Uploaded v1.4.2. New user-defined m-value for FA correction.

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [1.4.2]
+### Changed
+- Now using user-defined formamide m-value for wright correction.
+
+## [1.4.0]
+### Added
+- New feature: formamide correction.
+
+## [1.3.0]
+### Added
+- New feature: temperature curve calculation. Proper fasta input.
+
+## [1.2.2]
+### Fixed
+- Allawi and Freier thermodynamic tables.
+
+## [1.2.1]
+### Fixed
+- Introduced Sugimoto (DNA:RNA) thermodynamic table.
+
+## [1.2.0]
+### Added
+- New feature: DNA/RNA and RNA/DNA duplex calculation.
+
+## [1.1.0]
+### Added
+- New input file mode.
+
+### Fixed
+- Mg2+ correction now skips Na+ correction.
+
+## [1.0.0]
+
+[1.4.2] https://github.com/ggirelli/oligo-melting/releases/tag/v1.4.2
+[1.4.0] https://github.com/ggirelli/oligo-melting
+[1.3.0] https://github.com/ggirelli/oligo-melting
+[1.2.2] https://github.com/ggirelli/oligo-melting
+[1.2.1] https://github.com/ggirelli/oligo-melting
+[1.2.0] https://github.com/ggirelli/oligo-melting
+[1.1.0] https://github.com/ggirelli/oligo-melting
+[1.0.0] https://github.com/ggirelli/oligo-melting

README.md

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+oligo-melting-temperature
+===
+
+The `oligomelt.py` script, implemented in Python, allows to calculate the melting temperature of a nucleic acid duplex, provided the sequence of one of the two strands.
+
+The hybridization delta free energy calculation is based on the N-N thermodynamic values in literature and is available for DNA:DNA[^3], RNA:RNA[^1] and DNA:RNA[^2] duplexes. The melting temperature calculation is based on Santalucia, 1998[^4]. Sodium and cagnesium concentration correction is based on the work of Owczarzy et al[^5][^6]. Formamide correction can be performed based on two different published models[^7][^8].
+
+* Use the `-t` option to specify the **type of nucleic acid duplex**.
+* Use `--fa-mode` to switch between linear melting temperature **formamide-based correction**[^7] and linear δG formamide-based correction[^8].
+* Use `--fa-mvalue` together with `--fa-mode wright` to specify the **m-value** for the formamide-based correction.
+* Use the `-F` option and providing the path to a **fasta file** instead of a single sequence, the melting temperature is automatically calculated for every sequence in the file.
+* Use the `-v` option to trigger the verbose mode, which provides more **details** for every single sequence.
+* Use `-C` for the temperature in **degree Celsius** instead of Kelvin.
+* Use `--out-curve` to specify a file where to save estimated single-sequence **melting curves** with temperature range and step around the melting temperature as defined with `--t-curve`.
+
+### Help page
+
+```
+usage: oligomelt.py [-h] [-t {DNA:DNA,RNA:RNA,RNA:DNA,DNA:RNA}]
+                    [-o oligo_conc] [-n na_conc] [-m mg_conc]
+                    [-f fa_conc] [--fa-mode fa_mode] [--fa-mvalue m]
+                    [--t-curve range step] [--out-curve outname]
+                    [-C] [-F] [-v]
+                    seq
+
+Calculate melting temeprature of a DNA duplex at provided [oligo],
+[Na+], [Mg2+]. Either provide an oligo sequence or a file with one oligo
+per line (and use -F option). References:
+ [1] Freier et al, PNAS(83), 1986;
+ [2] Sugimoto et al, Biochemistry(34), 1995.
+ [3] Allawi & Santalucia, Biochemistry(36), 1997;
+ [4] SantaLucia, PNAS(95), 1998;
+ [5] Owczarzy et al, Biochemistry(43), 2004;
+ [6] Owczarzy et al, Biochemistry(47), 2008;
+ [7] McConaughy et al, Biochemistry(8), 1969;
+ [8] Wright et al, Appl. env. microbiol.(80), 2014.
+
+positional arguments:
+  seq                   DNA duplex sequence (one strand only) or path to a
+                        FASTA file (use with -F).
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -t {DNA:DNA,RNA:RNA,RNA:DNA,DNA:RNA}, --type {DNA:DNA,RNA:RNA,RNA:DNA,DNA:RNA}
+                        Duplex type. Possible values: DNA:DNA (based on ref.3,
+                        default), RNA:RNA (based on ref.1), DNA:RNA (based on
+                        ref.2., given DNA sequence) or RNA:DNA (based on
+                        ref.2, given RNA sequence). The first nucleic acid
+                        type indicates the provided sequence.
+  -o oligo_conc, --oconc oligo_conc
+                        Oligonucleotide concentration [M]. Default: 0.25e-6 M
+  -n na_conc, --naconc na_conc
+                        Na+ concentration [M]. Default: 50e-3 M
+  -m mg_conc, --mgconc mg_conc
+                        Mg2+ concentration [M]. Note: Mg2+ correction
+                        overwrites Na+ correction. Default: 0 M
+  -f fa_conc, --faconc fa_conc
+                        Formamide concentration in %(v,v).
+  --fa-mode fa_mode     Mode of formamide correction. "mcconaughy" for
+                        classical -0.72%FA correction from ref. 7, "wright"
+                        for single reaction model correction from ref.8
+                        (default).
+  --fa-mvalue m         Specify the formamide m-value to be used with the
+                        wright correction model. Use either a single value "x"
+                        or two values "xL+y" where L is the probe length.
+                        Default: 0.1734
+  --t-curve range step  Temperature range and step for melting curve
+                        generation. Use --make-curve option to generate the
+                        curve. Default: 20 degC range and 0.5 degC step.
+  --out-curve outname   Path to output table containing tabulated curves.
+  -C, --celsius         Output temperature in Celsius degrees. Default: Kelvin
+  -F, --usefile         Use when a file path is provided instead of a single
+                        sequence.
+  -v, --verbose         Verbose output.
+```
+
+### References
+
+[^1]: Freier et al, PNAS(83), 1986;
+[^2]: Sugimoto et al, Biochemistry(34), 1995.
+[^3]: Allawi & Santalucia, Biochemistry(36), 1997;
+[^4]: SantaLucia, PNAS(95), 1998;
+[^5]: Owczarzy et al, Biochemistry(43), 2004;
+[^6]: Owczarzy et al, Biochemistry(47), 2008;
+[^7]: McConaughy et al, Biochemistry(8), 1969;
+[^8]: Wright et al, Appl. env. microbiol.(80), 2014.