biocaml

The OCaml Bioinformatics Library
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Libraries

This package provides the following libraries (via dune):

biocaml.base

Documentation:

Dependencies: base, rresult, uri, ppx_sexp_conv.runtime-lib, sexplib0, ppx_inline_test.config, ppx_inline_test.runtime-lib

biocaml.ez

Documentation:

Dependencies: biocaml.unix, ppx_sexp_conv.runtime-lib, sexplib0, ppx_compare.runtime-lib, ppx_enumerate.runtime-lib, ppx_hash.runtime-lib, ppx_here.runtime-lib, ppx_assert.runtime-lib, ppx_bench.runtime-lib, bin_prot, fieldslib, ppx_inline_test.config, ppx_inline_test.runtime-lib, ppx_module_timer.runtime, typerep, variantslib, ppx_expect.collector, ppx_expect.config, ppx_log.types, base_quickcheck.ppx_quickcheck.runtime, base_quickcheck

biocaml.unix

Documentation:

  • Biocaml_unix.Accu A datastructure (based on Hashtbl) to accumulate values.
  • Biocaml_unix.Bam Read and write BAM format.
  • Biocaml_unix.Bamstats
  • Biocaml_unix.Bar Affymetrix's BAR files. Their Tiling Analysis Software (TAS) produces BAR files in binary format but this module supports only the text format generated by selecting the "Export probe analysis as TXT" option.
  • Biocaml_unix.Bed BED data files.
  • Biocaml_unix.Bgzf I/O on Blocked GNU Zip format (BGZF) files
  • Biocaml_unix.Bin_pred Performance measurement of binary classifiers.
  • Biocaml_unix.Biocaml_result Extension of Core's Result. Internal use only.
  • Biocaml_unix.Bpmap Affymetrix's BPMAP files. Only text format supported. Binary BPMAP files must first be converted to text using Affymetrix's probe exporter tool.
  • Biocaml_unix.Cel Affymetrix's CEL files. Only text format supported. Binary file must be converted using Affymetrix's conversion tool. This tool does not change file extension, so be sure your file really is in text format.
  • Biocaml_unix.Chr Chromosome names. A chromosome name, as defined by this module, consists of two parts. An optional prefix "chr" (case-insensitive), followed by a suffix identifying the chromosome. The possible suffixes (case-insensitive) are:
  • Biocaml_unix.Entrez Entrez Utilities API
  • Biocaml_unix.Fasta FASTA files. The FASTA family of file formats has different incompatible descriptions (1, 2, 3, 4, etc.). Roughly FASTA files are in the format:
  • Biocaml_unix.Fastq FASTQ files. The FASTQ file format is repeated sequence of 4 lines:
  • Biocaml_unix.File_mapper
  • Biocaml_unix.Future
  • Biocaml_unix.Future_unix
  • Biocaml_unix.GenomeMap Data structures to represent sets of (possibly annotated) genomic regions
  • Biocaml_unix.Gff GFF files.
  • Biocaml_unix.Histogram Histograms with polymorphic bin types.
  • Biocaml_unix.Interval_tree Interval tree (data structure)
  • Biocaml_unix.Iset DIET : Discrete Interval Encoding Trees
  • Biocaml_unix.Jaspar Access to Jaspar database
  • Biocaml_unix.Line
  • Biocaml_unix.Lines Manipulate the lines of a file.
  • Biocaml_unix.Math Numeric mathematics.
  • Biocaml_unix.Msg Consistent printing of errors, warnings, and bugs. An error is a user mistake that prevents continuing program execution, a warning is a milder problem that the program continues to execute through, and a bug is a mistake in the software.
  • Biocaml_unix.MzData
  • Biocaml_unix.Phred_score PHRED quality scores.
  • Biocaml_unix.Pos File positions. A position within a file is defined by:
  • Biocaml_unix.Psl
  • Biocaml_unix.Pwm Position-weight matrix
  • Biocaml_unix.RSet Efficient integer sets when many elements expected to be large contiguous sequences of integers.
  • Biocaml_unix.Range Ranges of contiguous integers (integer intervals). A range is a contiguous sequence of integers from a lower bound to an upper bound. For example, [2, 10] is the set of integers from 2 through 10, inclusive of 2 and 10.
  • Biocaml_unix.Roman_num Roman numerals. Values greater than or equal to 1 are valid roman numerals.
  • Biocaml_unix.Sam SAM files. Documentation here assumes familiarity with the SAM specification.
  • Biocaml_unix.Sbml SBML file parser. Currently only level 2 version 4 is supported.
  • Biocaml_unix.Seq Nucleic acid sequences. A nucleic acid code is any of A, C, G, T, U, R, Y, K, M, S, W, B, D, H, V, N, or X. See IUB/IUPAC standards for further information. Gaps are not supported. Internal representation uses uppercase, but constructors are case-insensitive. By convention the first nucleic acid in a sequence is numbered 1.
  • Biocaml_unix.Seq_range Range on a sequence, where the sequence is represented by an identifier.
  • Biocaml_unix.Sgr Sequence Graph (SGR) files.
  • Biocaml_unix.Solexa_score Solexa quality scores.
  • Biocaml_unix.Strand Strand names. There are various conventions for referring to the two strands of DNA. This module provides an of_string function that parses the various conventions into a canonical representation, which we define to be '-' or '+'.
  • Biocaml_unix.Table Generic “tables” (like CSV, TSV, Bed …).
  • Biocaml_unix.Tfxm Buffered transforms. A buffered transform represents a method for converting a stream of inputs to a stream of outputs. However, inputs can also be buffered, i.e. you can feed inputs to the transform and pull out outputs later. There is no requirement that 1 input produces exactly 1 output. It is common that multiple input values are needed to construct a single output, and vice versa.
  • Biocaml_unix.Track Track files in UCSC Genome Browser format. The following documentation assumes knowledge of concepts explained on the UCSC Genome Browser's website. Basically, a track file is one of several types of data (WIG, GFF, etc.), possibly preceded by comments, browser lines, and a track line. This module allows only a single data track within a file, although the UCSC specifies that multiple tracks may be provided together.
  • Biocaml_unix.Transcripts Transcripts are integer intervals containing a list of exons. Exons are themselves defined as a list of integer intervals.
  • Biocaml_unix.Vcf Parsing of VCF files.
  • Biocaml_unix.Wig WIG data.
  • Biocaml_unix.Zip Streaming interface to the Zlib library.

Dependencies: base64, biocaml.base, zip, cfstream, core, core_kernel.binary_packing, re.perl, xmlm, ppx_expect.evaluator, ppx_sexp_conv.runtime-lib, sexplib0, ppx_compare.runtime-lib, ppx_enumerate.runtime-lib, ppx_hash.runtime-lib, ppx_here.runtime-lib, ppx_assert.runtime-lib, ppx_bench.runtime-lib, bin_prot, fieldslib, ppx_inline_test.config, ppx_inline_test.runtime-lib, ppx_module_timer.runtime, typerep, variantslib, ppx_expect.collector, ppx_expect.config, ppx_log.types, base_quickcheck.ppx_quickcheck.runtime, base_quickcheck