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.TH "PYCHOPPER" "1" "Nov 19, 2022" "2.7.2" "package documentation"
.SH NAME
pychopper \- package documentation
.SH COMMAND LINE TOOLS
.SH FULL API REFERENCE
.SS pychopper
.SS pychopper package
.SS Subpackages
.SS pychopper.phmm_data package
.SS Module contents
.SS pychopper.primer_data package
.SS Module contents
.SS pychopper.scripts package
.SS Submodules
.SS pychopper.scripts.pychopper module
.INDENT 0.0
.TP
.B pychopper.scripts.pychopper.main()
Parse command line arguments.
.UNINDENT
.SS Module contents
.SS pychopper.tests package
.SS Submodules
.SS pychopper.tests.test_detector module
.INDENT 0.0
.TP
.B class  pychopper.tests.test_detector.TestDetector(methodName=\(aqrunTest\(aq)
Bases: \fBunittest.case.TestCase\fP
.sp
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.
.INDENT 7.0
.TP
.B testPairAlign()
.UNINDENT
.INDENT 7.0
.TP
.B testScoreCutoff()
.UNINDENT
.UNINDENT
.SS pychopper.tests.test_regression_simple module
.INDENT 0.0
.TP
.B class  pychopper.tests.test_regression_simple.TestIntegration(methodName=\(aqrunTest\(aq)
Bases: \fBunittest.case.TestCase\fP
.sp
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.
.INDENT 7.0
.TP
.B testIntegration()
Integration test.
.UNINDENT
.INDENT 7.0
.TP
.B testIntegration_umi()
Integration test.
.UNINDENT
.UNINDENT
.SS Module contents
.SS Submodules
.SS pychopper.alignment_hits module
.INDENT 0.0
.TP
.B pychopper.alignment_hits.process_hits(hits, max_score)
Process alignment hits by removing overlaps
.UNINDENT
.SS pychopper.chopper module
.INDENT 0.0
.TP
.B 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.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.chopper.chopper_edlib(reads, primers, config, max_ed, cutoff, pool, min_batch)
Segment using the edlib/parasail backend
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.chopper.chopper_phmm(reads, phmm_file, config, cutoff, threads, pool, min_batch)
Segment using the profile HMM backend
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.chopper.segments_to_reads(read, segments, keep_primers, bam_tags, detect_umis)
Convert segments to output reads with annotation
.UNINDENT
.SS pychopper.common_structures module
.INDENT 0.0
.TP
.B class  pychopper.common_structures.Hit(Ref, RefStart, RefEnd, Query, QueryStart, QueryEnd, Score)
Bases: \fBtuple\fP
.sp
Create new instance of Hit(Ref, RefStart, RefEnd, Query, QueryStart, QueryEnd, Score)
.INDENT 7.0
.TP
.B Query
Alias for field number 3
.UNINDENT
.INDENT 7.0
.TP
.B QueryEnd
Alias for field number 5
.UNINDENT
.INDENT 7.0
.TP
.B QueryStart
Alias for field number 4
.UNINDENT
.INDENT 7.0
.TP
.B Ref
Alias for field number 0
.UNINDENT
.INDENT 7.0
.TP
.B RefEnd
Alias for field number 2
.UNINDENT
.INDENT 7.0
.TP
.B RefStart
Alias for field number 1
.UNINDENT
.INDENT 7.0
.TP
.B Score
Alias for field number 6
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B class  pychopper.common_structures.Segment(Left, Start, End, Right, Strand, Len)
Bases: \fBtuple\fP
.sp
Create new instance of Segment(Left, Start, End, Right, Strand, Len)
.INDENT 7.0
.TP
.B End
Alias for field number 2
.UNINDENT
.INDENT 7.0
.TP
.B Left
Alias for field number 0
.UNINDENT
.INDENT 7.0
.TP
.B Len
Alias for field number 5
.UNINDENT
.INDENT 7.0
.TP
.B Right
Alias for field number 3
.UNINDENT
.INDENT 7.0
.TP
.B Start
Alias for field number 1
.UNINDENT
.INDENT 7.0
.TP
.B Strand
Alias for field number 4
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B class  pychopper.common_structures.Seq(Id, Name, Seq, Qual, Umi)
Bases: \fBtuple\fP
.sp
Create new instance of Seq(Id, Name, Seq, Qual, Umi)
.INDENT 7.0
.TP
.B Id
Alias for field number 0
.UNINDENT
.INDENT 7.0
.TP
.B Name
Alias for field number 1
.UNINDENT
.INDENT 7.0
.TP
.B Qual
Alias for field number 3
.UNINDENT
.INDENT 7.0
.TP
.B Seq
Alias for field number 2
.UNINDENT
.INDENT 7.0
.TP
.B Umi
Alias for field number 4
.UNINDENT
.UNINDENT
.SS pychopper.edlib_backend module
.INDENT 0.0
.TP
.B 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
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.edlib_backend.find_umi_single(params)
Find UMI in a single reads using the edlib/parasail backend
.UNINDENT
.SS pychopper.hmmer_backend module
.INDENT 0.0
.TP
.B 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
.UNINDENT
.SS pychopper.parasail_backend module
.INDENT 0.0
.TP
.B pychopper.parasail_backend.first_cigar(cigar)
Extract details of the first operation in a cigar string.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.parasail_backend.pair_align(reference, query, query_name, subs_mat, params)
Perform pairwise local alignment using parsail\-python
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.parasail_backend.process_alignment(aln, query, query_name, aln_params)
Process an alignment, extracting score, start and end.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.parasail_backend.refine_locations(read, all_primers, locations, aln_params={\(aqgap_extend\(aq: 1, \(aqgap_open\(aq: 1, \(aqmatch\(aq: 1, \(aqmismatch\(aq: \-2}, subs_mat=<parasail.bindings_v2.Matrix object>)
Refine alignment edges based on local alignment
.UNINDENT
.SS pychopper.report module
.INDENT 0.0
.TP
.B class  pychopper.report.Report(pdf)
Bases: \fBobject\fP
.sp
Class for plotting utilities on the top of matplotlib. Plots are saved in the specified file through the PDF backend.
.INDENT 7.0
.TP
.B Parameters
.INDENT 7.0
.IP \(bu 2
\fBself\fP \-\- object.
.IP \(bu 2
\fBpdf\fP \-\- Output pdf.
.UNINDENT
.TP
.B Returns
The report object.
.TP
.B Return type
\fI\%Report\fP
.UNINDENT
.INDENT 7.0
.TP
.B close()
Close PDF backend. Do not forget to call this at the end of your script or your output will be damaged!
.INDENT 7.0
.TP
.B Parameters
\fBself\fP \-\- object
.TP
.B Returns
None
.TP
.B Return type
object
.UNINDENT
.UNINDENT
.INDENT 7.0
.TP
.B plot_arrays(data_map, title=\(aq\(aq, xlab=\(aq\(aq, ylab=\(aq\(aq, marker=\(aq.\(aq, legend_loc=\(aqbest\(aq, legend=True, vlines=None, vlcolor=\(aqgreen\(aq, vlwitdh=0.5)
Plot multiple pairs of data arrays.
.INDENT 7.0
.TP
.B Parameters
.INDENT 7.0
.IP \(bu 2
\fBself\fP \-\- object.
.IP \(bu 2
\fBdata_map\fP \-\- A dictionary with labels as keys and tupples of data arrays (x,y) as values.
.IP \(bu 2
\fBtitle\fP \-\- Figure title.
.IP \(bu 2
\fBxlab\fP \-\- X axis label.
.IP \(bu 2
\fBylab\fP \-\- Y axis label.
.IP \(bu 2
\fBmarker\fP \-\- Marker passed to the plot function.
.IP \(bu 2
\fBlegend_loc\fP \-\- Location of legend.
.IP \(bu 2
\fBlegend\fP \-\- Plot legend if True
.IP \(bu 2
\fBvlines\fP \-\- Dictionary with labels and positions of vertical lines to draw.
.IP \(bu 2
\fBvlcolor\fP \-\- Color of vertical lines drawn.
.IP \(bu 2
\fBvlwidth\fP \-\- Width of vertical lines drawn.
.UNINDENT
.TP
.B Returns
None
.TP
.B Return type
object
.UNINDENT
.UNINDENT
.INDENT 7.0
.TP
.B plot_bars_simple(data_map, title=\(aq\(aq, xlab=\(aq\(aq, ylab=\(aq\(aq, alpha=0.6, xticks_rotation=0, auto_limit=False)
Plot simple bar chart from input dictionary.
.INDENT 7.0
.TP
.B Parameters
.INDENT 7.0
.IP \(bu 2
\fBself\fP \-\- object.
.IP \(bu 2
\fBdata_map\fP \-\- A dictionary with labels as keys and data as values.
.IP \(bu 2
\fBtitle\fP \-\- Figure title.
.IP \(bu 2
\fBxlab\fP \-\- X axis label.
.IP \(bu 2
\fBylab\fP \-\- Y axis label.
.IP \(bu 2
\fBalpha\fP \-\- Alpha value.
.IP \(bu 2
\fBxticks_rotation\fP \-\- Rotation value for x tick labels.
.IP \(bu 2
\fBauto_limit\fP \-\- Set y axis limits automatically.
.UNINDENT
.TP
.B Returns
None
.TP
.B Return type
object
.UNINDENT
.UNINDENT
.INDENT 7.0
.TP
.B plot_histograms(data_map, title=\(aq\(aq, xlab=\(aq\(aq, ylab=\(aq\(aq, bins=50, alpha=0.7, legend_loc=\(aqbest\(aq, legend=True, vlines=None)
Plot histograms of multiple data arrays.
.INDENT 7.0
.TP
.B Parameters
.INDENT 7.0
.IP \(bu 2
\fBself\fP \-\- object.
.IP \(bu 2
\fBdata_map\fP \-\- A dictionary with labels as keys and data arrays as values.
.IP \(bu 2
\fBtitle\fP \-\- Figure title.
.IP \(bu 2
\fBxlab\fP \-\- X axis label.
.IP \(bu 2
\fBylab\fP \-\- Y axis label.
.IP \(bu 2
\fBbins\fP \-\- Number of bins.
.IP \(bu 2
\fBalpha\fP \-\- Transparency value for histograms.
.IP \(bu 2
\fBlegend_loc\fP \-\- Location of legend.
.IP \(bu 2
\fBlegend\fP \-\- Plot legend if True.
.IP \(bu 2
\fBvlines\fP \-\- Dictionary with labels and positions of vertical lines to draw.
.UNINDENT
.TP
.B Returns
None
.TP
.B Return type
object
.UNINDENT
.UNINDENT
.INDENT 7.0
.TP
.B save_close()
Utility method to save and close figure.
.UNINDENT
.UNINDENT
.SS pychopper.seq_utils module
.INDENT 0.0
.TP
.B pychopper.seq_utils.base_complement(k)
Return complement of base.
.sp
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.
.INDENT 7.0
.TP
.B Parameters
\fBk\fP \-\- A base.
.TP
.B Returns
Complement of base.
.TP
.B Return type
str
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.errs_tab(n)
Generate list of error rates for qualities less than equal than n.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.get_primers(primers)
Load primers from fasta file
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.get_runid(desc)
Parse out runid from sequence description.
.UNINDENT
.INDENT 0.0
.TP
.B 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
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.random(size=None)
Return random floats in the half\-open interval [0.0, 1.0). Alias for
\fIrandom_sample\fP to ease forward\-porting to the new random API.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.readfq(fp, sample=None, min_qual=None, rfq_sup={})
Below function taken from \fI\%https://github.com/lh3/readfq/blob/master/readfq.py\fP
Much faster parsing of large files compared to Biopyhton.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.record_size(read, in_format=\(aqfastq\(aq)
Calculate record size.
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.revcomp_seq(seq)
Reverse complement sequence record
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.reverse_complement(seq)
Return reverse complement of a string (base) sequence.
.INDENT 7.0
.TP
.B Parameters
\fBseq\fP \-\- Input sequence.
.TP
.B Returns
Reverse complement of input sequence.
.TP
.B Return type
str
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.seq_utils.writefq(r, fh)
Write read to fastq file
.UNINDENT
.SS pychopper.utils module
.INDENT 0.0
.TP
.B pychopper.utils.batch(iterable, size)
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.utils.check_command(cmd)
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.utils.check_min_hmmer_version(major, minor)
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.utils.count_fastq_records(fname, size=128000000, opener=<built\-in function open>)
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.utils.hit2bed(hit, read)
.UNINDENT
.INDENT 0.0
.TP
.B pychopper.utils.parse_config_string(s)
.UNINDENT
.SS Module contents
.INDENT 0.0
.IP \(bu 2
\fI\%Index\fP
.IP \(bu 2
\fI\%Module Index\fP
.IP \(bu 2
\fI\%Search Page\fP
.UNINDENT
.SH AUTHOR
ONT Applications Group
.SH COPYRIGHT
2022, Oxford Nanopore Technologies Ltd.
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