAG: 0 +ATTA: 0 +ATTT: 0 +ATTC: 0 +ATTG: 0 +ATCA: 0 +ATCT: 0 +ATCC: 0 +ATCG: 5 +ATGA: 0 +ATGT: 0 +ATGC: 0 +ATGG: 0 +ACAA: 0 +ACAT: 0 +ACAC: 0 +ACAG: 0 +ACTA: 0 +ACTT: 0 +ACTC: 0 +ACTG: 0 +ACCA: 0 +ACCT: 0 +ACCC: 0 +ACCG: 0 +ACGA: 0 +ACGT: 0 +ACGC: 0 +ACGG: 0 +AGAA: 0 +AGAT: 0 +AGAC: 0 +AGAG: 0 +AGTA: 0 +AGTT: 0 +AGTC: 0 +AGTG: 0 +AGCA: 0 +AGCT: 0 +AGCC: 0 +AGCG: 0 +AGGA: 0 +AGGT: 0 +AGGC: 0 +AGGG: 0 +TAAA: 0 +TAAT: 0 +TAAC: 0 +TAAG: 0 +TATA: 0 +TATT: 0 +TATC: 0 +TATG: 0 +TACA: 0 +TACT: 0 +TACC: 0 +TACG: 0 +TAGA: 0 +TAGT: 0 +TAGC: 0 +TAGG: 0 +TTAA: 0 +TTAT: 0 +TTAC: 0 +TTAG: 0 +TTTA: 0 +TTTT: 0 +TTTC: 0 +TTTG: 0 +TTCA: 0 +TTCT: 0 +TTCC: 0 +TTCG: 0 +TTGA: 0 +TTGT: 0 +TTGC: 0 +TTGG: 0 +TCAA: 0 +TCAT: 0 +TCAC: 0 +TCAG: 0 +TCTA: 0 +TCTT: 0 +TCTC: 0 +TCTG: 0 +TCCA: 0 +TCCT: 0 +TCCC: 0 +TCCG: 0 +TCGA: 5 +TCGT: 0 +TCGC: 0 +TCGG: 0 +TGAA: 0 +TGAT: 0 +TGAC: 0 +TGAG: 0 +TGTA: 0 +TGTT: 0 +TGTC: 0 +TGTG: 0 +TGCA: 0 +TGCT: 0 +TGCC: 0 +TGCG: 0 +TGGA: 0 +TGGT: 0 +TGGC: 0 +TGGG: 0 +CAAA: 0 +CAAT: 0 +CAAC: 0 +CAAG: 0 +CATA: 0 +CATT: 0 +CATC: 0 +CATG: 0 +CACA: 0 +CACT: 0 +CACC: 0 +CACG: 0 +CAGA: 0 +CAGT: 0 +CAGC: 0 +CAGG: 0 +CTAA: 0 +CTAT: 0 +CTAC: 0 +CTAG: 0 +CTTA: 0 +CTTT: 0 +CTTC: 0 +CTTG: 0 +CTCA: 0 +CTCT: 0 +CTCC: 0 +CTCG: 0 +CTGA: 0 +CTGT: 0 +CTGC: 0 +CTGG: 0 +CCAA: 0 +CCAT: 0 +CCAC: 0 +CCAG: 0 +CCTA: 0 +CCTT: 0 +CCTC: 0 +CCTG: 0 +CCCA: 0 +CCCT: 0 +CCCC: 0 +CCCG: 0 +CCGA: 0 +CCGT: 0 +CCGC: 0 +CCGG: 0 +CGAA: 0 +CGAT: 5 +CGAC: 0 +CGAG: 0 +CGTA: 0 +CGTT: 0 +CGTC: 0 +CGTG: 0 +CGCA: 0 +CGCT: 0 +CGCC: 0 +CGCG: 0 +CGGA: 0 +CGGT: 0 +CGGC: 0 +CGGG: 0 +GAAA: 0 +GAAT: 0 +GAAC: 0 +GAAG: 0 +GATA: 0 +GATT: 0 +GATC: 5 +GATG: 0 +GACA: 0 +GACT: 0 +GACC: 0 +GACG: 0 +GAGA: 0 +GAGT: 0 +GAGC: 0 +GAGG: 0 +GTAA: 0 +GTAT: 0 +GTAC: 0 +GTAG: 0 +GTTA: 0 +GTTT: 0 +GTTC: 0 +GTTG: 0 +GTCA: 0 +GTCT: 0 +GTCC: 0 +GTCG: 0 +GTGA: 0 +GTGT: 0 +GTGC: 0 +GTGG: 0 +GCAA: 0 +GCAT: 0 +GCAC: 0 +GCAG: 0 +GCTA: 0 +GCTT: 0 +GCTC: 0 +GCTG: 0 +GCCA: 0 +GCCT: 0 +GCCC: 0 +GCCG: 0 +GCGA: 0 +GCGT: 0 +GCGC: 0 +GCGG: 0 +GGAA: 0 +GGAT: 0 +GGAC: 0 +GGAG: 0 +GGTA: 0 +GGTT: 0 +GGTC: 0 +GGTG: 0 +GGCA: 0 +GGCT: 0 +GGCC: 0 +GGCG: 0 +GGGA: 0 +GGGT: 0 +GGGC: 0 +GGGG: 0 +--- diff --git a/bp_test/out/kmer_freq.out.2 b/bp_test/out/kmer_freq.out.2 new file mode 100644 index 0000000..411af63 --- /dev/null +++ b/bp_test/out/kmer_freq.out.2 @@ -0,0 +1,38 @@ +DUMMY: nothing +--- +SEQ: atcgatcgatcg +AA: 0 +AT: 3 +AC: 0 +AG: 0 +TA: 0 +TT: 0 +TC: 3 +TG: 0 +CA: 0 +CT: 0 +CC: 0 +CG: 2 +GA: 2 +GT: 0 +GC: 0 +GG: 0 +--- +SEQ: atcgatcgatcgATCGATCGATCG +AA: 0 +AT: 6 +AC: 0 +AG: 0 +TA: 0 +TT: 0 +TC: 6 +TG: 0 +CA: 0 +CT: 0 +CC: 0 +CG: 5 +GA: 5 +GT: 0 +GC: 0 +GG: 0 +--- diff --git a/bp_test/out/kmer_freq.out.3 b/bp_test/out/kmer_freq.out.3 new file mode 100644 index 0000000..a697e78 --- /dev/null +++ b/bp_test/out/kmer_freq.out.3 @@ -0,0 +1,38 @@ +DUMMY: nothing +--- +SEQ: atcgatcgatcg +AA: 0 +AU: 0 +AC: 0 +AG: 0 +UA: 0 +UU: 0 +UC: 0 +UG: 0 +CA: 0 +CU: 0 +CC: 0 +CG: 2 +GA: 2 +GU: 0 +GC: 0 +GG: 0 +--- +SEQ: atcgatcgatcgATCGATCGATCG +AA: 0 +AU: 0 +AC: 0 +AG: 0 +UA: 0 +UU: 0 +UC: 0 +UG: 0 +CA: 0 +CU: 0 +CC: 0 +CG: 5 +GA: 5 +GU: 0 +GC: 0 +GG: 0 +--- diff --git a/bp_test/out/kmer_freq.out.4 b/bp_test/out/kmer_freq.out.4 new file mode 100644 index 0000000..b18313e --- /dev/null +++ b/bp_test/out/kmer_freq.out.4 @@ -0,0 +1,806 @@ +DUMMY: nothing +--- +SEQ: atcgatcgatcg +FF: 0 +FL: 0 +FS: 0 +FY: 0 +FC: 0 +FW: 0 +FP: 0 +FH: 0 +FQ: 0 +FR: 0 +FI: 0 +FM: 0 +FT: 0 +FN: 0 +FK: 0 +FV: 0 +FA: 0 +FD: 0 +FE: 0 +FG: 0 +LF: 0 +LL: 0 +LS: 0 +LY: 0 +LC: 0 +LW: 0 +LP: 0 +LH: 0 +LQ: 0 +LR: 0 +LI: 0 +LM: 0 +LT: 0 +LN: 0 +LK: 0 +LV: 0 +LA: 0 +LD: 0 +LE: 0 +LG: 0 +SF: 0 +SL: 0 +SS: 0 +SY: 0 +SC: 0 +SW: 0 +SP: 0 +SH: 0 +SQ: 0 +SR: 0 +SI: 0 +SM: 0 +ST: 0 +SN: 0 +SK: 0 +SV: 0 +SA: 0 +SD: 0 +SE: 0 +SG: 0 +YF: 0 +YL: 0 +YS: 0 +YY: 0 +YC: 0 +YW: 0 +YP: 0 +YH: 0 +YQ: 0 +YR: 0 +YI: 0 +YM: 0 +YT: 0 +YN: 0 +YK: 0 +YV: 0 +YA: 0 +YD: 0 +YE: 0 +YG: 0 +CF: 0 +CL: 0 +CS: 0 +CY: 0 +CC: 0 +CW: 0 +CP: 0 +CH: 0 +CQ: 0 +CR: 0 +CI: 0 +CM: 0 +CT: 0 +CN: 0 +CK: 0 +CV: 0 +CA: 0 +CD: 0 +CE: 0 +CG: 2 +WF: 0 +WL: 0 +WS: 0 +WY: 0 +WC: 0 +WW: 0 +WP: 0 +WH: 0 +WQ: 0 +WR: 0 +WI: 0 +WM: 0 +WT: 0 +WN: 0 +WK: 0 +WV: 0 +WA: 0 +WD: 0 +WE: 0 +WG: 0 +PF: 0 +PL: 0 +PS: 0 +PY: 0 +PC: 0 +PW: 0 +PP: 0 +PH: 0 +PQ: 0 +PR: 0 +PI: 0 +PM: 0 +PT: 0 +PN: 0 +PK: 0 +PV: 0 +PA: 0 +PD: 0 +PE: 0 +PG: 0 +HF: 0 +HL: 0 +HS: 0 +HY: 0 +HC: 0 +HW: 0 +HP: 0 +HH: 0 +HQ: 0 +HR: 0 +HI: 0 +HM: 0 +HT: 0 +HN: 0 +HK: 0 +HV: 0 +HA: 0 +HD: 0 +HE: 0 +HG: 0 +QF: 0 +QL: 0 +QS: 0 +QY: 0 +QC: 0 +QW: 0 +QP: 0 +QH: 0 +QQ: 0 +QR: 0 +QI: 0 +QM: 0 +QT: 0 +QN: 0 +QK: 0 +QV: 0 +QA: 0 +QD: 0 +QE: 0 +QG: 0 +RF: 0 +RL: 0 +RS: 0 +RY: 0 +RC: 0 +RW: 0 +RP: 0 +RH: 0 +RQ: 0 +RR: 0 +RI: 0 +RM: 0 +RT: 0 +RN: 0 +RK: 0 +RV: 0 +RA: 0 +RD: 0 +RE: 0 +RG: 0 +IF: 0 +IL: 0 +IS: 0 +IY: 0 +IC: 0 +IW: 0 +IP: 0 +IH: 0 +IQ: 0 +IR: 0 +II: 0 +IM: 0 +IT: 0 +IN: 0 +IK: 0 +IV: 0 +IA: 0 +ID: 0 +IE: 0 +IG: 0 +MF: 0 +ML: 0 +MS: 0 +MY: 0 +MC: 0 +MW: 0 +MP: 0 +MH: 0 +MQ: 0 +MR: 0 +MI: 0 +MM: 0 +MT: 0 +MN: 0 +MK: 0 +MV: 0 +MA: 0 +MD: 0 +ME: 0 +MG: 0 +TF: 0 +TL: 0 +TS: 0 +TY: 0 +TC: 3 +TW: 0 +TP: 0 +TH: 0 +TQ: 0 +TR: 0 +TI: 0 +TM: 0 +TT: 0 +TN: 0 +TK: 0 +TV: 0 +TA: 0 +TD: 0 +TE: 0 +TG: 0 +NF: 0 +NL: 0 +NS: 0 +NY: 0 +NC: 0 +NW: 0 +NP: 0 +NH: 0 +NQ: 0 +NR: 0 +NI: 0 +NM: 0 +NT: 0 +NN: 0 +NK: 0 +NV: 0 +NA: 0 +ND: 0 +NE: 0 +NG: 0 +KF: 0 +KL: 0 +KS: 0 +KY: 0 +KC: 0 +KW: 0 +KP: 0 +KH: 0 +KQ: 0 +KR: 0 +KI: 0 +KM: 0 +KT: 0 +KN: 0 +KK: 0 +KV: 0 +KA: 0 +KD: 0 +KE: 0 +KG: 0 +VF: 0 +VL: 0 +VS: 0 +VY: 0 +VC: 0 +VW: 0 +VP: 0 +VH: 0 +VQ: 0 +VR: 0 +VI: 0 +VM: 0 +VT: 0 +VN: 0 +VK: 0 +VV: 0 +VA: 0 +VD: 0 +VE: 0 +VG: 0 +AF: 0 +AL: 0 +AS: 0 +AY: 0 +AC: 0 +AW: 0 +AP: 0 +AH: 0 +AQ: 0 +AR: 0 +AI: 0 +AM: 0 +AT: 3 +AN: 0 +AK: 0 +AV: 0 +AA: 0 +AD: 0 +AE: 0 +AG: 0 +DF: 0 +DL: 0 +DS: 0 +DY: 0 +DC: 0 +DW: 0 +DP: 0 +DH: 0 +DQ: 0 +DR: 0 +DI: 0 +DM: 0 +DT: 0 +DN: 0 +DK: 0 +DV: 0 +DA: 0 +DD: 0 +DE: 0 +DG: 0 +EF: 0 +EL: 0 +ES: 0 +EY: 0 +EC: 0 +EW: 0 +EP: 0 +EH: 0 +EQ: 0 +ER: 0 +EI: 0 +EM: 0 +ET: 0 +EN: 0 +EK: 0 +EV: 0 +EA: 0 +ED: 0 +EE: 0 +EG: 0 +GF: 0 +GL: 0 +GS: 0 +GY: 0 +GC: 0 +GW: 0 +GP: 0 +GH: 0 +GQ: 0 +GR: 0 +GI: 0 +GM: 0 +GT: 0 +GN: 0 +GK: 0 +GV: 0 +GA: 2 +GD: 0 +GE: 0 +GG: 0 +--- +SEQ: atcgatcgatcgATCGATCGATCG +FF: 0 +FL: 0 +FS: 0 +FY: 0 +FC: 0 +FW: 0 +FP: 0 +FH: 0 +FQ: 0 +FR: 0 +FI: 0 +FM: 0 +FT: 0 +FN: 0 +FK: 0 +FV: 0 +FA: 0 +FD: 0 +FE: 0 +FG: 0 +LF: 0 +LL: 0 +LS: 0 +LY: 0 +LC: 0 +LW: 0 +LP: 0 +LH: 0 +LQ: 0 +LR: 0 +LI: 0 +LM: 0 +LT: 0 +LN: 0 +LK: 0 +LV: 0 +LA: 0 +LD: 0 +LE: 0 +LG: 0 +SF: 0 +SL: 0 +SS: 0 +SY: 0 +SC: 0 +SW: 0 +SP: 0 +SH: 0 +SQ: 0 +SR: 0 +SI: 0 +SM: 0 +ST: 0 +SN: 0 +SK: 0 +SV: 0 +SA: 0 +SD: 0 +SE: 0 +SG: 0 +YF: 0 +YL: 0 +YS: 0 +YY: 0 +YC: 0 +YW: 0 +YP: 0 +YH: 0 +YQ: 0 +YR: 0 +YI: 0 +YM: 0 +YT: 0 +YN: 0 +YK: 0 +YV: 0 +YA: 0 +YD: 0 +YE: 0 +YG: 0 +CF: 0 +CL: 0 +CS: 0 +CY: 0 +CC: 0 +CW: 0 +CP: 0 +CH: 0 +CQ: 0 +CR: 0 +CI: 0 +CM: 0 +CT: 0 +CN: 0 +CK: 0 +CV: 0 +CA: 0 +CD: 0 +CE: 0 +CG: 5 +WF: 0 +WL: 0 +WS: 0 +WY: 0 +WC: 0 +WW: 0 +WP: 0 +WH: 0 +WQ: 0 +WR: 0 +WI: 0 +WM: 0 +WT: 0 +WN: 0 +WK: 0 +WV: 0 +WA: 0 +WD: 0 +WE: 0 +WG: 0 +PF: 0 +PL: 0 +PS: 0 +PY: 0 +PC: 0 +PW: 0 +PP: 0 +PH: 0 +PQ: 0 +PR: 0 +PI: 0 +PM: 0 +PT: 0 +PN: 0 +PK: 0 +PV: 0 +PA: 0 +PD: 0 +PE: 0 +PG: 0 +HF: 0 +HL: 0 +HS: 0 +HY: 0 +HC: 0 +HW: 0 +HP: 0 +HH: 0 +HQ: 0 +HR: 0 +HI: 0 +HM: 0 +HT: 0 +HN: 0 +HK: 0 +HV: 0 +HA: 0 +HD: 0 +HE: 0 +HG: 0 +QF: 0 +QL: 0 +QS: 0 +QY: 0 +QC: 0 +QW: 0 +QP: 0 +QH: 0 +QQ: 0 +QR: 0 +QI: 0 +QM: 0 +QT: 0 +QN: 0 +QK: 0 +QV: 0 +QA: 0 +QD: 0 +QE: 0 +QG: 0 +RF: 0 +RL: 0 +RS: 0 +RY: 0 +RC: 0 +RW: 0 +RP: 0 +RH: 0 +RQ: 0 +RR: 0 +RI: 0 +RM: 0 +RT: 0 +RN: 0 +RK: 0 +RV: 0 +RA: 0 +RD: 0 +RE: 0 +RG: 0 +IF: 0 +IL: 0 +IS: 0 +IY: 0 +IC: 0 +IW: 0 +IP: 0 +IH: 0 +IQ: 0 +IR: 0 +II: 0 +IM: 0 +IT: 0 +IN: 0 +IK: 0 +IV: 0 +IA: 0 +ID: 0 +IE: 0 +IG: 0 +MF: 0 +ML: 0 +MS: 0 +MY: 0 +MC: 0 +MW: 0 +MP: 0 +MH: 0 +MQ: 0 +MR: 0 +MI: 0 +MM: 0 +MT: 0 +MN: 0 +MK: 0 +MV: 0 +MA: 0 +MD: 0 +ME: 0 +MG: 0 +TF: 0 +TL: 0 +TS: 0 +TY: 0 +TC: 6 +TW: 0 +TP: 0 +TH: 0 +TQ: 0 +TR: 0 +TI: 0 +TM: 0 +TT: 0 +TN: 0 +TK: 0 +TV: 0 +TA: 0 +TD: 0 +TE: 0 +TG: 0 +NF: 0 +NL: 0 +NS: 0 +NY: 0 +NC: 0 +NW: 0 +NP: 0 +NH: 0 +NQ: 0 +NR: 0 +NI: 0 +NM: 0 +NT: 0 +NN: 0 +NK: 0 +NV: 0 +NA: 0 +ND: 0 +NE: 0 +NG: 0 +KF: 0 +KL: 0 +KS: 0 +KY: 0 +KC: 0 +KW: 0 +KP: 0 +KH: 0 +KQ: 0 +KR: 0 +KI: 0 +KM: 0 +KT: 0 +KN: 0 +KK: 0 +KV: 0 +KA: 0 +KD: 0 +KE: 0 +KG: 0 +VF: 0 +VL: 0 +VS: 0 +VY: 0 +VC: 0 +VW: 0 +VP: 0 +VH: 0 +VQ: 0 +VR: 0 +VI: 0 +VM: 0 +VT: 0 +VN: 0 +VK: 0 +VV: 0 +VA: 0 +VD: 0 +VE: 0 +VG: 0 +AF: 0 +AL: 0 +AS: 0 +AY: 0 +AC: 0 +AW: 0 +AP: 0 +AH: 0 +AQ: 0 +AR: 0 +AI: 0 +AM: 0 +AT: 6 +AN: 0 +AK: 0 +AV: 0 +AA: 0 +AD: 0 +AE: 0 +AG: 0 +DF: 0 +DL: 0 +DS: 0 +DY: 0 +DC: 0 +DW: 0 +DP: 0 +DH: 0 +DQ: 0 +DR: 0 +DI: 0 +DM: 0 +DT: 0 +DN: 0 +DK: 0 +DV: 0 +DA: 0 +DD: 0 +DE: 0 +DG: 0 +EF: 0 +EL: 0 +ES: 0 +EY: 0 +EC: 0 +EW: 0 +EP: 0 +EH: 0 +EQ: 0 +ER: 0 +EI: 0 +EM: 0 +ET: 0 +EN: 0 +EK: 0 +EV: 0 +EA: 0 +ED: 0 +EE: 0 +EG: 0 +GF: 0 +GL: 0 +GS: 0 +GY: 0 +GC: 0 +GW: 0 +GP: 0 +GH: 0 +GQ: 0 +GR: 0 +GI: 0 +GM: 0 +GT: 0 +GN: 0 +GK: 0 +GV: 0 +GA: 5 +GD: 0 +GE: 0 +GG: 0 +--- diff --git a/bp_test/test/test_kmer_freq b/bp_test/test/test_kmer_freq new file mode 100755 index 0000000..4af9bf6 --- /dev/null +++ b/bp_test/test/test_kmer_freq @@ -0,0 +1,19 @@ +#!/bin/bash + +source "$BP_DIR/bp_test/lib/test.sh" + +run "$bp -I $in -O $tmp" +assert_no_diff $tmp $out.1 +clean + +run "$bp -I $in -s 2 -O $tmp" +assert_no_diff $tmp $out.2 +clean + +run "$bp -I $in -s 2 -t rna -O $tmp" +assert_no_diff $tmp $out.3 +clean + +run "$bp -I $in -s 2 -t protein -O $tmp" +assert_no_diff $tmp $out.4 +clean -- 2.39.5