sequence-formats (empty) → 1.1.4.1
raw patch · 10 files changed
+1396/−0 lines, 10 filesdep +MissingHdep +attoparsecdep +base
Dependencies added: MissingH, attoparsec, base, bytestring, containers, data-memocombinators, errors, exceptions, foldl, hslogger, lens-family, pipes, pipes-attoparsec, pipes-bytestring, pipes-safe, pipes-text, split, text, transformers, turtle, vector
Files
- Changelog.md +1/−0
- LICENSE +674/−0
- README.md +3/−0
- sequence-formats.cabal +48/−0
- src/SequenceFormats/Eigenstrat.hs +168/−0
- src/SequenceFormats/Fasta.hs +67/−0
- src/SequenceFormats/FreqSum.hs +109/−0
- src/SequenceFormats/RareAlleleHistogram.hs +116/−0
- src/SequenceFormats/Utils.hs +53/−0
- src/SequenceFormats/VCF.hs +157/−0
+ Changelog.md view
@@ -0,0 +1,1 @@+V 1.1.4.1: First entry in the Changelog. Added Haddock documentation to all modules and prepare for releasing on Hackage.
+ LICENSE view
@@ -0,0 +1,674 @@+ GNU GENERAL PUBLIC LICENSE+ Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++ Preamble++ The GNU General Public License is a free, copyleft license for+software and other kinds of works.++ The licenses for most software and other practical works are designed+to take away your freedom to share and change the works. By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users. We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors. You can apply it to+your programs, too.++ When we speak of free software, we are referring to freedom, not+price. Our General Public Licenses are designed to make sure that you+have the freedom to distribute copies of free software (and charge for+them if you wish), that you receive source code or can get it if you+want it, that you can change the software or use pieces of it in new+free programs, and that you know you can do these things.++ To protect your rights, we need to prevent others from denying you+these rights or asking you to surrender the rights. Therefore, you have+certain responsibilities if you distribute copies of the software, or if+you modify it: responsibilities to respect the freedom of others.++ For example, if you distribute copies of such a program, whether+gratis or for a fee, you must pass on to the recipients the same+freedoms that you received. You must make sure that they, too, receive+or can get the source code. And you must show them these terms so they+know their rights.++ Developers that use the GNU GPL protect your rights with two steps:+(1) assert copyright on the software, and (2) offer you this License+giving you legal permission to copy, distribute and/or modify it.++ For the developers' and authors' protection, the GPL clearly explains+that there is no warranty for this free software. For both users' and+authors' sake, the GPL requires that modified versions be marked as+changed, so that their problems will not be attributed erroneously to+authors of previous versions.++ Some devices are designed to deny users access to install or run+modified versions of the software inside them, although the manufacturer+can do so. This is fundamentally incompatible with the aim of+protecting users' freedom to change the software. The systematic+pattern of such abuse occurs in the area of products for individuals to+use, which is precisely where it is most unacceptable. Therefore, we+have designed this version of the GPL to prohibit the practice for those+products. If such problems arise substantially in other domains, we+stand ready to extend this provision to those domains in future versions+of the GPL, as needed to protect the freedom of users.++ Finally, every program is threatened constantly by software patents.+States should not allow patents to restrict development and use of+software on general-purpose computers, but in those that do, we wish to+avoid the special danger that patents applied to a free program could+make it effectively proprietary. To prevent this, the GPL assures that+patents cannot be used to render the program non-free.++ The precise terms and conditions for copying, distribution and+modification follow.++ TERMS AND CONDITIONS++ 0. Definitions.++ "This License" refers to version 3 of the GNU General Public License.++ "Copyright" also means copyright-like laws that apply to other kinds of+works, such as semiconductor masks.++ "The Program" refers to any copyrightable work licensed under this+License. Each licensee is addressed as "you". "Licensees" and+"recipients" may be individuals or organizations.++ To "modify" a work means to copy from or adapt all or part of the work+in a fashion requiring copyright permission, other than the making of an+exact copy. The resulting work is called a "modified version" of the+earlier work or a work "based on" the earlier work.++ A "covered work" means either the unmodified Program or a work based+on the Program.++ To "propagate" a work means to do anything with it that, without+permission, would make you directly or secondarily liable for+infringement under applicable copyright law, except executing it on a+computer or modifying a private copy. Propagation includes copying,+distribution (with or without modification), making available to the+public, and in some countries other activities as well.++ To "convey" a work means any kind of propagation that enables other+parties to make or receive copies. Mere interaction with a user through+a computer network, with no transfer of a copy, is not conveying.++ An interactive user interface displays "Appropriate Legal Notices"+to the extent that it includes a convenient and prominently visible+feature that (1) displays an appropriate copyright notice, and (2)+tells the user that there is no warranty for the work (except to the+extent that warranties are provided), that licensees may convey the+work under this License, and how to view a copy of this License. If+the interface presents a list of user commands or options, such as a+menu, a prominent item in the list meets this criterion.++ 1. Source Code.++ The "source code" for a work means the preferred form of the work+for making modifications to it. "Object code" means any non-source+form of a work.++ A "Standard Interface" means an interface that either is an official+standard defined by a recognized standards body, or, in the case of+interfaces specified for a particular programming language, one that+is widely used among developers working in that language.++ The "System Libraries" of an executable work include anything, other+than the work as a whole, that (a) is included in the normal form of+packaging a Major Component, but which is not part of that Major+Component, and (b) serves only to enable use of the work with that+Major Component, or to implement a Standard Interface for which an+implementation is available to the public in source code form. A+"Major Component", in this context, means a major essential component+(kernel, window system, and so on) of the specific operating system+(if any) on which the executable work runs, or a compiler used to+produce the work, or an object code interpreter used to run it.++ The "Corresponding Source" for a work in object code form means all+the source code needed to generate, install, and (for an executable+work) run the object code and to modify the work, including scripts to+control those activities. However, it does not include the work's+System Libraries, or general-purpose tools or generally available free+programs which are used unmodified in performing those activities but+which are not part of the work. For example, Corresponding Source+includes interface definition files associated with source files for+the work, and the source code for shared libraries and dynamically+linked subprograms that the work is specifically designed to require,+such as by intimate data communication or control flow between those+subprograms and other parts of the work.++ The Corresponding Source need not include anything that users+can regenerate automatically from other parts of the Corresponding+Source.++ The Corresponding Source for a work in source code form is that+same work.++ 2. Basic Permissions.++ All rights granted under this License are granted for the term of+copyright on the Program, and are irrevocable provided the stated+conditions are met. This License explicitly affirms your unlimited+permission to run the unmodified Program. The output from running a+covered work is covered by this License only if the output, given its+content, constitutes a covered work. This License acknowledges your+rights of fair use or other equivalent, as provided by copyright law.++ You may make, run and propagate covered works that you do not+convey, without conditions so long as your license otherwise remains+in force. You may convey covered works to others for the sole purpose+of having them make modifications exclusively for you, or provide you+with facilities for running those works, provided that you comply with+the terms of this License in conveying all material for which you do+not control copyright. Those thus making or running the covered works+for you must do so exclusively on your behalf, under your direction+and control, on terms that prohibit them from making any copies of+your copyrighted material outside their relationship with you.++ Conveying under any other circumstances is permitted solely under+the conditions stated below. Sublicensing is not allowed; section 10+makes it unnecessary.++ 3. Protecting Users' Legal Rights From Anti-Circumvention Law.++ No covered work shall be deemed part of an effective technological+measure under any applicable law fulfilling obligations under article+11 of the WIPO copyright treaty adopted on 20 December 1996, or+similar laws prohibiting or restricting circumvention of such+measures.++ When you convey a covered work, you waive any legal power to forbid+circumvention of technological measures to the extent such circumvention+is effected by exercising rights under this License with respect to+the covered work, and you disclaim any intention to limit operation or+modification of the work as a means of enforcing, against the work's+users, your or third parties' legal rights to forbid circumvention of+technological measures.++ 4. Conveying Verbatim Copies.++ You may convey verbatim copies of the Program's source code as you+receive it, in any medium, provided that you conspicuously and+appropriately publish on each copy an appropriate copyright notice;+keep intact all notices stating that this License and any+non-permissive terms added in accord with section 7 apply to the code;+keep intact all notices of the absence of any warranty; and give all+recipients a copy of this License along with the Program.++ You may charge any price or no price for each copy that you convey,+and you may offer support or warranty protection for a fee.++ 5. Conveying Modified Source Versions.++ You may convey a work based on the Program, or the modifications to+produce it from the Program, in the form of source code under the+terms of section 4, provided that you also meet all of these conditions:++ a) The work must carry prominent notices stating that you modified+ it, and giving a relevant date.++ b) The work must carry prominent notices stating that it is+ released under this License and any conditions added under section+ 7. This requirement modifies the requirement in section 4 to+ "keep intact all notices".++ c) You must license the entire work, as a whole, under this+ License to anyone who comes into possession of a copy. This+ License will therefore apply, along with any applicable section 7+ additional terms, to the whole of the work, and all its parts,+ regardless of how they are packaged. This License gives no+ permission to license the work in any other way, but it does not+ invalidate such permission if you have separately received it.++ d) If the work has interactive user interfaces, each must display+ Appropriate Legal Notices; however, if the Program has interactive+ interfaces that do not display Appropriate Legal Notices, your+ work need not make them do so.++ A compilation of a covered work with other separate and independent+works, which are not by their nature extensions of the covered work,+and which are not combined with it such as to form a larger program,+in or on a volume of a storage or distribution medium, is called an+"aggregate" if the compilation and its resulting copyright are not+used to limit the access or legal rights of the compilation's users+beyond what the individual works permit. Inclusion of a covered work+in an aggregate does not cause this License to apply to the other+parts of the aggregate.++ 6. Conveying Non-Source Forms.++ You may convey a covered work in object code form under the terms+of sections 4 and 5, provided that you also convey the+machine-readable Corresponding Source under the terms of this License,+in one of these ways:++ a) Convey the object code in, or embodied in, a physical product+ (including a physical distribution medium), accompanied by the+ Corresponding Source fixed on a durable physical medium+ customarily used for software interchange.++ b) Convey the object code in, or embodied in, a physical product+ (including a physical distribution medium), accompanied by a+ written offer, valid for at least three years and valid for as+ long as you offer spare parts or customer support for that product+ model, to give anyone who possesses the object code either (1) a+ copy of the Corresponding Source for all the software in the+ product that is covered by this License, on a durable physical+ medium customarily used for software interchange, for a price no+ more than your reasonable cost of physically performing this+ conveying of source, or (2) access to copy the+ Corresponding Source from a network server at no charge.++ c) Convey individual copies of the object code with a copy of the+ written offer to provide the Corresponding Source. This+ alternative is allowed only occasionally and noncommercially, and+ only if you received the object code with such an offer, in accord+ with subsection 6b.++ d) Convey the object code by offering access from a designated+ place (gratis or for a charge), and offer equivalent access to the+ Corresponding Source in the same way through the same place at no+ further charge. You need not require recipients to copy the+ Corresponding Source along with the object code. If the place to+ copy the object code is a network server, the Corresponding Source+ may be on a different server (operated by you or a third party)+ that supports equivalent copying facilities, provided you maintain+ clear directions next to the object code saying where to find the+ Corresponding Source. Regardless of what server hosts the+ Corresponding Source, you remain obligated to ensure that it is+ available for as long as needed to satisfy these requirements.++ e) Convey the object code using peer-to-peer transmission, provided+ you inform other peers where the object code and Corresponding+ Source of the work are being offered to the general public at no+ charge under subsection 6d.++ A separable portion of the object code, whose source code is excluded+from the Corresponding Source as a System Library, need not be+included in conveying the object code work.++ A "User Product" is either (1) a "consumer product", which means any+tangible personal property which is normally used for personal, family,+or household purposes, or (2) anything designed or sold for incorporation+into a dwelling. In determining whether a product is a consumer product,+doubtful cases shall be resolved in favor of coverage. For a particular+product received by a particular user, "normally used" refers to a+typical or common use of that class of product, regardless of the status+of the particular user or of the way in which the particular user+actually uses, or expects or is expected to use, the product. A product+is a consumer product regardless of whether the product has substantial+commercial, industrial or non-consumer uses, unless such uses represent+the only significant mode of use of the product.++ "Installation Information" for a User Product means any methods,+procedures, authorization keys, or other information required to install+and execute modified versions of a covered work in that User Product from+a modified version of its Corresponding Source. The information must+suffice to ensure that the continued functioning of the modified object+code is in no case prevented or interfered with solely because+modification has been made.++ If you convey an object code work under this section in, or with, or+specifically for use in, a User Product, and the conveying occurs as+part of a transaction in which the right of possession and use of the+User Product is transferred to the recipient in perpetuity or for a+fixed term (regardless of how the transaction is characterized), the+Corresponding Source conveyed under this section must be accompanied+by the Installation Information. But this requirement does not apply+if neither you nor any third party retains the ability to install+modified object code on the User Product (for example, the work has+been installed in ROM).++ The requirement to provide Installation Information does not include a+requirement to continue to provide support service, warranty, or updates+for a work that has been modified or installed by the recipient, or for+the User Product in which it has been modified or installed. Access to a+network may be denied when the modification itself materially and+adversely affects the operation of the network or violates the rules and+protocols for communication across the network.++ Corresponding Source conveyed, and Installation Information provided,+in accord with this section must be in a format that is publicly+documented (and with an implementation available to the public in+source code form), and must require no special password or key for+unpacking, reading or copying.++ 7. Additional Terms.++ "Additional permissions" are terms that supplement the terms of this+License by making exceptions from one or more of its conditions.+Additional permissions that are applicable to the entire Program shall+be treated as though they were included in this License, to the extent+that they are valid under applicable law. If additional permissions+apply only to part of the Program, that part may be used separately+under those permissions, but the entire Program remains governed by+this License without regard to the additional permissions.++ When you convey a copy of a covered work, you may at your option+remove any additional permissions from that copy, or from any part of+it. (Additional permissions may be written to require their own+removal in certain cases when you modify the work.) You may place+additional permissions on material, added by you to a covered work,+for which you have or can give appropriate copyright permission.++ Notwithstanding any other provision of this License, for material you+add to a covered work, you may (if authorized by the copyright holders of+that material) supplement the terms of this License with terms:++ a) Disclaiming warranty or limiting liability differently from the+ terms of sections 15 and 16 of this License; or++ b) Requiring preservation of specified reasonable legal notices or+ author attributions in that material or in the Appropriate Legal+ Notices displayed by works containing it; or++ c) Prohibiting misrepresentation of the origin of that material, or+ requiring that modified versions of such material be marked in+ reasonable ways as different from the original version; or++ d) Limiting the use for publicity purposes of names of licensors or+ authors of the material; or++ e) Declining to grant rights under trademark law for use of some+ trade names, trademarks, or service marks; or++ f) Requiring indemnification of licensors and authors of that+ material by anyone who conveys the material (or modified versions of+ it) with contractual assumptions of liability to the recipient, for+ any liability that these contractual assumptions directly impose on+ those licensors and authors.++ All other non-permissive additional terms are considered "further+restrictions" within the meaning of section 10. If the Program as you+received it, or any part of it, contains a notice stating that it is+governed by this License along with a term that is a further+restriction, you may remove that term. If a license document contains+a further restriction but permits relicensing or conveying under this+License, you may add to a covered work material governed by the terms+of that license document, provided that the further restriction does+not survive such relicensing or conveying.++ If you add terms to a covered work in accord with this section, you+must place, in the relevant source files, a statement of the+additional terms that apply to those files, or a notice indicating+where to find the applicable terms.++ Additional terms, permissive or non-permissive, may be stated in the+form of a separately written license, or stated as exceptions;+the above requirements apply either way.++ 8. Termination.++ You may not propagate or modify a covered work except as expressly+provided under this License. Any attempt otherwise to propagate or+modify it is void, and will automatically terminate your rights under+this License (including any patent licenses granted under the third+paragraph of section 11).++ However, if you cease all violation of this License, then your+license from a particular copyright holder is reinstated (a)+provisionally, unless and until the copyright holder explicitly and+finally terminates your license, and (b) permanently, if the copyright+holder fails to notify you of the violation by some reasonable means+prior to 60 days after the cessation.++ Moreover, your license from a particular copyright holder is+reinstated permanently if the copyright holder notifies you of the+violation by some reasonable means, this is the first time you have+received notice of violation of this License (for any work) from that+copyright holder, and you cure the violation prior to 30 days after+your receipt of the notice.++ Termination of your rights under this section does not terminate the+licenses of parties who have received copies or rights from you under+this License. If your rights have been terminated and not permanently+reinstated, you do not qualify to receive new licenses for the same+material under section 10.++ 9. Acceptance Not Required for Having Copies.++ You are not required to accept this License in order to receive or+run a copy of the Program. Ancillary propagation of a covered work+occurring solely as a consequence of using peer-to-peer transmission+to receive a copy likewise does not require acceptance. However,+nothing other than this License grants you permission to propagate or+modify any covered work. These actions infringe copyright if you do+not accept this License. Therefore, by modifying or propagating a+covered work, you indicate your acceptance of this License to do so.++ 10. Automatic Licensing of Downstream Recipients.++ Each time you convey a covered work, the recipient automatically+receives a license from the original licensors, to run, modify and+propagate that work, subject to this License. You are not responsible+for enforcing compliance by third parties with this License.++ An "entity transaction" is a transaction transferring control of an+organization, or substantially all assets of one, or subdividing an+organization, or merging organizations. If propagation of a covered+work results from an entity transaction, each party to that+transaction who receives a copy of the work also receives whatever+licenses to the work the party's predecessor in interest had or could+give under the previous paragraph, plus a right to possession of the+Corresponding Source of the work from the predecessor in interest, if+the predecessor has it or can get it with reasonable efforts.++ You may not impose any further restrictions on the exercise of the+rights granted or affirmed under this License. For example, you may+not impose a license fee, royalty, or other charge for exercise of+rights granted under this License, and you may not initiate litigation+(including a cross-claim or counterclaim in a lawsuit) alleging that+any patent claim is infringed by making, using, selling, offering for+sale, or importing the Program or any portion of it.++ 11. Patents.++ A "contributor" is a copyright holder who authorizes use under this+License of the Program or a work on which the Program is based. The+work thus licensed is called the contributor's "contributor version".++ A contributor's "essential patent claims" are all patent claims+owned or controlled by the contributor, whether already acquired or+hereafter acquired, that would be infringed by some manner, permitted+by this License, of making, using, or selling its contributor version,+but do not include claims that would be infringed only as a+consequence of further modification of the contributor version. For+purposes of this definition, "control" includes the right to grant+patent sublicenses in a manner consistent with the requirements of+this License.++ Each contributor grants you a non-exclusive, worldwide, royalty-free+patent license under the contributor's essential patent claims, to+make, use, sell, offer for sale, import and otherwise run, modify and+propagate the contents of its contributor version.++ In the following three paragraphs, a "patent license" is any express+agreement or commitment, however denominated, not to enforce a patent+(such as an express permission to practice a patent or covenant not to+sue for patent infringement). To "grant" such a patent license to a+party means to make such an agreement or commitment not to enforce a+patent against the party.++ If you convey a covered work, knowingly relying on a patent license,+and the Corresponding Source of the work is not available for anyone+to copy, free of charge and under the terms of this License, through a+publicly available network server or other readily accessible means,+then you must either (1) cause the Corresponding Source to be so+available, or (2) arrange to deprive yourself of the benefit of the+patent license for this particular work, or (3) arrange, in a manner+consistent with the requirements of this License, to extend the patent+license to downstream recipients. "Knowingly relying" means you have+actual knowledge that, but for the patent license, your conveying the+covered work in a country, or your recipient's use of the covered work+in a country, would infringe one or more identifiable patents in that+country that you have reason to believe are valid.++ If, pursuant to or in connection with a single transaction or+arrangement, you convey, or propagate by procuring conveyance of, a+covered work, and grant a patent license to some of the parties+receiving the covered work authorizing them to use, propagate, modify+or convey a specific copy of the covered work, then the patent license+you grant is automatically extended to all recipients of the covered+work and works based on it.++ A patent license is "discriminatory" if it does not include within+the scope of its coverage, prohibits the exercise of, or is+conditioned on the non-exercise of one or more of the rights that are+specifically granted under this License. You may not convey a covered+work if you are a party to an arrangement with a third party that is+in the business of distributing software, under which you make payment+to the third party based on the extent of your activity of conveying+the work, and under which the third party grants, to any of the+parties who would receive the covered work from you, a discriminatory+patent license (a) in connection with copies of the covered work+conveyed by you (or copies made from those copies), or (b) primarily+for and in connection with specific products or compilations that+contain the covered work, unless you entered into that arrangement,+or that patent license was granted, prior to 28 March 2007.++ Nothing in this License shall be construed as excluding or limiting+any implied license or other defenses to infringement that may+otherwise be available to you under applicable patent law.++ 12. No Surrender of Others' Freedom.++ If conditions are imposed on you (whether by court order, agreement or+otherwise) that contradict the conditions of this License, they do not+excuse you from the conditions of this License. If you cannot convey a+covered work so as to satisfy simultaneously your obligations under this+License and any other pertinent obligations, then as a consequence you may+not convey it at all. For example, if you agree to terms that obligate you+to collect a royalty for further conveying from those to whom you convey+the Program, the only way you could satisfy both those terms and this+License would be to refrain entirely from conveying the Program.++ 13. Use with the GNU Affero General Public License.++ Notwithstanding any other provision of this License, you have+permission to link or combine any covered work with a work licensed+under version 3 of the GNU Affero General Public License into a single+combined work, and to convey the resulting work. The terms of this+License will continue to apply to the part which is the covered work,+but the special requirements of the GNU Affero General Public License,+section 13, concerning interaction through a network will apply to the+combination as such.++ 14. Revised Versions of this License.++ The Free Software Foundation may publish revised and/or new versions of+the GNU General Public License from time to time. Such new versions will+be similar in spirit to the present version, but may differ in detail to+address new problems or concerns.++ Each version is given a distinguishing version number. If the+Program specifies that a certain numbered version of the GNU General+Public License "or any later version" applies to it, you have the+option of following the terms and conditions either of that numbered+version or of any later version published by the Free Software+Foundation. If the Program does not specify a version number of the+GNU General Public License, you may choose any version ever published+by the Free Software Foundation.++ If the Program specifies that a proxy can decide which future+versions of the GNU General Public License can be used, that proxy's+public statement of acceptance of a version permanently authorizes you+to choose that version for the Program.++ Later license versions may give you additional or different+permissions. However, no additional obligations are imposed on any+author or copyright holder as a result of your choosing to follow a+later version.++ 15. Disclaimer of Warranty.++ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.++ 16. Limitation of Liability.++ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF+SUCH DAMAGES.++ 17. Interpretation of Sections 15 and 16.++ If the disclaimer of warranty and limitation of liability provided+above cannot be given local legal effect according to their terms,+reviewing courts shall apply local law that most closely approximates+an absolute waiver of all civil liability in connection with the+Program, unless a warranty or assumption of liability accompanies a+copy of the Program in return for a fee.++ END OF TERMS AND CONDITIONS++ How to Apply These Terms to Your New Programs++ If you develop a new program, and you want it to be of the greatest+possible use to the public, the best way to achieve this is to make it+free software which everyone can redistribute and change under these terms.++ To do so, attach the following notices to the program. It is safest+to attach them to the start of each source file to most effectively+state the exclusion of warranty; and each file should have at least+the "copyright" line and a pointer to where the full notice is found.++ <one line to give the program's name and a brief idea of what it does.>+ Copyright (C) <year> <name of author>++ 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 3 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, see <http://www.gnu.org/licenses/>.++Also add information on how to contact you by electronic and paper mail.++ If the program does terminal interaction, make it output a short+notice like this when it starts in an interactive mode:++ <program> Copyright (C) <year> <name of author>+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.+ This is free software, and you are welcome to redistribute it+ under certain conditions; type `show c' for details.++The hypothetical commands `show w' and `show c' should show the appropriate+parts of the General Public License. Of course, your program's commands+might be different; for a GUI interface, you would use an "about box".++ You should also get your employer (if you work as a programmer) or school,+if any, to sign a "copyright disclaimer" for the program, if necessary.+For more information on this, and how to apply and follow the GNU GPL, see+<http://www.gnu.org/licenses/>.++ The GNU General Public License does not permit incorporating your program+into proprietary programs. If your program is a subroutine library, you+may consider it more useful to permit linking proprietary applications with+the library. If this is what you want to do, use the GNU Lesser General+Public License instead of this License. But first, please read+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+ README.md view
@@ -0,0 +1,3 @@+Sequence-Formats is a Haskell package to provide file parsers and writers for some commonly, and less commonly used file formats in Bioinformatics, speficially population genetics.++The library makes heavy use of the [pipes library](http://hackage.haskell.org/package/pipes) to provide Producers and Consumers for reading and writing files.
+ sequence-formats.cabal view
@@ -0,0 +1,48 @@+cabal-version: >=1.10+name: sequence-formats+version: 1.1.4.1+license: GPL-3+license-file: LICENSE+maintainer: stephan.schiffels@mac.com+author: Stephan Schiffels+synopsis: A package with basic parsing utilities for several Bioinformatic data formats.+description:+ Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF and other file formats used in population genetics analyses.+category: Bioinformatics+build-type: Simple+extra-source-files:+ README.md+ Changelog.md++library+ exposed-modules:+ SequenceFormats.RareAlleleHistogram+ SequenceFormats.FreqSum+ SequenceFormats.Fasta+ SequenceFormats.VCF+ SequenceFormats.Eigenstrat+ SequenceFormats.Utils+ hs-source-dirs: src+ default-language: Haskell2010+ build-depends:+ base >=4.7 && <5,+ containers >=0.5.10.2 && <0.6,+ errors >=2.2.2 && <2.3,+ text >=1.2.2.2 && <1.3,+ attoparsec >=0.13.2.2 && <0.14,+ pipes >=4.3.7 && <4.4,+ pipes-text >=0.0.2.5 && <0.1,+ transformers >=0.5.2.0 && <0.6,+ turtle >=1.4.5 && <1.5,+ bytestring >=0.10.8.2 && <0.11,+ lens-family >=1.2.2 && <1.3,+ pipes-bytestring >=2.1.6 && <2.2,+ foldl >=1.3.7 && <1.4,+ exceptions >=0.8.3 && <0.9,+ pipes-safe >=2.2.6 && <2.3,+ pipes-attoparsec >=0.5.1.5 && <0.6,+ vector >=0.12.0.1 && <0.13,+ data-memocombinators >=0.5.1 && <0.6,+ split >=0.2.3.3 && <0.3,+ MissingH >=1.4.0.1 && <1.5,+ hslogger >=1.2.10 && <1.3
+ src/SequenceFormats/Eigenstrat.hs view
@@ -0,0 +1,168 @@+{-# LANGUAGE OverloadedStrings #-}++{-|Module to read and parse Eigenstrat-formatted genotype data. The Eigenstrat format is defined at <https://github.com/argriffing/eigensoft/blob/master/CONVERTF/README>.++-}++module SequenceFormats.Eigenstrat (EigenstratSnpEntry(..), EigenstratIndEntry(..), + readEigenstratInd, GenoEntry(..), GenoLine, Sex(..), + readEigenstratSnpStdIn, readEigenstratSnpFile, readEigenstrat, writeEigenstrat) where++import SequenceFormats.Utils (consumeProducer, FormatException(..), Chrom(..))++import Control.Applicative ((<|>))+import Control.Monad (void, forM_)+import Control.Monad.Catch (MonadThrow, throwM)+import Control.Monad.IO.Class (MonadIO, liftIO)+import qualified Data.Attoparsec.Text as A+import Data.Char (isSpace)+import Data.Vector (Vector, fromList, toList)+import qualified Data.Text as T+import qualified Data.Text.IO as T+import Pipes (Producer, Pipe, (>->), for, cat, yield, Consumer)+import Pipes.Safe (MonadSafe)+import qualified Pipes.Prelude as P+import qualified Pipes.Text.IO as PT+import System.IO (withFile, IOMode(..))+import Turtle (format, w, d, (%), s)++-- |A datatype to represent a single genomic SNP. The constructor arguments are:+-- Chromosome, Position, Reference Allele, Alternative Allele.+data EigenstratSnpEntry = EigenstratSnpEntry Chrom Int Char Char deriving (Eq, Show)++-- |A datatype to represent a single individual. The constructor arguments are:+-- Name, Sex and Population Name+data EigenstratIndEntry = EigenstratIndEntry T.Text Sex T.Text deriving (Show)++-- |A datatype to represent Sex in an Eigenstrat Individual file+data Sex = Male | Female | Unknown deriving (Show)++-- |A datatype to represent the genotype of an individual at a SNP.+data GenoEntry = HomRef | Het | HomAlt | Missing deriving (Eq, Show)++-- |Vector of the genotypes of all individuals at a single SNP.+type GenoLine = Vector GenoEntry++eigenstratSnpParser :: A.Parser EigenstratSnpEntry+eigenstratSnpParser = do+ A.skipMany A.space+ void word+ A.skipMany1 A.space+ chrom <- word+ A.skipMany1 A.space+ void word+ A.skipMany1 A.space+ pos <- A.decimal+ A.skipMany1 A.space+ ref <- A.satisfy (A.inClass "ACTGN")+ A.skipMany1 A.space+ alt <- A.satisfy (A.inClass "ACTGX")+ void A.endOfLine+ return $ EigenstratSnpEntry (Chrom chrom) pos ref alt++word :: A.Parser T.Text+word = A.takeTill isSpace++eigenstratIndParser :: A.Parser EigenstratIndEntry+eigenstratIndParser = do+ A.skipMany A.space+ name <- word+ A.skipMany1 A.space+ sex <- parseSex+ A.skipMany1 A.space+ popName <- word+ void A.endOfLine+ return $ EigenstratIndEntry name sex popName++parseSex :: A.Parser Sex+parseSex = parseMale <|> parseFemale <|> parseUnknown+ where+ parseMale = A.char 'M' >> return Male+ parseFemale = A.char 'F' >> return Female+ parseUnknown = A.char 'U' >> return Unknown++-- |Function to read an Eigenstrat individual file. Returns the Eigenstrat Individual Entries as list.+readEigenstratInd :: (MonadIO m) => FilePath -> m [EigenstratIndEntry]+readEigenstratInd fn = do+ liftIO . withFile fn ReadMode $ \handle -> do+ P.toListM $ consumeProducer eigenstratIndParser (PT.fromHandle handle)++eigenstratGenoParser :: A.Parser GenoLine+eigenstratGenoParser = do+ line <- A.takeWhile1 isValidNum+ void A.endOfLine+ return . fromList $ do+ l <- T.unpack line+ case l of+ '0' -> return HomAlt+ '1' -> return Het+ '2' -> return HomRef+ '9' -> return Missing+ _ -> error "this should never happen"+ where+ isValidNum c = c == '0' || c == '1' || c == '2' || c == '9'++-- |Function to read a Snp File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.+readEigenstratSnpStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()+readEigenstratSnpStdIn = consumeProducer eigenstratSnpParser PT.stdin++-- |Function to read a Snp File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.+readEigenstratSnpFile :: (MonadSafe m) => FilePath -> Producer EigenstratSnpEntry m ()+readEigenstratSnpFile = consumeProducer eigenstratSnpParser . PT.readFile++-- |Function to read a full Eigenstrat database from files. Returns a pair of the Eigenstrat Individual Entries, and a joint Producer over the snp entries and the genotypes.+readEigenstrat :: (MonadSafe m) => FilePath -- ^The Genotype file+ -> FilePath -- ^The Snp File+ -> FilePath -- ^The Ind file+ -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ()) -- The return pair of individual entries and a joint Snp/Geno Producer.+readEigenstrat genoFile snpFile indFile = do+ indEntries <- readEigenstratInd indFile+ let snpProd = readEigenstratSnpFile snpFile+ genoProd = consumeProducer eigenstratGenoParser (PT.readFile genoFile) >-> + validateEigenstratEntries (length indEntries)+ return (indEntries, P.zip snpProd genoProd)++validateEigenstratEntries :: (MonadThrow m) => Int -> Pipe GenoLine GenoLine m ()+validateEigenstratEntries nr = for cat $ \line -> do+ if length line /= nr+ then do+ let msg = format ("inconsistent nr of genotypes ("%d%", but should be "%d%") in \+ \genotype line "%w) (length line) nr line+ throwM $ FormatException msg+ else+ yield line++-- |Function to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines.+writeEigenstrat :: (MonadSafe m) => FilePath -- ^The Genotype file+ -> FilePath -- ^The Snp File+ -> FilePath -- ^The Ind file+ -> [EigenstratIndEntry] -- ^The list of individual entries+ -> Consumer (EigenstratSnpEntry, GenoLine) m () -- ^A consumer to read joint Snp/Genotype entries.+writeEigenstrat genoFile snpFile indFile indEntries = do+ liftIO $ writeEigenstratIndFile indFile indEntries+ let snpOutTextConsumer = PT.writeFile snpFile+ genoOutTextConsumer = PT.writeFile genoFile+ toTextPipe = P.map (\(EigenstratSnpEntry chrom pos ref alt, genoLine) ->+ let n = format (s%"_"%d) (unChrom chrom) pos+ snpLine = format (s%"\t"%s%"\t0\t"%d%"\t"%s%"\t"%s%"\n") n (unChrom chrom) pos+ (T.singleton ref) (T.singleton alt)+ genoLineStr = T.concat . map (format d . toEigenStratNum) . toList $ genoLine+ in (snpLine, format (s%"\n") genoLineStr))+ toTextPipe >-> P.tee (P.map fst >-> snpOutTextConsumer) >-> P.map snd >-> genoOutTextConsumer+ where+ toEigenStratNum c = case c of+ HomRef -> 2 :: Int+ Het -> 1+ HomAlt -> 0+ Missing -> 9++writeEigenstratIndFile :: (MonadIO m) => FilePath -> [EigenstratIndEntry] -> m ()+writeEigenstratIndFile f indEntries = do+ liftIO . withFile f WriteMode $ \h -> do+ forM_ indEntries $ \(EigenstratIndEntry name sex popName) -> do+ liftIO . T.hPutStrLn h $ format (s%"\t"%s%"\t"%s) name (sexToStr sex) popName+ where+ sexToStr sex = case sex of+ Male -> "M"+ Female -> "F"+ Unknown -> "U"
+ src/SequenceFormats/Fasta.hs view
@@ -0,0 +1,67 @@+{-# LANGUAGE OverloadedStrings #-}++{-| Module to read and parse through a Fasta file. The Fasta format is defined here:+<https://en.wikipedia.org/wiki/FASTA_format>+-}+module SequenceFormats.Fasta (readNextFastaEntry, loadFastaChrom) where++import SequenceFormats.Utils (Chrom(..))++import Control.Exception.Base (throwIO, AssertionFailed(..))+import Control.Monad (void)+import Control.Monad.IO.Class (liftIO, MonadIO)+import Control.Monad.Trans.State.Strict (runStateT)+import qualified Data.Attoparsec.ByteString.Char8 as A+import qualified Data.ByteString.Char8 as B+import Data.Char (isAlphaNum)+import qualified Data.Text as T+import Lens.Family2 (view)+import Pipes (Producer, next, (>->), runEffect)+import Pipes.Attoparsec (parse)+import qualified Pipes.ByteString as P+import Pipes.Prelude (drain)+import System.IO (Handle)+import Turtle.Format (format, (%), s)+import Turtle.Prelude (err)+import Turtle.Line (unsafeTextToLine)++-- |A function to select out a specific chromosome from a Fasta File. Expects a file handle to the +-- file and a chromosome. Note that by Chromosome I simply denote a fasta header line, as is the +-- case for example for the human reference genome. Returns a Bytestring-Producer over the single sequence followed the specified header (the chromosome).+loadFastaChrom :: Handle -> Chrom -> IO (Producer B.ByteString IO ())+loadFastaChrom refFileHandle chrom = do+ let prod = P.fromHandle refFileHandle+ go prod+ where+ go prod = do+ (chrom_, prod') <- readNextFastaEntry prod+ err . unsafeTextToLine $ format ("found chromosome "%s) (unChrom chrom_)+ if chrom_ == chrom+ then return (void prod')+ else do+ newProd <- runEffect $ prod' >-> drain+ go newProd++-- |This function takes a Bytestring-Producer over a Fasta-file, reads in the first header and then returns a produer over its sequence. The return of that producer is the Bytestring-Producer of the rest of the fasta file.+readNextFastaEntry :: (MonadIO m) => Producer B.ByteString m () ->+ m (Chrom, Producer B.ByteString m (Producer B.ByteString m ()))+readNextFastaEntry prod = do+ (res, rest) <- runStateT (parse fastaHeaderLineParser) prod+ header <- case res of+ Nothing -> liftIO . throwIO $ AssertionFailed "Could not find chromosome. Fasta file exhausted."+ Just (Left e_) -> do+ Right (chunk, _) <- next rest+ let msg = show e_ ++ B.unpack chunk+ liftIO . throwIO $ AssertionFailed ("Fasta header parsing error: " ++ msg)+ Just (Right h) -> return h+ return (header, view (P.break (==62)) rest >-> P.filter (\c -> c /= 10 && c /= 13))+-- '>' == 62, '\n' == 10, \r == 13++fastaHeaderLineParser :: A.Parser Chrom+fastaHeaderLineParser = do+ _ <- A.char '>'+ chrom <- A.takeWhile isAlphaNum+ A.skipSpace+ A.skipWhile (\c -> c /= '\n' && c /= '\r')+ A.endOfLine+ return . Chrom . T.pack . B.unpack $ chrom
+ src/SequenceFormats/FreqSum.hs view
@@ -0,0 +1,109 @@+{-# LANGUAGE OverloadedStrings #-}++{-| Module to parse and write freqSum files. The freqsum format is defined here:+<https://rarecoal-docs.readthedocs.io/en/latest/rarecoal-tools.html#vcf2freqsum>+-}++module SequenceFormats.FreqSum (readFreqSumStdIn, readFreqSumFile, FreqSumEntry(..), + FreqSumHeader(..), printFreqSumStdOut, printFreqSumFile, freqSumEntryToText) where++import SequenceFormats.Utils (consumeProducer, Chrom(..))++import Control.Applicative ((<|>))+import Control.Monad.Catch (MonadThrow, throwM)+import Control.Monad.IO.Class (MonadIO, liftIO)+import Control.Monad.Trans.State.Strict (runStateT)+import qualified Data.Attoparsec.Text as A+import Data.Char (isAlphaNum, isSpace)+import Data.Text (Text, intercalate, singleton)+import Data.Text.IO (putStr, hPutStr)+import Pipes (Producer, (>->), Consumer)+import Pipes.Attoparsec (parse, ParsingError(..))+import qualified Pipes.Prelude as P+import Pipes.Safe (MonadSafe)+import Pipes.Safe.Prelude (withFile)+import qualified Pipes.Text.IO as PT+import Prelude hiding (putStr)+import System.IO (IOMode(..))+import Turtle (format, s, d, (%))++-- |A Datatype representing the Header+data FreqSumHeader = FreqSumHeader {+ fshNames :: [Text], -- ^A list of individual or group names+ fshCounts :: [Int] -- ^A list of haplotype counts per individual/group.+} deriving (Eq)++freqSumHeaderToText :: FreqSumHeader -> Text+freqSumHeaderToText (FreqSumHeader names nCounts) =+ format ("#CHROM\tPOS\tREF\tALT\t"%s%"\n") (intercalate "\t" tuples)+ where+ tuples = zipWith (\n c -> format (s%"("%d%")") n c) names nCounts++-- |A Datatype to denote a single freqSum line+data FreqSumEntry = FreqSumEntry {+ fsChrom :: Chrom, -- ^The chromosome of the site+ fsPos :: Int, -- ^The position of the site+ fsRef :: Char, -- ^The reference allele+ fsAlt :: Char, -- ^The alternative allele+ fsCounts :: [Maybe Int] -- ^A list of allele counts in each group. Nothing denotes missing data.+}++-- |This function converts a single freqSum entry to a printable freqSum line.+freqSumEntryToText :: FreqSumEntry -> Text+freqSumEntryToText (FreqSumEntry chrom pos ref alt maybeCounts) =+ format (s%"\t"%d%"\t"%s%"\t"%s%"\t"%s%"\n") (unChrom chrom) pos (singleton ref) (singleton alt) + countStr + where+ countStr = intercalate "\t" . map (format d . convertToNum) $ maybeCounts + convertToNum Nothing = -1+ convertToNum (Just a) = a++readFreqSumProd :: (MonadThrow m) =>+ Producer Text m () -> m (FreqSumHeader, Producer FreqSumEntry m ())+readFreqSumProd prod = do+ (res, rest) <- runStateT (parse parseFreqSumHeader) prod+ header <- case res of+ Nothing -> throwM $ ParsingError [] "freqSum file exhausted"+ Just (Left e) -> throwM e+ Just (Right h) -> return h+ return (header, consumeProducer parseFreqSumEntry rest)++-- |A function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.+readFreqSumStdIn :: (MonadIO m, MonadThrow m) => m (FreqSumHeader, Producer FreqSumEntry m ())+readFreqSumStdIn = readFreqSumProd PT.stdin++-- |A function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.+readFreqSumFile :: (MonadSafe m) => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ())+readFreqSumFile = readFreqSumProd . PT.readFile++parseFreqSumHeader :: A.Parser FreqSumHeader+parseFreqSumHeader = do+ tuples <- A.string "#CHROM\tPOS\tREF\tALT\t" >> A.sepBy' tuple A.space <* A.endOfLine+ let names = map fst tuples+ counts = map snd tuples+ return $ FreqSumHeader names counts+ where+ tuple = (,) <$> A.takeWhile (\c -> isAlphaNum c || c == '_' || c == '-') <* A.char '(' <*> A.decimal <* A.char ')'++parseFreqSumEntry :: A.Parser FreqSumEntry+parseFreqSumEntry = FreqSumEntry <$> (Chrom <$> A.takeTill isSpace) <* A.skipSpace <*> A.decimal <*+ A.skipSpace <*> base <* A.skipSpace <*> baseOrDot <* A.skipSpace <*> counts <* A.endOfLine+ where+ counts = (parseMissing <|> parseCount) `A.sepBy` A.char '\t'+ parseMissing = A.string "-1" *> pure Nothing+ parseCount = Just <$> A.decimal+ base = A.satisfy (A.inClass "ACTGN")+ baseOrDot = A.satisfy (A.inClass "ACTG.")++-- |A function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.+printFreqSumStdOut :: (MonadIO m) => FreqSumHeader -> Consumer FreqSumEntry m ()+printFreqSumStdOut fsh = do+ liftIO . putStr . freqSumHeaderToText $ fsh+ P.map freqSumEntryToText >-> PT.stdout++-- |A function that writes a freqSum file. Expects the FilePath and the freqSum header as arguments, and then returns a Consumer that accepts freqSum entries.+printFreqSumFile :: (MonadSafe m) => FilePath -> FreqSumHeader -> Consumer FreqSumEntry m ()+printFreqSumFile outFile fsh = do+ outFileH <- withFile outFile WriteMode return+ liftIO . hPutStr outFileH . freqSumHeaderToText $ fsh+ P.map freqSumEntryToText >-> PT.toHandle outFileH
+ src/SequenceFormats/RareAlleleHistogram.hs view
@@ -0,0 +1,116 @@+{-# LANGUAGE OverloadedStrings #-}++{-| A module to read and write allele sharing histograms, as defined here:+<https://rarecoal-docs.readthedocs.io/en/latest/rarecoal.html#histogram-files>+-}++module SequenceFormats.RareAlleleHistogram (RareAlleleHistogram(..), readHistogramFromHandle,+ SitePattern, readHistogram, showHistogram, showSitePattern) where++import Control.Applicative (optional)+import Control.Error (Script, scriptIO, assertErr, throwE)+import Control.Monad.Trans.State.Strict (evalStateT)+import qualified Data.Attoparsec.Text as A+import Data.Char (isAlphaNum)+import Data.Int (Int64)+import Data.List (intercalate, sortBy)+import qualified Data.Map.Strict as Map+import qualified Data.Text as T+import Pipes.Attoparsec (parse)+import qualified Pipes.Text.IO as PT+import System.IO (Handle, openFile, IOMode(..), hClose)+import Turtle.Format ((%), w, format)++-- |A datatype to represent an Allele Sharing Histogram:+data RareAlleleHistogram = RareAlleleHistogram {+ raNames :: [T.Text], -- ^A list of branch names+ raNVec :: [Int], -- ^A list of haploid sample sizes.+ raMinAf :: Int, -- ^The minimum allele count+ raMaxAf :: Int, -- ^The maximum allele count+ raConditionOn :: [Int], -- ^A list of branch indices that were used to condition the allele + --sharing pattern+ raExcludePatterns :: [SitePattern], -- ^A list of patterns that are excluded.+ raTotalNrSites :: Int64, -- ^The total number of non-missing sites in the genome.+ raCounts :: Map.Map SitePattern Int64, -- ^The actual data, a dictionary from allele sharing patterns to observed numbers.+ raJackknifeEstimates :: Maybe (Map.Map SitePattern (Double, Double)) -- ^An optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency.+}++-- |A simple type synonym for the SitePattern, represented as a list of Integers that represents +-- each pattern across the branches.+type SitePattern = [Int]++-- |A simple function to convert a pattern into a String.+showSitePattern :: SitePattern -> String+showSitePattern nVec = intercalate "," . map show $ nVec++-- |Function to convert a Rare Allele Histogram to text. Returns an error if attempting to print a +-- histogram with non-standard settings. Many settings, such as minAf>1, are only meant for +-- in-memory representations, but are not compatible with the file format itself.+showHistogram :: RareAlleleHistogram -> Either T.Text T.Text+showHistogram hist = do+ assertErr "can only print histogram with minAf=1 due to format-legacy" $ raMinAf hist == 1+ assertErr "can only print histogram with no conditioning due to format-legacy" $+ null (raConditionOn hist)+ assertErr "can only print histogram with no exclude pattern due to format-legacy" $+ null (raExcludePatterns hist)+ let head0 = T.concat ["NAMES=", T.intercalate "," . raNames $ hist]+ head1 = T.concat ["N=", T.pack . intercalate "," . map show . raNVec $ hist]+ head2 = T.concat ["MAX_M=", T.pack . show . raMaxAf $ hist]+ head3 = T.concat ["TOTAL_SITES=", T.pack . show . raTotalNrSites $ hist]+ body = do+ (k, v) <- sorted+ case raJackknifeEstimates hist of+ Nothing -> [T.intercalate " " [T.pack . showSitePattern $ k, T.pack . show $ v]]+ Just jkHist -> do+ let Just (jkMean, jkSE) = k `Map.lookup` jkHist+ return $ T.intercalate " " [T.pack . showSitePattern $ k, T.pack . show $ v,+ T.pack . show $ jkMean, T.pack . show $ jkSE]+ return $ T.unlines (head0:head1:head2:head3:body)+ where+ sorted = sortBy (\(_, v1) (_, v2) -> compare v2 v1) $ Map.toList (raCounts hist)++-- |Read a histogram from a FilePath+readHistogram :: FilePath -> Script RareAlleleHistogram+readHistogram path = do+ h <- scriptIO $ openFile path ReadMode+ hist <- readHistogramFromHandle h+ scriptIO $ hClose h+ return hist++-- |Read a histogram from a File Handle.+readHistogramFromHandle :: Handle -> Script RareAlleleHistogram+readHistogramFromHandle handle = do+ res <- evalStateT (parse parseHistogram) . PT.fromHandle $ handle+ case res of+ Nothing -> throwE "histogram file exhausted too early"+ Just (Left err) -> throwE $ format ("Histogram parsing error: "%w) err+ Just (Right hist) -> return hist++parseHistogram :: A.Parser RareAlleleHistogram+parseHistogram = do+ names <- parseNames+ nVec <- parseNVec+ maxM <- parseMaxM+ totalNrSites <- parseTotalNrSites+ body <- parseBody+ let countHist = Map.fromList $ [(k, c) | (k, c, _) <- body]+ jkHist = case head body of+ (_, _, Just _) -> Just . Map.fromList $ [(k, (jkMean, jkSE)) |+ (k, _, Just (jkMean, jkSE)) <- body]+ _ -> Nothing+ return $ RareAlleleHistogram names nVec 1 maxM [][] totalNrSites countHist jkHist+ where+ parseNames = A.string "NAMES=" *> name `A.sepBy1` A.char ',' <* A.endOfLine+ name = A.takeWhile1 (\c -> isAlphaNum c || c == '_' || c == '-')+ parseNVec = A.string "N=" *> A.decimal `A.sepBy1` A.char ',' <* A.endOfLine+ parseMaxM = A.string "MAX_M=" *> A.decimal <* A.endOfLine+ parseTotalNrSites = A.string "TOTAL_SITES=" *> A.decimal <* A.endOfLine++parseBody :: A.Parser [(SitePattern, Int64, Maybe (Double, Double))]+parseBody = A.many1 patternLine+ where+ patternLine = (,,) <$> parsePattern <* A.space <*> parseLargeInt <*> optional parseJackknife <*+ A.endOfLine+ parsePattern = A.decimal `A.sepBy1` A.char ','+ parseLargeInt = read <$> A.many1 A.digit+ parseJackknife = (,) <$> (A.space *> A.double) <* A.space <*> A.double
+ src/SequenceFormats/Utils.hs view
@@ -0,0 +1,53 @@+{-# LANGUAGE OverloadedStrings #-}++-- |This module contains helper functions for file parsing.++module SequenceFormats.Utils (liftParsingErrors,+ consumeProducer,+ FormatException(..),+ Chrom(..)) where++import Control.Exception (Exception)+import Control.Monad.Catch (MonadThrow, throwM)+import Control.Monad.Trans.Class (lift)+import qualified Data.Text as T+import qualified Data.Attoparsec.Text as A+import Pipes (Producer, next)+import Pipes.Attoparsec (ParsingError(..), parsed)++-- |A wrapper datatype for Chromosome names.+newtype Chrom = Chrom {unChrom :: T.Text} deriving (Eq)++-- |Show instance for Chrom+instance Show Chrom where+ show (Chrom c) = show c++-- |Ord instance for Chrom+instance Ord Chrom where+ compare (Chrom c1) (Chrom c2) = + let c1' = if T.take 3 c1 == "chr" then T.drop 3 c1 else c1+ c2' = if T.take 3 c2 == "chr" then T.drop 3 c2 else c2+ cn1 = read . T.unpack $ c1' :: Int+ cn2 = read . T.unpack $ c2' :: Int+ in cn1 `compare` cn2++-- |An exception type for parsing BioInformatic file formats.+data FormatException = FormatException T.Text+ deriving Show++instance Exception FormatException++-- |A function to help with reporting parsing errors to stderr. Returns a clean Producer over the +-- parsed datatype.+liftParsingErrors :: (MonadThrow m) =>+ Either (ParsingError, Producer T.Text m r) () -> Producer a m ()+liftParsingErrors res = case res of+ Left (ParsingError cont msg, restProd) -> do+ Right (chunk, _) <- lift $ next restProd+ let msg' = msg ++ " Error occurred while trying to parse this chunk: " ++ show chunk+ throwM (ParsingError cont msg')+ Right () -> return ()++-- |A helper function to parse a text producer, properly reporting all errors to stderr.+consumeProducer :: (MonadThrow m) => A.Parser a -> Producer T.Text m () -> Producer a m ()+consumeProducer parser prod = parsed parser prod >>= liftParsingErrors
+ src/SequenceFormats/VCF.hs view
@@ -0,0 +1,157 @@+{-# LANGUAGE OverloadedStrings #-}++{-| A module to help with parsing VCF files. The VCF format is defined here:+<https://en.wikipedia.org/wiki/Variant_Call_Format>+-}++module SequenceFormats.VCF (VCFheader(..),+ VCFentry(..),+ readVCFfromStdIn,+ readVCFfromFile,+ getGenotypes,+ getDosages,+ isTransversionSnp,+ vcfToFreqSumEntry,+ isBiallelicSnp) where++import SequenceFormats.Utils (consumeProducer, Chrom(..))+import SequenceFormats.FreqSum (FreqSumEntry(..))++import Control.Applicative ((<|>), empty)+import Control.Error (headErr, assertErr)+import Control.Monad (void)+import Control.Monad.Catch (MonadThrow, throwM)+import Control.Monad.Trans.State.Strict (runStateT)+import Control.Monad.IO.Class (MonadIO)+import qualified Data.Attoparsec.Text as A+import Data.Char (isSpace)+import qualified Data.Text as T+import Pipes (Producer)+import Pipes.Attoparsec (parse, ParsingError(..))+import Pipes.Safe (MonadSafe)+import qualified Pipes.Text.IO as PT++-- |A datatype to represent the VCF Header. Most comments are simply parsed as entire lines, but the very last comment line, containing the sample names, is separated out+data VCFheader = VCFheader {+ vcfHeaderComments :: [T.Text], -- ^A list of containing all comments starting with a single '#'+ vcfSampleNames :: [T.Text] -- ^The list of sample names parsed from the last comment line + -- starting with '##'+} deriving (Show)++-- |A Datatype representing a single VCF entry.+data VCFentry = VCFentry {+ vcfChrom :: Chrom, -- ^The chromosome+ vcfPos :: Int, -- ^The position+ vcfId :: Maybe T.Text, -- ^The SNP ID if non-missing+ vcfRef :: T.Text, -- ^ The reference allele (supports also multi-character alleles for Indels)+ vcfAlt :: [T.Text], -- ^The alternative alleles, each one possible of multiple characters + vcfQual :: Double, -- ^The quality value+ vcfFilter :: Maybe T.Text, -- ^The Filter value, if non-missing.+ vcfInfo :: [T.Text], -- ^A list of Info fields+ vcfFormatString :: [T.Text], -- ^A list of format tags+ vcfGenotypeInfo :: [[T.Text]] -- ^A list of format fields for each sapmle.+} deriving (Show)++readVCFfromProd :: (MonadThrow m) =>+ Producer T.Text m () -> m (VCFheader, Producer VCFentry m ())+readVCFfromProd prod = do+ (res, rest) <- runStateT (parse vcfHeaderParser) prod+ header <- case res of+ Nothing -> throwM $ ParsingError [] "freqSum file exhausted"+ Just (Left e) -> throwM e+ Just (Right h) -> return h+ return (header, consumeProducer vcfEntryParser rest)++-- |Reading a VCF from StdIn. Returns a VCFHeader and a Producer over VCFentries.+readVCFfromStdIn :: (MonadIO m, MonadThrow m) => m (VCFheader, Producer VCFentry m ())+readVCFfromStdIn = readVCFfromProd PT.stdin++-- |Reading a VCF from a file. Returns a VCFHeader and a Producer over VCFentries.+readVCFfromFile :: (MonadSafe m) => FilePath -> m (VCFheader, Producer VCFentry m ())+readVCFfromFile = readVCFfromProd . PT.readFile++vcfHeaderParser :: A.Parser VCFheader+vcfHeaderParser = VCFheader <$> A.many1' doubleCommentLine <*> singleCommentLine+ where+ doubleCommentLine = do+ c1 <- A.string "##"+ s_ <- A.takeWhile1 (not . A.isEndOfLine)+ A.endOfLine+ return $ T.append c1 s_+ singleCommentLine = do+ void $ A.char '#'+ s_ <- A.takeWhile1 (not . A.isEndOfLine)+ A.endOfLine+ let fields = T.splitOn "\t" s_+ return . drop 9 $ fields++vcfEntryParser :: A.Parser VCFentry+vcfEntryParser = VCFentry <$> (Chrom <$> word) <* sp <*> A.decimal <* sp <*> parseId <* sp <*>+ word <* sp <*> parseAlternativeAlleles <* sp <*> A.double <* sp <*> parseFilter <* sp <*> + parseInfoFields <* sp <*> parseFormatStrings <* sp <*> parseGenotypeInfos <* A.endOfLine+ where+ word = A.takeTill A.isHorizontalSpace+ sp = A.satisfy A.isHorizontalSpace+ parseId = parseDot <|> (Just <$> word)+ parseDot = A.char '.' *> empty+ parseAlternativeAlleles = parseDot <|> (parseAllele `A.sepBy1` A.char ',')+ parseAllele = A.takeTill (\c -> c == ',' || A.isHorizontalSpace c)+ parseFilter = parseDot <|> (Just <$> word)+ parseInfoFields = parseDot <|> (parseInfoField `A.sepBy1` A.char ';')+ parseInfoField = A.takeTill (\c -> c == ';' || A.isHorizontalSpace c)+ parseFormatStrings = A.takeTill (\c -> c == ':' || A.isHorizontalSpace c) `A.sepBy1` A.char ':'+ parseGenotypeInfos = parseGenotype `A.sepBy1` (A.satisfy A.isHorizontalSpace)+ parseGenotype = parseGenoField `A.sepBy1` (A.char ':')+ parseGenoField = A.takeTill (\c -> c == ':' || isSpace c) ++-- |returns True if the SNP is biallelic.+isBiallelicSnp :: T.Text -> [T.Text] -> Bool+isBiallelicSnp ref alt = validRef && validAlt+ where+ validRef = (ref `elem` ["A", "C", "G", "T"])+ validAlt = case alt of+ [alt'] -> alt' `elem` ["A", "C", "G", "T"]+ _ -> False++-- |returns True if the SNp is a biallelic Transversion SNP (i.e. one of G/T, G/C, A/T, A/C)+isTransversionSnp :: T.Text -> [T.Text] -> Bool+isTransversionSnp ref alt =+ case alt of+ [alt'] -> isBiallelicSnp ref alt && (not $ isTransition ref alt')+ _ -> False+ where+ isTransition r a = ((r == "A") && (a == "G")) || ((r == "G") && (a == "A")) ||+ ((r == "C") && (a == "T")) || ((r == "T") && (a == "C"))++-- |Extracts the genotype fields (for each sapmle) from a VCF entry+getGenotypes :: VCFentry -> Either String [T.Text]+getGenotypes vcfEntry = do+ gtIndex <- fmap fst . headErr "GT format field not found" . filter ((=="GT") . snd) .+ zip [0..] . vcfFormatString $ vcfEntry+ return $ map (!!gtIndex) (vcfGenotypeInfo vcfEntry)++-- |Extracts the dosages (the sum of non-reference alleles) per sample (returns a Left Error if it fails.)+getDosages :: VCFentry -> Either String [Maybe Int]+getDosages vcfEntry = do+ genotypes <- getGenotypes vcfEntry+ let dosages = do+ gen <- genotypes+ if '.' `elem` (T.unpack gen) then+ return Nothing+ else+ return . Just $ T.count "1" gen+ return dosages++-- |Converts a VCFentry to the simpler FreqSum format (returns a Left Error if it fails.)+vcfToFreqSumEntry :: VCFentry -> Either String FreqSumEntry+vcfToFreqSumEntry vcfEntry = do+ dosages <- getDosages vcfEntry+ assertErr "multi-site reference allele" $ T.length (vcfRef vcfEntry) == 1+ assertErr "need exactly one alternative allele" $ length (vcfAlt vcfEntry) == 1+ assertErr "multi-site alternative allele" $ T.length (head . vcfAlt $ vcfEntry) == 1+ let ref = T.head (vcfRef vcfEntry)+ let alt = T.head . head . vcfAlt $ vcfEntry+ assertErr "Invalid Reference Allele" $ ref `elem` ['A', 'C', 'T', 'G', 'N']+ assertErr "Invalid Alternative Allele" $ alt `elem` ['A', 'C', 'T', 'G', '.']+ return $ FreqSumEntry (vcfChrom vcfEntry) (vcfPos vcfEntry) ref alt dosages+