heatitup-complete (empty) → 0.5.3.3
raw patch · 9 files changed
+1857/−0 lines, 9 filesdep +basedep +bytestringdep +cassavasetup-changed
Dependencies added: base, bytestring, cassava, containers, fasta, foldl, heatitup-complete, lens, optparse-applicative, pipes, pipes-text, safe, text, text-show, turtle, vector
Files
- LICENSE +674/−0
- Setup.hs +2/−0
- app/Main.hs +686/−0
- heatitup-complete.cabal +60/−0
- src/Blast.hs +66/−0
- src/Merge.hs +113/−0
- src/Parse.hs +75/−0
- src/Types.hs +76/−0
- src/Utility.hs +105/−0
+ 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:++ {project} Copyright (C) {year} {fullname}+ 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>.
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ app/Main.hs view
@@ -0,0 +1,686 @@+{- heatitup-complete+Gregory W. Schwartz++Find duplications a sequence with assembly. Requires all to be in path:+heatitup, Trinity, samtools (if input is a bam), rsem-prepare-reference,+rsem-calculate-expression, and bowtie2. Cleans up at the end by deleting all+files with INPUT.* pattern, the new period being the main difference.+-}++{-# LANGUAGE ViewPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Main where++-- Standard+import Data.Bool+import Data.Maybe+import qualified Data.List.NonEmpty as NE+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set++-- Cabal+import Data.Fasta.Text+import Pipes+import qualified Pipes.Prelude as P+import qualified Pipes.Text as PT+import qualified Pipes.Text.IO as PT+import qualified Control.Foldl as Fold+import qualified Data.ByteString.Lazy.Char8 as B+import qualified Data.Csv as CSV+import qualified Data.Text as T+import qualified Data.Vector as V+import qualified Options.Applicative as O+import Turtle+import Turtle.Line++-- Local+import Types+import Parse+import Merge+import Blast+import Utility++-- | Command line arguments+data Options = Options { input :: String+ , spacerFlag :: Bool+ , refInput :: Maybe String+ , blacklistInput :: Maybe String+ , output :: Maybe String+ , outputPlot :: Maybe String+ , outputLabel :: String+ , refField :: Int+ , posField :: Maybe Int+ , ignoreField :: Maybe Int+ , inputMinSize :: Int+ , gaussWindow :: Int+ , gaussTime :: Double+ , gaussThreshold :: Double+ , inputMinMut :: Maybe Int+ , inputDistance :: Int+ , refCheckBlacklistFlag :: Bool+ , refRecBlacklistFlag :: Bool+ , minRichness :: Int+ , inputColorDupL :: String+ , inputColorDupR :: String+ , inputColorMut :: String+ , inputColorSpacer :: String+ , inputColorBackground :: String+ , inputColorForeground :: String+ , preprocessType :: Preprocess+ , blastCommand :: Maybe String+ , blastArgs :: Maybe String+ , trinityCommand :: String+ , trinityArgs :: TrinityArgs+ , trinityAbundance :: String+ , dirtyFlag :: Bool+ , cigarFlag :: Bool+ , headers :: Maybe String+ }++-- | Command line options+options :: O.Parser Options+options = Options+ <$> O.strOption+ ( O.long "input"+ <> O.short 'i'+ <> O.metavar "FILE"+ <> O.help "The input file"+ )+ <*> O.switch+ ( O.long "spacer"+ <> O.short 's'+ <> O.help "Whether to characterize the spacer. Requires\+ \ reference-input and matching labels for the input and\+ \ reference-input to compare."+ )+ <*> O.optional ( O.strOption+ ( O.long "reference-input"+ <> O.short 'I'+ <> O.metavar "[Nothing] | FILE"+ <> O.help "The input file containing the reference sequences to compare\+ \ to. The first entry in the field must be the accession and\+ \ match the requested field from reference-field for the\+ \ input. With no supplied file, no spacer will be annotated."+ )+ )+ <*> O.optional ( O.strOption+ ( O.long "blacklist-input"+ <> O.short 'b'+ <> O.metavar "[Nothing] | FILE"+ <> O.help "The input fasta file containing possible false positives --\+ \ sequences which may be duplicate nucleotides in the\+ \ reference sequence."+ )+ )+ <*> O.optional ( O.strOption+ ( O.long "output"+ <> O.short 'o'+ <> O.metavar "FILE"+ <> O.help "The output file"+ )+ )+ <*> O.optional ( O.strOption+ ( O.long "output-plot"+ <> O.short 'O'+ <> O.metavar "FILE"+ <> O.help "The output file for the plot. Each new plot gets a new number\+ \ on it: output_1.svg, output_2.svg, etc. Each plot uses the\+ \ first entry in the fasta header as the label."+ )+ )+ <*> O.strOption+ ( O.long "label"+ <> O.short 'l'+ <> O.metavar "STRING"+ <> O.value ""+ <> O.help "The label to use in the label column for the output"+ )+ <*> O.option O.auto+ ( O.long "reference-field"+ <> O.short 'f'+ <> O.metavar "[1] | INT"+ <> O.value 1+ <> O.help "The field in each input header that contains the reference\+ \ accession number to compare to. Results in an out of bounds\+ \ if this field does not exist."+ )+ <*> O.optional ( O.option O.auto+ ( O.long "position-field"+ <> O.short 'p'+ <> O.metavar "[Nothing] | INT"+ <> O.help "The field in each input header that contains the starting\+ \ position of the read. Added to the annotations. Results\+ \ in out of bounds if this field does not exist."+ )+ )+ <*> O.optional ( O.option O.auto+ ( O.long "ignore-field"+ <> O.short 'g'+ <> O.metavar "[Nothing] | INT"+ <> O.help "The field in each input header that contains a 0 or a 1:\+ \ 0 means to ignore this read (assign as Normal) and 1\+ \ means to find a duplication in this read.\+ \ Used for reads where there is known to be no duplication\+ \ and thus helps remove false positives."+ )+ )+ <*> O.option O.auto+ ( O.long "min-size"+ <> O.short 's'+ <> O.metavar "[15] | INT"+ <> O.value 15+ <> O.help "The minimum size of a duplication"+ )+ <*> O.option O.auto+ ( O.long "gaussian-window"+ <> O.short 'w'+ <> O.metavar "[4] | Double"+ <> O.value 3+ <> O.help "The window for the discrete gaussian kernel atypical spacer\+ \ determination"+ )+ <*> O.option O.auto+ ( O.long "gaussian-time"+ <> O.short 't'+ <> O.metavar "[2] | Double"+ <> O.value 2+ <> O.help "The time for the discrete gaussian kernel atypical spacer\+ \ determination"+ )+ <*> O.option O.auto+ ( O.long "gaussian-threshold"+ <> O.short 'T'+ <> O.metavar "[0.4] | Double"+ <> O.value 0.4+ <> O.help "The cutoff to be considered a mutation for the discrete\+ \ gaussian kernel atypical spacer determination"+ )+ <*> O.optional ( O.option O.auto+ ( O.long "min-mutations"+ <> O.short 'm'+ <> O.metavar "INT"+ <> O.help "The minimum number of nucleotides between mutations"+ )+ )+ <*> O.option O.auto+ ( O.long "levenshtein-distance"+ <> O.short 'L'+ <> O.metavar "[2] | INT"+ <> O.value 2+ <> O.help "The minimum Levenshtein distance to the false positive\+ \ checker. If the distance to the false positive string\+ \ is less than or equal to this number,\+ \ the duplication is considered\+ \ a false positive. Compares candidates against each sequence\+ \ in --blacklist-input"+ )+ <*> O.switch+ ( O.long "reference-check-blacklist"+ <> O.short 'c'+ <> O.help "Whether to use the reference as a blacklist in addition to\+ \ the supplied blacklist. That is, we check if the duplication\+ \ can be found twice or more in the reference input."+ )+ <*> O.switch+ ( O.long "reference-recursive-blacklist"+ <> O.short 'r'+ <> O.help "Whether to use the reference as a recursive\+ \ blacklist in addition to\+ \ the supplied blacklist. That is, the reference sequences\+ \ are inputed with the same parameters (except distance, which\+ \ here is 0)\+ \ to the duplication finder, and those duplications found are\+ \ added to the blacklist. This process is recursive, executed\+ \ until no more duplications are found in the reference.\+ \ Beware, too many blacklist entries can slow down the finder\+ \ significantly, as each blacklist entry is compared with each\+ \ candidate."+ )+ <*> O.option O.auto+ ( O.long "min-richness"+ <> O.short 'R'+ <> O.metavar "[1] | INT"+ <> O.value 1+ <> O.help "The minimum nucleotide richness (number of different types of\+ \ nucleotides) allowed in the duplication to be considered\+ \ real. Useful if the user knows that a sequence like\+ \ \"TTTTTTTTCTTTTTTTTC\" is not likely to be real."+ )+ <*> O.strOption+ ( O.long "color-left-duplication"+ <> O.metavar "[#a6cae3] | COLOR"+ <> O.help "The color of the left side of the repeated sequence."+ <> O.value "#a6cae3"+ )+ <*> O.strOption+ ( O.long "color-right-duplication"+ <> O.metavar "[#b0de8a] | COLOR"+ <> O.help "The color of the right side of the repeated sequence."+ <> O.value "#b0de8a"+ )+ <*> O.strOption+ ( O.long "color-difference"+ <> O.metavar "[#1978b3] | COLOR"+ <> O.help "The color of discrepancies between the left and right side of\+ \ the duplication."+ <> O.value "#1978b3"+ )+ <*> O.strOption+ ( O.long "color-spacer"+ <> O.metavar "[#fdbd6e] | COLOR"+ <> O.help "The color of the exogenous nucleotides within the spacer."+ <> O.value "#fdbd6e"+ )+ <*> O.strOption+ ( O.long "color-background"+ <> O.metavar "[#ffffff] | COLOR"+ <> O.help "The color of the background."+ <> O.value "#ffffff"+ )+ <*> O.strOption+ ( O.long "color-foreground"+ <> O.metavar "[#000000] | COLOR"+ <> O.help "The color of the foreground."+ <> O.value "#000000"+ )+ <*> O.option O.auto+ ( O.long "type"+ <> O.short 'P'+ <> O.metavar "Assembly | NonAssembly CHAR"+ <> O.help "The type of preprocessing before duplication finding.\+ \ Assembly would be used on exome sequencing, RNA-seq, etc.\+ \ while NonAssembly would be for certain paired end\+ \ sequencing like amplicon based. Basically, are the reads\+ \ fragmented across a location (Assembly) or are they\+ \ all piled up (NonAssembly)? Paired end is required for\+ \ NonAssembly, otherwise just use the duplication finding\+ \ program directly on the reads for best results.\+ \ NonAssembly additionally requires a character to use as\+ \ filler between non-overlapping mate pairs, as the\+ \ program will remove duplications containing that\+ \ character. Input would look like \"NonAssembly 'X'\"."+ )+ <*> O.optional ( O.strOption+ ( O.long "blast-command"+ <> O.short 'B'+ <> O.metavar "[Nothing] | PATH"+ <> O.help "The command used for blastn. Useful if not in path.\+ \ Used for filtering out reads from irrelevant locations.\+ \ If using small sequences, be sure to set blast-args\+ \ to \"-task blastn-short\"."+ )+ )+ <*> O.optional ( O.strOption+ ( O.long "blast-args"+ <> O.short 'z'+ <> O.metavar "[Nothing] | STRING"+ <> O.help "The additional arguments used for blastn. Separated by space.\+ \ Use \"-task blastn-short\" for small sequences."+ )+ )+ <*> O.strOption+ ( O.long "trinity-command"+ <> O.short 'C'+ <> O.metavar "[Trinity] | PATH"+ <> O.value "Trinity"+ <> O.help "The command used for Trinity. Useful if not in path."+ )+ <*> O.option O.auto+ ( O.long "trinity-args"+ <> O.short 'A'+ <> O.metavar "[TrinityBase] | TrinityGenome | TrinityCustom STRING"+ <> O.value TrinityBase+ <> O.help "The arguments used for Trinity.\+ \ TrinityBase is --seqType fq --run_as_paired --max_memory 10G --no_version_check --single,\+ \ TrinityGenome is --genome_guided_max_intron 10000 --max_memory 10G --no_version_check --genome_guided_bam,\+ \ and TrinityCustom STRING is STRING.\+ \ Make sure the input argument\+ \ is last and points to nothing (like in the default)."+ )+ <*> O.strOption+ ( O.long "trinity-abundance"+ <> O.short 'a'+ <> O.metavar "[align_and_estimate_abundance.pl] | PATH"+ <> O.value "align_and_estimate_abundance.pl"+ <> O.help "The command used for align_and_estimate_abundance.pl\+ \ in Trinity's util folder. Useful if not in path. Make sure\+ \ kallisto is in the path."+ )+ <*> O.switch+ ( O.long "dirty"+ <> O.short 'd'+ <> O.help "Leave behind the INPUT.* files at the end (but the trinity\+ \ output is still deleted)."+ )+ <*> O.switch+ ( O.long "no-cigar-filter"+ <> O.short 'G'+ <> O.help "Skip the CIGAR based filtering, that is, look at all reads\+ \ and not just reads without all M's in the CIGAR."+ )+ <*> O.optional ( O.strOption+ ( O.long "header"+ <> O.short 'H'+ <> O.metavar "[Nothing] | STRING"+ <> O.help "The headers used when converting bam to fasta.\+ \ The order in the resulting header is\+ \ \">FILE|ACCESSION|POSITION|IGNORE|HEADER\".\+ \ So take that order\+ \ into account for field options with positions and the\+ \ rest. Also, make sure this string has fields separated by\+ \ a pipe \"|\" character. So if you have HEADER as the\+ \ \"ENSE00000SOMETHING\" reference accession that\+ \ agrees with --input-reference, that would be\+ \ field 5."+ )+ )++-- | Get the Trinity arguments.+defTrinityArgs :: TrinityArgs -> T.Text+defTrinityArgs TrinityBase = T.pack "--seqType fq\+ \ --run_as_paired\+ \ --max_memory 10G\+ \ --no_version_check\+ \ --single"+defTrinityArgs TrinityGenome = T.pack "--genome_guided_max_intron 10000\+ \ --max_memory 10G\+ \ --no_version_check\+ \ --genome_guided_bam"+defTrinityArgs (TrinityCustom x) = T.pack x++-- | Run the trinity command.+runTrinity :: Options -> Turtle.FilePath -> Turtle.FilePath -> IO ()+runTrinity opts tempFile tempDir = do+ let modifiedArgs = (T.words . defTrinityArgs . trinityArgs $ opts)+ <> [ format fp tempFile+ , "--output"+ , format fp tempDir+ ]++ stderr . inproc (T.pack $ trinityCommand opts) modifiedArgs $ mempty++ return ()++-- | Run samtools if the input is a bam file.+runSamtools :: Options -> Turtle.FilePath -> IO Turtle.FilePath+runSamtools opts tempFasta = do+ let inputFile = T.pack . Main.input $ opts+ outputType = case preprocessType opts of+ Assembly -> "fastq"+ (NonAssembly _) -> "fasta"++ fastFile <- if hasExtension (fromText inputFile) "bam"+ then strict $ do+ Turtle.output tempFasta+ . inproc "samtools" [outputType, inputFile]+ $ mempty+ return . NE.head . textToLines . format fp $ tempFasta+ else+ return inputFile++ return . fromText . T.strip $ fastFile++-- | Run the abundance command.+runAlignContig :: Options -> Turtle.FilePath -> Turtle.FilePath -> Shell Line+runAlignContig opts tempDir trinityFastaFile = do+ tempFasta <- mktempfile tempDir "trinity.fasta"++ inputFasta <- liftIO . runSamtools opts $ tempFasta+ fastaMap <-+ fmap (fastaToMap ' ') -- Trinity outputs ' ' as a separator.+ . liftIO+ . PT.runSafeT+ . runEffect+ . P.toListM+ $ pipesFasta (PT.readFile . T.unpack . format fp $ trinityFastaFile)++ bamOutput <- strict+ . inproc "samtools" ["view", "-F", "4", "-"] -- No headers and unmapped reads+ . inproc+ (T.pack $ trinityAbundance opts)+ [ "--transcripts", format fp trinityFastaFile+ , "--seqType", "fa"+ , "--single", format fp inputFasta+ , "--est_method", "kallisto"+ , "--kallisto_add_opts", "--pseudobam"+ , "--trinity_mode"+ , "--prep_reference"+ , "--output_dir", format fp tempDir+ ]+ $ mempty++ let bamRows' = fmap (BamRow . T.splitOn "\t") . T.lines $ bamOutput++ bamRows <- case blastCommand opts of+ (Just cmd) -> filterBlastBamRows+ 2+ (Command . T.pack $ cmd)+ (fmap Args . blastArgs $ opts)+ ( Subject+ . fromText+ . T.pack+ . fromMaybe (error "Need --reference-input for blast.")+ . refInput+ $ opts+ )+ (QueryFile trinityFastaFile)+ bamRows'+ Nothing -> return bamRows'++ let matchMap = getMatchMap bamRows++ select+ . concatMap (NE.toList . textToLines)+ . concat+ . nub'+ . fmap+ ( bamToFasta+ (Just fastaMap)+ (bool (Just matchMap) Nothing . cigarFlag $ opts)+ (T.pack $ Main.input opts)+ (fmap (Headers . T.pack) . headers $ opts)+ )+ $ bamRows++-- | Find duplications in the Trinity output.+runFindDuplication :: Options -> Shell Line -> Shell Line+runFindDuplication opts streamIn =+ inproc "heatitup" commandList streamIn+ where+ commandList =+ fmap T.pack+ . concat+ . catMaybes+ $ [ fmap (("--reference-input" :) . (:[])) . refInput $ opts+ , bool Nothing (Just ["--spacer"]) . spacerFlag $ opts+ , fmap (("--blacklist-input" :) . (:[])) . blacklistInput $ opts+ , fmap (("--output" :) . (:[])) . Main.output $ opts+ , fmap (("--output-plot" :) . (:[])) . outputPlot $ opts+ , Just ["--label", outputLabel opts]+ , Just ["--reference-field", show . refField $ opts]+ , fmap (("--position-field" :) . (:[]) . show) . posField $ opts+ , fmap (("--ignore-field" :) . (:[]) . show) . ignoreField $ opts+ , Just ["--min-size", show . inputMinSize $ opts]+ , Just ["--gaussian-window", show . gaussWindow $ opts]+ , Just ["--gaussian-time", show . gaussTime $ opts]+ , Just ["--gaussian-threshold", show . gaussThreshold $ opts]+ , fmap (("--min-mutations" :) . (:[]) . show) . inputMinMut $ opts+ , Just ["--levenshtein-distance", show . inputDistance $ opts]+ , bool Nothing (Just ["--reference-check-blacklist"])+ . refCheckBlacklistFlag+ $ opts+ , bool Nothing (Just ["--reference-recursive-blacklist"])+ . refRecBlacklistFlag+ $ opts+ , Just ["--min-richness", show . minRichness $ opts]+ , Just ["--color-left-duplication", inputColorDupL $ opts]+ , Just ["--color-right-duplication", inputColorDupR $ opts]+ , Just ["--color-difference", inputColorMut $ opts]+ , Just ["--color-spacer", inputColorSpacer $ opts]+ , Just ["--color-background", inputColorBackground $ opts]+ , Just ["--color-foreground", inputColorForeground $ opts]+ ]+++-- | Cleanup the intermediate files.+cleanup :: Options -> Shell ()+cleanup opts = sh $ do+ removableHere <-+ fold ( grep (has . text $ T.pack (Main.input opts) <> ".")+ . join+ . fmap (select . textToLines . format fp)+ . ls+ $ "."+ )+ Fold.list+ removableThere <-+ fold ( grep (has . text $ T.pack (Main.input opts) <> ".")+ . join+ . fmap (select . textToLines . format fp)+ . ls+ . directory+ . fromText+ . T.pack+ . Main.input+ $ opts+ )+ Fold.list++ mapM_ (rm . fromText . lineToText) $ removableHere <> removableThere++ return ()++assembly :: Options -> IO ()+assembly opts = sh $ do+ tempDir <- mktempdir "." "trinity"+ tempFile' <- mktempfile "." "tmp.fq"+ tempFile <-+ case trinityArgs opts of+ TrinityBase -> liftIO . runSamtools opts $ tempFile'+ TrinityGenome ->+ return . fromText . T.pack . Main.input $ opts+ (TrinityCustom _) ->+ return . fromText . T.pack . Main.input $ opts++ liftIO . runTrinity opts tempFile $ tempDir+ trinityFastaFile <-+ fold (find (has "/Trinity" <> suffix ".fasta") tempDir) Fold.head++ _ <- if isNothing trinityFastaFile+ then error "Fasta not generated."+ else return ()++ duplicationOutput <- strict+ . runFindDuplication opts+ . runAlignContig opts tempDir+ . fromJust+ $ trinityFastaFile++ unless (dirtyFlag opts) . cleanup $ opts++ abundances <-+ strict+ . maybe mempty (Turtle.input . const (tempDir </> "abundance.tsv"))+ $ trinityFastaFile++ unless (dirtyFlag opts) . cleanup $ opts++ let abundanceMap' = getAbundanceMap . B.pack . T.unpack $ abundances+ (dupHeader, dupRows) =+ parseDuplications . B.pack . T.unpack $ duplicationOutput+ accSet = getAccSet dupRows+ abundanceMap = --We only want the frequency of valid contigs+ AbundanceMap+ . Map.filterWithKey (\k _ -> Set.member k . unAccSet $ accSet)+ . unAbundanceMap+ $ abundanceMap'+ frequencyMap = getFrequencyMap abundanceMap+ newRows = fmap (mergeAbundance frequencyMap) dupRows+ finalOutput = CSV.encodeByName (V.snoc dupHeader "frequency")+ . fmap unDuplicationRow+ $ newRows++ liftIO . B.putStrLn $ finalOutput++-- | Remove rows where the duplication contains the filler.+removeFillDups :: Fill -> WithHeader Line -> Maybe Line+removeFillDups _ (Header x) = Just x+removeFillDups (Fill fill) (Row h row) =+ if T.isInfixOf (T.singleton fill)+ . fromMaybe (error "dSubstring column not found.")+ . lookup "dSubstring"+ . zip (getCols h)+ . getCols+ $ row+ then Nothing+ else Just row+ where+ getCols = T.splitOn "," . lineToText++nonAssembly :: Options -> Fill -> IO ()+nonAssembly opts fill = sh $ do+ bamOutput <- strict+ . inproc "samtools" ["view", "-"] -- No headers+ . inproc "samtools" [ "sort"+ , "-n"+ , "-O", "sam"+ , T.pack $ Main.input opts+ ]+ $ mempty++ let bamRows' = parseBAM bamOutput+ query = QueryShell+ . select+ . concatMap (NE.toList . textToLines)+ . concatMap blastBamToFasta+ $ bamRows'++ -- Get rid of sequences that don't blast to the reference.+ bamRows <- case blastCommand opts of+ (Just cmd) -> filterBlastBamRows+ 0+ (Command . T.pack $ cmd)+ (fmap Args . blastArgs $ opts)+ ( Subject+ . fromText+ . T.pack+ . fromMaybe (error "Need --reference-input for blast.")+ . refInput+ $ opts+ )+ query+ bamRows'+ Nothing -> return bamRows'++ let mergedMates = mergeMates fill bamRows+ fastaOutput = select+ . concatMap (NE.toList . textToLines)+ . concatMap ( bamToFasta+ Nothing+ Nothing+ (T.pack $ Main.input opts)+ (fmap (Headers . T.pack) . headers $ opts)+ )+ $ mergedMates++ stdout+ . fmap fromJust+ . mfilter isJust+ . fmap (removeFillDups fill)+ . Turtle.header+ . runFindDuplication opts+ $ fastaOutput++mainFunc :: Options -> IO ()+mainFunc opts@(preprocessType -> Assembly) = assembly opts+mainFunc opts@(preprocessType -> NonAssembly fill) =+ nonAssembly opts (Fill fill)++main :: IO ()+main = O.execParser opts >>= mainFunc+ where+ opts = O.info (O.helper <*> Main.options)+ ( O.fullDesc+ <> O.progDesc "Finds duplications in a sequence with assembly"+ <> O.header "heatitup-complete, Gregory W. Schwartz" )
+ heatitup-complete.cabal view
@@ -0,0 +1,60 @@+name: heatitup-complete+version: 0.5.3.3+synopsis: Find and annotate ITDs with assembly or read pair joining.+description: Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.+homepage: http://github.com/GregorySchwartz/heatitup-complete#readme+license: GPL-3+license-file: LICENSE+author: Gregory W. Schwartz+maintainer: gsch@pennmedicine.upenn.edu+copyright: Copyright: (c) 2018 Gregory W. Schwartz+category: Bioinformatics+build-type: Simple+-- extra-source-files:+cabal-version: >=1.10++library+ hs-source-dirs: src+ exposed-modules: Types+ , Utility+ , Parse+ , Merge+ , Blast+ build-depends: base >= 4.7 && < 5+ , bytestring+ , cassava+ , containers+ , fasta+ , foldl+ , lens+ , safe+ , text+ , text-show+ , turtle+ , vector+ ghc-options: -O2+ default-language: Haskell2010++executable heatitup-complete+ hs-source-dirs: app+ main-is: Main.hs+ ghc-options: -threaded -rtsopts -O2+ build-depends: base+ , heatitup-complete+ , bytestring+ , cassava+ , containers+ , fasta+ , foldl+ , optparse-applicative+ , pipes+ , pipes-text+ , safe+ , text+ , turtle+ , vector+ default-language: Haskell2010++source-repository head+ type: git+ location: https://github.com/GregorySchwartz/heatitup-complete
+ src/Blast.hs view
@@ -0,0 +1,66 @@+{- Blast+Gregory W. Schwartz++Collects the functions pertaining to Blasting sequences.+-}++{-# LANGUAGE OverloadedStrings #-}++module Blast+ ( filterBlastBamRows+ , blastBamToFasta+ ) where++-- Standard+import Data.Maybe+import qualified Data.Set as Set++-- Cabal+import qualified Control.Foldl as Fold+import qualified Data.Text as T+import Safe+import Turtle+import Turtle.Line++-- Local+import Types++-- | Get the accessions that successfully align to the reference.+getBlastSet :: Command -> Maybe Args -> Subject -> Query -> Shell BlastSet+getBlastSet (Command cmd) args (Subject sub) query = do+ let queryIn (QueryFile x) = input x+ queryIn (QueryShell x) = x+ argsIn = maybe [] (fmap T.pack . words . unArgs) args+ blastOutput = fmap fromJust+ . mfilter isJust+ . fmap (headMay . cut "\t" . lineToText)+ . inproc cmd ( [ "-subject", format fp sub+ , "-outfmt", "6"+ , "-max_target_seqs", "1"+ ]+ <> argsIn+ )+ . queryIn+ $ query+ blastSet <- fmap (BlastSet . Set.fromList) . fold blastOutput $ Fold.list++ return blastSet++-- | Filter out BamRows that do not successfully align to the reference.+filterBlastBamRows :: Int -> Command -> Maybe Args -> Subject -> Query -> [BamRow] -> Shell [BamRow]+filterBlastBamRows accField cmd args sub query rows = do+ blastSet <- getBlastSet cmd args sub $ query++ let newRows =+ filter+ (flip Set.member (unBlastSet blastSet) . (`at` accField) . unBamRow)+ rows++ return newRows++-- | Convert a bam row to fasta for a quick blast check.+blastBamToFasta :: BamRow -> [T.Text]+blastBamToFasta (BamRow row) =+ [ ">" <> (fromMaybe (error "No accession in bam.") . headMay $ row)+ , fromMaybe (error "No sequence in bam.") $ row `atMay` 9+ ]
+ src/Merge.hs view
@@ -0,0 +1,113 @@+{- Merge+Gregory W. Schwartz++Collects the functions pertaining to the merging of headers with abundances.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Merge+ ( mergeAbundance+ , mergeMates+ , bamToFasta+ ) where++-- Standard+import Data.Function (on)+import Data.List+import Data.Maybe+import Data.Monoid+import qualified Data.IntMap.Strict as IMap+import qualified Data.Map.Strict as Map++-- Cabal+import Control.Lens+import qualified Data.Text as T+import qualified Data.Text.Read as T+import Safe+import TextShow++-- Local+import Types+import Utility++mergeAbundance :: FrequencyMap -> DuplicationRow -> DuplicationRow+mergeAbundance (FrequencyMap m) (DuplicationRow row) =+ DuplicationRow+ . Map.insert "frequency" (showt . findWithError rowAccession $ m)+ $ row+ where+ rowAccession =+ flip (Safe.at) 1 . T.splitOn "|" . findWithError "fHeader" $ row++-- | Get the position map of a sequence.+getPositionMap :: Position -> Sequence -> PositionMap+getPositionMap (Position p) =+ PositionMap . IMap.fromList . zip [p..] . T.unpack . unSequence++-- | Fill the gaps in a position sequence list with a character.+fillGapsWith :: Fill+ -> [(Position, Char)]+ -> [(Position, Char)]+ -> [(Position, Char)]+fillGapsWith _ !acc [] = reverse acc+fillGapsWith fill [] (x:xs) = fillGapsWith fill [x] xs+fillGapsWith+ fill+ acc@((Position !previousPos, _):_)+ allNext@((Position !currentPos, !currentChar):xs) =+ if abs (currentPos - previousPos) > 1+ then fillGapsWith+ fill+ ((Position (previousPos + 1), unFill fill) : acc)+ allNext+ else fillGapsWith+ fill+ ((Position currentPos, currentChar) : acc)+ xs++-- | Merge two sequences by their positions.+mergeSequences :: Fill+ -> (Position, Sequence)+ -> (Position, Sequence)+ -> Sequence+mergeSequences fill left =+ Sequence+ . T.pack+ . fmap snd+ . fillGapsWith fill []+ . fmap (over _1 Position)+ . IMap.toAscList+ . IMap.union (unPositionMap . uncurry getPositionMap $ left)+ . unPositionMap+ . uncurry getPositionMap++-- | Merge a mate pair. Assumes that the lines are sorted by mate pair already+-- (samtools sort -n). Also assumes that the left mate appears first. Removes+-- supplementary alignments.+mergePair :: Fill -> [BamRow] -> Maybe BamRow+mergePair fill xs =+ case filter (not . isSupplementary) xs of+ [] -> Nothing+ [x] -> Just x+ [BamRow left, BamRow right] ->+ Just+ . BamRow+ . set (ix 9) ( unSequence+ $ mergeSequences fill (posSeq left) (posSeq right)+ )+ $ left+ xs -> error ("Too many mate pairs (even after supplementary removal) for: " <> show xs)+ where+ posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3+ , Sequence $ xs !! 9+ )+ isSupplementary =+ (== "1") . drop 11 . decodeSAMFlag . read . T.unpack . (!! 1) . unBamRow++-- | Merge all mate pairs. Assumes that the lines are sorted by mate pair already+-- (samtools sort -n).+mergeMates :: Fill -> [BamRow] -> [BamRow]+mergeMates fill =+ catMaybes . fmap (mergePair fill) . groupBy ((==) `on` (head . unBamRow))
+ src/Parse.hs view
@@ -0,0 +1,75 @@+{- Parse+Gregory W. Schwartz++Collects the functions pertaining to the parsing of the abundance output.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Parse+ ( getAbundanceMap+ , getFrequencyMap+ , getAccSet+ , parseDuplications+ , parseBAM+ ) where++-- Standard+import Data.Char+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set++-- Cabal+import Control.Lens+import Data.Csv+import Data.Text.Read+import qualified Data.ByteString.Lazy.Char8 as B+import qualified Data.Text as T+import qualified Data.Vector as V+import Safe++-- Local+import Types+import Utility++-- | Get the abundance map from the contents of the abundance output.+getAbundanceMap :: B.ByteString -> AbundanceMap+getAbundanceMap =+ AbundanceMap+ . Map.unions+ . fmap (\ !m -> Map.singleton+ (findWithError ("target_id" :: T.Text) m)+ (getDouble . findWithError ("est_counts" :: T.Text) $ m)+ )+ . V.toList+ . either error snd+ . decodeByNameWith decodeOpts+ where+ decodeOpts = defaultDecodeOptions { decDelimiter = fromIntegral (ord '\t') }+ getDouble = either error fst . double++-- | Convert an abundance map to a frequency map.+getFrequencyMap :: AbundanceMap -> FrequencyMap+getFrequencyMap (AbundanceMap m) = FrequencyMap . Map.map (/ totalCount) $ m+ where+ totalCount = Map.foldl (+) 0 m++-- | Get the list of accessions from a duplication row post-Trinity.+getAccSet :: [DuplicationRow] -> AccSet+getAccSet = AccSet+ . Set.fromList+ . fmap ( flip (Safe.at) 1+ . T.splitOn "|"+ . findWithError "fHeader"+ . unDuplicationRow+ )+ +-- | Get the duplications in an easy to read format.+parseDuplications :: B.ByteString -> (Header, [DuplicationRow])+parseDuplications =+ over _2 (fmap DuplicationRow . V.toList) . either error id . decodeByName++-- | Parse bam rows.+parseBAM :: T.Text -> [BamRow]+parseBAM = fmap (BamRow . T.splitOn "\t") . T.lines
+ src/Types.hs view
@@ -0,0 +1,76 @@+{- Types+Gregory W. Schwartz++Collects the types used in the program+-}++module Types where++-- Standard+import qualified Data.IntMap.Strict as IMap+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set++-- Cabal+import qualified Data.Text as T+import Turtle++-- Local+++-- Algebraic+data Preprocess = Assembly | NonAssembly Char deriving (Read, Show)+data TrinityArgs = TrinityBase | TrinityGenome | TrinityCustom String deriving (Read, Show)+data Query = QueryFile Turtle.FilePath | QueryShell (Shell Line)++-- Basic+newtype Position = Position+ { unPosition :: Int+ } deriving (Show)+newtype Sequence = Sequence+ { unSequence :: T.Text+ } deriving (Show)+newtype Fill = Fill+ { unFill :: Char+ } deriving (Show)+newtype Command = Command+ { unCommand :: T.Text+ } deriving (Show)+newtype Args = Args+ { unArgs :: String+ } deriving (Show)+newtype Subject = Subject+ { unSubject :: Turtle.FilePath+ } deriving (Show)++-- Advanced+newtype BamRow = BamRow+ { unBamRow :: [T.Text]+ } deriving (Read, Show)+newtype Headers = Headers+ { unHeaders :: T.Text+ }+newtype AbundanceMap = AbundanceMap+ { unAbundanceMap :: Map.Map T.Text Double+ }+newtype FrequencyMap = FrequencyMap+ { unFrequencyMap :: Map.Map T.Text Double+ }+newtype DuplicationRow = DuplicationRow+ { unDuplicationRow :: Map.Map T.Text T.Text+ }+newtype PositionMap = PositionMap+ { unPositionMap :: IMap.IntMap Char+ }+newtype AccessionMap = AccessionMap+ { unAccessionMap :: Map.Map T.Text T.Text+ } deriving (Read, Show)+newtype BlastSet = BlastSet+ { unBlastSet :: Set.Set T.Text+ }+newtype AccSet = AccSet+ { unAccSet :: Set.Set T.Text+ }+newtype MatchMap = MatchMap+ { unMatchMap :: Map.Map T.Text Bool+ }
+ src/Utility.hs view
@@ -0,0 +1,105 @@+{- Utility+Gregory W. Schwartz++Collects the functions pertaining to utility helper functions.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE ViewPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Utility+ ( findWithError+ , bamToFasta+ , appendHeader+ , fastaToMap+ , getMatchMap+ , nub'+ , decodeSAMFlag+ ) where++-- Standard+import Data.Bool+import Data.Char+import Data.Maybe+import Data.Monoid+import Numeric+import qualified Data.ByteString.Char8 as B+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set++-- Cabal+import qualified Control.Foldl as Fold+import qualified Data.Text as T+import Data.Fasta.Text+import Safe+import Turtle.Line++-- Local+import Types++-- | Return a specific error when the text key is not found.+findWithError :: (Eq a, Ord a, Show a) => a -> Map.Map a b -> b+findWithError x = Map.findWithDefault (error (show x <> " not found.")) x++-- | Whether to ignore the read based on the cigar (0 is ignore 1 is don't+-- ignore).+isIgnore :: T.Text -> Bool+isIgnore = (== "M") . T.filter isAlpha++-- | Convert a line in a bam file to a fasta format for duplication input. Uses+-- values from the maps if Assembly.+bamToFasta :: Maybe AccessionMap+ -> Maybe MatchMap+ -> T.Text+ -> Maybe Headers+ -> BamRow+ -> [T.Text]+bamToFasta aMap mMap fileHeader headers (BamRow row) =+ [ ">" <> header+ , maybe (row `at` 9) (lookupErr (row `at` 2) . unAccessionMap) aMap+ ]+ where+ header = T.intercalate "|"+ . catMaybes+ $ [ Just fileHeader+ , Just $ if isJust aMap then (row `at` 2) else (row `at` 0)+ , Just $ if isJust aMap then "" else (row `at` 3)+ , Just . bool "1" "0"+ . maybe+ (isIgnore $ row `at` 5)+ (lookupErr (row `at` 2) . unMatchMap)+ $ mMap+ , fmap unHeaders headers+ ]++-- | Append a header to the end of the header line in a fasta row.+appendHeader :: Maybe Headers -> Line -> Line+appendHeader Nothing row = row+appendHeader (Just (Headers h)) row@((T.take 1 . lineToText) -> ">") =+ unsafeTextToLine $ lineToText row <> "|" <> h+appendHeader _ row = row++-- | Create a mapping from accession number to sequence. Trinity outputs ' ' as+-- a separator.+fastaToMap :: Char -> [FastaSequence] -> AccessionMap+fastaToMap sep =+ AccessionMap . Map.fromList . fmap (\ !x -> (getField 1 sep x, fastaSeq x))++-- | Get a mapping from accession to if the cigar has all matching.+getMatchMap :: [BamRow] -> MatchMap+getMatchMap = MatchMap+ . Map.fromListWith (&&)+ . fmap (\ (BamRow !x) -> (x `at` 2, isIgnore $ x `at` 5))++-- | Better lookup error message.+lookupErr :: (Ord k, Show k) => k -> Map.Map k a -> a+lookupErr k = fromMaybe (error $ "Cannot find: " <> (show k)) . Map.lookup k++-- | Better nub.+nub' :: (Eq a, Ord a) => [a] -> [a]+nub' = Set.toList . Set.fromList++-- | Decode a SAM flag into the bit representation (as a string).+decodeSAMFlag :: Int -> String+decodeSAMFlag x = showIntAtBase 2 intToDigit x ""