--- name: "pychopper" section: "1" platform: "linux" package: "python3-pychopper" version: "2.7.2-1" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/pychopper" --- # pychopper(1) package documentation ## NAME pychopper - package documentation ## COMMAND LINE TOOLS ## FULL API REFERENCE ### pychopper ### pychopper package ### Subpackages ### pychopper.phmm\_data package ### Module contents ### pychopper.primer\_data package ### Module contents ### pychopper.scripts package ### Submodules ### pychopper.scripts.pychopper module - **pychopper.scripts.pychopper.main()** Parse command line arguments. ### Module contents ### pychopper.tests package ### Submodules ### pychopper.tests.test\_detector module - **class pychopper.tests.test\_detector.TestDetector(methodName='runTest')** Bases: **unittest.case.TestCase** Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name. - **testPairAlign()** - **testScoreCutoff()** ### pychopper.tests.test\_regression\_simple module - **class pychopper.tests.test\_regression\_simple.TestIntegration(methodName='runTest')** Bases: **unittest.case.TestCase** Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name. - **testIntegration()** Integration test. - **testIntegration\_umi()** Integration test. ### Module contents ### Submodules ### pychopper.alignment\_hits module - **pychopper.alignment\_hits.process\_hits(hits, max\_score)** Process alignment hits by removing overlaps ### pychopper.chopper module - **pychopper.chopper.analyse\_hits(hits, config)** Segment reads based on alignment hits using dynamic programming. The algorithm is based on the rule that each primer alignment hit can be used only once. Hence if a segment is included, the next one has to be excluded. - **pychopper.chopper.chopper\_edlib(reads, primers, config, max\_ed, cutoff, pool, min\_batch)** Segment using the edlib/parasail backend - **pychopper.chopper.chopper\_phmm(reads, phmm\_file, config, cutoff, threads, pool, min\_batch)** Segment using the profile HMM backend - **pychopper.chopper.segments\_to\_reads(read, segments, keep\_primers, bam\_tags, detect\_umis)** Convert segments to output reads with annotation ### pychopper.common\_structures module - **class pychopper.common\_structures.Hit(Ref, RefStart, RefEnd, Query, QueryStart, QueryEnd, Score)** Bases: **tuple** Create new instance of Hit(Ref, RefStart, RefEnd, Query, QueryStart, QueryEnd, Score) - **Query** Alias for field number 3 - **QueryEnd** Alias for field number 5 - **QueryStart** Alias for field number 4 - **Ref** Alias for field number 0 - **RefEnd** Alias for field number 2 - **RefStart** Alias for field number 1 - **Score** Alias for field number 6 - **class pychopper.common\_structures.Segment(Left, Start, End, Right, Strand, Len)** Bases: **tuple** Create new instance of Segment(Left, Start, End, Right, Strand, Len) - **End** Alias for field number 2 - **Left** Alias for field number 0 - **Len** Alias for field number 5 - **Right** Alias for field number 3 - **Start** Alias for field number 1 - **Strand** Alias for field number 4 - **class pychopper.common\_structures.Seq(Id, Name, Seq, Qual, Umi)** Bases: **tuple** Create new instance of Seq(Id, Name, Seq, Qual, Umi) - **Id** Alias for field number 0 - **Name** Alias for field number 1 - **Qual** Alias for field number 3 - **Seq** Alias for field number 2 - **Umi** Alias for field number 4 ### pychopper.edlib\_backend module - **pychopper.edlib\_backend.find\_locations(reads, all\_primers, max\_ed, pool, min\_batch)** Find alignment hits of all primers in all reads using the edlib/parasail backend - **pychopper.edlib\_backend.find\_umi\_single(params)** Find UMI in a single reads using the edlib/parasail backend ### pychopper.hmmer\_backend module - **pychopper.hmmer\_backend.find\_locations(reads, phmm\_file, E, pool, min\_batch)** Find alignment hits of all primers in all reads using the pHMM/nhmmscan backend ### pychopper.parasail\_backend module - **pychopper.parasail\_backend.first\_cigar(cigar)** Extract details of the first operation in a cigar string. - **pychopper.parasail\_backend.pair\_align(reference, query, query\_name, subs\_mat, params)** Perform pairwise local alignment using parsail-python - **pychopper.parasail\_backend.process\_alignment(aln, query, query\_name, aln\_params)** Process an alignment, extracting score, start and end. - **pychopper.parasail\_backend.refine\_locations(read, all\_primers, locations, aln\_params={'gap\_extend': 1, 'gap\_open': 1, 'match': 1, 'mismatch': -2}, subs\_mat=\)** Refine alignment edges based on local alignment ### pychopper.report module - **class pychopper.report.Report(pdf)** Bases: **object** Class for plotting utilities on the top of matplotlib. Plots are saved in the specified file through the PDF backend. - **Parameters** - • **self** -- object. - • **pdf** -- Output pdf. - **Returns** The report object. - **Return type** *Report* - **close()** Close PDF backend. Do not forget to call this at the end of your script or your output will be damaged! - **Parameters** **self** -- object - **Returns** None - **Return type** object - **plot\_arrays(data\_map, title='', xlab='', ylab='', marker='.', legend\_loc='best', legend=True, vlines=None, vlcolor='green', vlwitdh=0.5)** Plot multiple pairs of data arrays. - **Parameters** - • **self** -- object. - • **data\_map** -- A dictionary with labels as keys and tupples of data arrays (x,y) as values. - • **title** -- Figure title. - • **xlab** -- X axis label. - • **ylab** -- Y axis label. - • **marker** -- Marker passed to the plot function. - • **legend\_loc** -- Location of legend. - • **legend** -- Plot legend if True - • **vlines** -- Dictionary with labels and positions of vertical lines to draw. - • **vlcolor** -- Color of vertical lines drawn. - • **vlwidth** -- Width of vertical lines drawn. - **Returns** None - **Return type** object - **plot\_bars\_simple(data\_map, title='', xlab='', ylab='', alpha=0.6, xticks\_rotation=0, auto\_limit=False)** Plot simple bar chart from input dictionary. - **Parameters** - • **self** -- object. - • **data\_map** -- A dictionary with labels as keys and data as values. - • **title** -- Figure title. - • **xlab** -- X axis label. - • **ylab** -- Y axis label. - • **alpha** -- Alpha value. - • **xticks\_rotation** -- Rotation value for x tick labels. - • **auto\_limit** -- Set y axis limits automatically. - **Returns** None - **Return type** object - **plot\_histograms(data\_map, title='', xlab='', ylab='', bins=50, alpha=0.7, legend\_loc='best', legend=True, vlines=None)** Plot histograms of multiple data arrays. - **Parameters** - • **self** -- object. - • **data\_map** -- A dictionary with labels as keys and data arrays as values. - • **title** -- Figure title. - • **xlab** -- X axis label. - • **ylab** -- Y axis label. - • **bins** -- Number of bins. - • **alpha** -- Transparency value for histograms. - • **legend\_loc** -- Location of legend. - • **legend** -- Plot legend if True. - • **vlines** -- Dictionary with labels and positions of vertical lines to draw. - **Returns** None - **Return type** object - **save\_close()** Utility method to save and close figure. ### pychopper.seq\_utils module - **pychopper.seq\_utils.base\_complement(k)** Return complement of base. Performs the subsitutions: A\<=\>T, C\<=\>G, X=\>X for both upper and lower case. The return value is identical to the argument for all other values. - **Parameters** **k** -- A base. - **Returns** Complement of base. - **Return type** str - **pychopper.seq\_utils.errs\_tab(n)** Generate list of error rates for qualities less than equal than n. - **pychopper.seq\_utils.get\_primers(primers)** Load primers from fasta file - **pychopper.seq\_utils.get\_runid(desc)** Parse out runid from sequence description. - **pychopper.seq\_utils.mean\_qual(quals, qround=False, tab=\[1.0, 0.7943282347242815, 0.6309573444801932, 0.5011872336272722, 0.3981071705534972, 0.31622776601683794, 0.251188643150958, 0.19952623149688797, 0.15848931924611134, 0.12589254117941673, 0.1, 0.07943282347242814, 0.06309573444801933, 0.05011872336272722, 0.039810717055349734, 0.03162277660168379, 0.025118864315095794, 0.0199526231496888, 0.015848931924611134, 0.012589254117941675, 0.01, 0.007943282347242814, 0.00630957344480193, 0.005011872336272725, 0.003981071705534973, 0.0031622776601683794, 0.0025118864315095794, 0.001995262314968879, 0.001584893192461114, 0.0012589254117941675, 0.001, 0.0007943282347242813, 0.000630957344480193, 0.0005011872336272725, 0.00039810717055349735, 0.00031622776601683794, 0.00025118864315095795, 0.00019952623149688788, 0.00015848931924611142, 0.00012589254117941674, 0.0001, 7.943282347242822e-05, 6.309573444801929e-05, 5.011872336272725e-05, 3.9810717055349695e-05, 3.1622776601683795e-05, 2.5118864315095822e-05, 1.9952623149688786e-05, 1.584893192461114e-05, 1.2589254117941661e-05, 1e-05, 7.943282347242822e-06, 6.30957344480193e-06, 5.011872336272725e-06, 3.981071705534969e-06, 3.162277660168379e-06, 2.5118864315095823e-06, 1.9952623149688787e-06, 1.584893192461114e-06, 1.2589254117941661e-06, 1e-06, 7.943282347242822e-07, 6.30957344480193e-07, 5.011872336272725e-07, 3.981071705534969e-07, 3.162277660168379e-07, 2.5118864315095823e-07, 1.9952623149688787e-07, 1.584893192461114e-07, 1.2589254117941662e-07, 1e-07, 7.943282347242822e-08, 6.30957344480193e-08, 5.011872336272725e-08, 3.981071705534969e-08, 3.162277660168379e-08, 2.511886431509582e-08, 1.9952623149688786e-08, 1.5848931924611143e-08, 1.2589254117941661e-08, 1e-08, 7.943282347242822e-09, 6.309573444801943e-09, 5.011872336272715e-09, 3.981071705534969e-09, 3.1622776601683795e-09, 2.511886431509582e-09, 1.9952623149688828e-09, 1.584893192461111e-09, 1.2589254117941663e-09, 1e-09, 7.943282347242822e-10, 6.309573444801942e-10, 5.011872336272714e-10, 3.9810717055349694e-10, 3.1622776601683795e-10, 2.511886431509582e-10, 1.9952623149688828e-10, 1.584893192461111e-10, 1.2589254117941662e-10, 1e-10, 7.943282347242822e-11, 6.309573444801942e-11, 5.011872336272715e-11, 3.9810717055349695e-11, 3.1622776601683794e-11, 2.5118864315095823e-11, 1.9952623149688828e-11, 1.5848931924611107e-11, 1.2589254117941662e-11, 1e-11, 7.943282347242821e-12, 6.309573444801943e-12, 5.011872336272715e-12, 3.9810717055349695e-12, 3.1622776601683794e-12, 2.5118864315095823e-12, 1.9952623149688827e-12, 1.584893192461111e-12, 1.258925411794166e-12, 1e-12, 7.943282347242822e-13, 6.309573444801942e-13, 5.011872336272715e-13, 3.981071705534969e-13, 3.162277660168379e-13, 2.511886431509582e-13, 1.9952623149688827e-13, 1.584893192461111e-13\])** Calculate average basecall quality of a read. Receive the ascii quality scores of a read and return the average quality for that read First convert Phred scores to probabilities, calculate average error probability convert average back to Phred scale - **pychopper.seq\_utils.random(size=None)** Return random floats in the half-open interval \[0.0, 1.0). Alias for *random\_sample* to ease forward-porting to the new random API. - **pychopper.seq\_utils.readfq(fp, sample=None, min\_qual=None, rfq\_sup={})** Below function taken from *https://github.com/lh3/readfq/blob/master/readfq.py* Much faster parsing of large files compared to Biopyhton. - **pychopper.seq\_utils.record\_size(read, in\_format='fastq')** Calculate record size. - **pychopper.seq\_utils.revcomp\_seq(seq)** Reverse complement sequence record - **pychopper.seq\_utils.reverse\_complement(seq)** Return reverse complement of a string (base) sequence. - **Parameters** **seq** -- Input sequence. - **Returns** Reverse complement of input sequence. - **Return type** str - **pychopper.seq\_utils.writefq(r, fh)** Write read to fastq file ### pychopper.utils module - **pychopper.utils.batch(iterable, size)** - **pychopper.utils.check\_command(cmd)** - **pychopper.utils.check\_min\_hmmer\_version(major, minor)** - **pychopper.utils.count\_fastq\_records(fname, size=128000000, opener=\)** - **pychopper.utils.hit2bed(hit, read)** - **pychopper.utils.parse\_config\_string(s)** ### Module contents - • *Index* - • *Module Index* - • *Search Page* ## AUTHOR ONT Applications Group ## COPYRIGHT 2022, Oxford Nanopore Technologies Ltd.