Saravanan666/pypi-org huggingface dataset:
Package: tnote-cli
tnote-cliA simple notes Command line tool, because I really got tired of either:A. going from the terminal into another app to write something down for later
or
B. Forgetting which configuration file is where and not having a convenient place where all my notes could be keptPlus I really just wanted a project to work on.Installationpip install tnote-cliUsageUsing tnote is pretty simple when it really comes down to it as there is only one command that has several options.IndexThe index of all the notes you've created can be accessed by$ tnotewith no arguments.
At any point you can use$ tnas it is the same because who has time for all those extra keystrokes.$ tnote 
|-------------------------INDEX-------------------------|


|-------------------------RECENT------------------------|
 Note ID: todo
 Name: todo.md
 Path: /Users/username/.tnote/notes/todo.md
|-------------------------------------------------------|
    
            _________________________________
            

|-------------------------------------------------------|
 Note ID: todo
 Name: todo.md
 Path: /Users/username/.tnote/notes/todo.md
|-------------------------------------------------------|At first your index obviously won't look like this but create a note and you'll be good.
Up at the top there it will show you want is your most recently edited note which can be accessed
using the$ -rflag.Creating and Editing NotesTo create a new note you need only type in a name for a note like so$ tn EXAMPLEand a note will be created and
you'll begin editing it. You can also specify editing with the$ -eflag. The editor used will be the$EDITORenvironment variable but it can also be changed in the config at~/.tnote.json$ tnote -e Example$ tn ExampleViewTnote was designed with using markdown in mind as it is how I frequently take notes as
such if you wish to render it from your terminal use the view flag.$ tnote -v ExampleMoving and RenamingIf you wish to rename a file simply do so by passing the same path other than the filename to the move option:$ tnote Example -m ~/tnote/notes/new_name.mdotherwise just pass a fully qualified path with filename to move the file:$ tnote Example -m ~/Example.mdDeleteTo permenantly delete a note:$ tnote -d ExampleChange IDIF you want to change the Id you use to access notes you do so as shown below$ tnote Example -i new-idto access this note in the future you'll usenew-idExecuteFrom time to time I like to have some simple scripts on-hand for quick access
so I have allowed a way to simply execute from my notesExecute a file that has permissions:tnote Script -xGive a file permission (chmod) and execute it:tnote Script -xx
Package: tnote-plus
tnote_________ _        _______ _________ _______       _    
             \__   __/( (    /|(  ___  )\__   __/(  ____ \     ( )   
                ) (   |  \  ( || (   ) |   ) (   | (    \/     | |   
                | |   |   \ | || |   | |   | |   | (__       __| |__ 
                | |   | (\ \) || |   | |   | |   |  __)     (__   __)
                | |   | | \   || |   | |   | |   | (           | |   
                | |   | )  \  || (___) |   | |   | (____/\     | |   
                )_(   |/    )_)(_______)   )_(   (_______/     (_)A dead simple command line note taking app built for you! The original project lives here:https://github.com/tasdikrahman/tnoteAt the time of forking the project, there had been not updates in 4 years with 11 issues. I thought it was interesting
enough to at least fork it and give it a shot.IndexDemoFeaturesInstallationInstalling dependenciesClone itRun itSupported platformsContributingTo-doContributersIssuesLicenseFeatures:arrow_up: Back to topDead simple to use: Even your granny would be able to use it. No seriously!Feature richAdd your precious note with it'stitle,content,tagsNOTEThis was built and testing in Linux - use on other OS's at your own riskText Highlighting is cross platform- Supports Linux, Windows, MAC for the terminal based highlighting.Searching for notes is hassle freeintnote: It supports full text search for notes based oncontent,tagsThe search query if found in the database will be highlighted if found. Looks pleasing to the eyesAbility to add and remove tags for each note.Adds timestamp for each note which has been added.Written in uncomplicated python.Need I say more?Installation:arrow_up: Back to topIf poetry is on the system:poetry installRun itFire it up! :volcano:poetry run ./tnote_plus/tnote.pyContributing:arrow_up: Back to topThis project was originally created in a few hours and utilizespeewee (ORM). It
was then forked by acherrera to do more work.DependenciesDependencies are managed withPython Poetry. This is also used to publish the package.Install poetry withcurl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -Deploymentpoetry buildwill build the project.poetry publishwill publish the package to a repository.To-doConvert color handling to RichAdd initial testsAdd github actions for testsMake it pip installableAbility to edit the content of a noteAdd option to remove title for notesAdd option to search for notes using titleAdd option to search for notes using timestampList titles with number and open based on numberContributersA big shout out to all the contributers, more specifically to these guysOG contributers:@maxwellgerber@BrandtMMotivation:arrow_up: Back to topOriginal project had not had updates for 4 years, so I thought I would try my hand at understanding what was going on
and expanding upon the project.Issues:arrow_up: Back to topYou can report the bugs at theissue trackerLicense:arrow_up: Back to topYou can find a copy of the License athttp://prodicus.mit-license.org/
Package: t-notes
TNotesProgram for quick terminal-based notes.UsageAfter installing with$ pip install t-notescreate/choose a note with$ tnotes note [note name](default is firstnote, and folders are accepted).To see the current note,$ tnotes currentTo create a note entry, simply$ t [your note]To modify it, just$ tt [index]where the index starts from 0 (last entry). If no index is entered, default is 0.To save it to a file,$ tnotes save [filename]To change any of the settings,$ tnotes config [config name] [new value](config file in .tnotes)Note: Every entry is saved with a timestamp, and modifications do not delete the old version, which can be accessed in the tnotes folder (in home)
Package: tnprofanity
tn-profanity-pythonSupport Python3,
for Python2 please use version 0.3.4 or belowfilter profane word in Thai / English by censoring blacklist wordsThai profane words are provided !How To> from tnprofanity.tnprofanity import Profane

> Profane.censor(u"สวัสดีครับ คุณควาย เป็นยังไงบ้างครับ", whitelist =[u"บ้าง"],  blacklist = [u"บ้า", u"ควาย"], mode = "preserve")
u"สวัสดีครับ คุณ**** เป็นยังไงบ้างครับ")

> Profane.censor(u"แม่งเอ้ย อย่ามาถุยน้ำลายใส่กับข้าวของลูกค้าสิครับ", whitelist =[u"น้ำ"],  blacklist = [u"แม่ง", u"ถุยน้ำลาย"], mode = "preserve", mark="X")
u"XXXXเอ้ย อย่ามาXXXXXXXXXใส่กับข้าวของลูกค้าสิครับ"

> Profane.censor(u"boobs size porn", blacklist = [u"boobs", u"porn"])
u"***** size ****"

> Profane.check(u"มาทำไมอีก อีควาย", whitelist=[u"อีก"], blacklist=[])
[(u'\\u0e2d\\u0e35', 10, 12), (u'\\u0e04\\u0e27\\u0e32\\u0e22', 12, 16)]
# [(u"อี", 10, 12), (u"ควาย", 12, 16)]mode for merging whitelist / blacklist conflict"preserve" : (default) preserve white term if conflict with black term"overlap" : preserve white term but still censor partial of black term"ignore" : ignore white termfor very positive-case exampleinput text ได้จากhttps://th.uncyclopedia.info/wiki/%E0%B8%84%E0%B8%B3%E0%B8%AB%E0%B8%A2%E0%B8%B2%E0%B8%9A%E0%B8%84%E0%B8%B2%E0%B8%A2ที่หัวข้อคำหยาบอันตรายcensor text :****พ่อ**********เอง เอาปืนพกยิง**ยิง*******พ่อ**********สิ **จะเอาปืนยิง*** **สัตว์ ******เป็ด **แตด ดูด***ปลิ้น สิ้นน้ำเชื้อ เจืออสุจิ หัว*** นรก******* ช้างลากกระโดด**** **นกเป็ดน้ำ ****ต่ำช้า *******สิ้นชีพ สก**** เศษนรก ***ยมทูต ******* ******* ****ไม่เลือก*****ตลอด ยอด***** **วาฬ **โรส ********จิ๊กโกะ **จะเอาปืนกลไปยิง****สะ โอตะ **หน้า**** **ซวยแปดตลบ ****กลบทราย ***สิงโต********* **พระราม ***พระลักษมณ์ ***นนทก **สุครีพ ***นางสีดา **ทศกัณฐ์ **ไมยราพ ***หนุมาน ***มัจฉานุ หันแตด*** **กระทิงเปลี่ยว เลี้ยว**ลงรู **จะเอาปืนกลไปยิงใส่พ่อ***สิ ไซเรนตำรวจดัง**** **จะเฟี่ยงระเบิดใส่*** **จะเอารถถังไปยิง*****หูหมี**ปลาเอ๋ง **กระหรี่ไขมันจุกแตด **ฟันจระเข้ **มังกรคอมมานโด้ ไอ*****แม้ว กวน****** **วาฬสีน้ำเงิน *****สะพานขาว ******ไบซั่น **ลาวลืมชาติ **มีดบาด** **ฟัน***บ้า **แตดแสบสันต์ **ฟันฉลาม ************** **พล่อยทะเล**** **ปลาเงือก *****พะยูน *****ปลาวาฬ การะบูนลูบ** ******จุกปาก **ลาก******* **เบ็ดไม่มีที่สิ้นสุด **ทรุดกลางฟลอร์ **ดอเหม็น **เมนส์ ย้อนกลับ **ตับแดง **แฝง*****บ้า **หมัดเกาะ** **โลนเซาะ**** **ผังผืดหนอน **อ้วนนรกแตก **กระเทย******* ***คิดว่าคำด่าพ่อด่า****ันสะกดยากนักสิ อย่าให้**เห็น*****กนะ อย่านึกว่า**ไม่รู้หรือ***เหมือน****เหง้าศักราชญาติ*** ***** **แก่หนัง***** **พจมาน
Package: tnpy
tnpyDocumentation|This project is a python implementation of Tensor Network,
a numerical approach to quantum many-body systems.tnpyis built on top ofquimb,
along withTensorNetworkfor tensor contractions,
with optimized support for various backend engines (TensorFlow, JAX, PyTorch, and Numpy).
For eigen-solver we adoptprimme,
an iterative multi-method solver with preconditioning.Currently, we support Matrix Product State (MPS) algorithms,
with more are coming...Finite-sized Density Matrix Renormalization Group (fDMRG)Tree tensor Strong Disorder Renormalization Group (tSDRG)fDMRG & tSDRG are on alpha-release.
For others, please expect edge cases.RequirmentsSeepyproject.tomlfor more details.
But these two are essential building blocks.jcmgray/quimbgoogle/Tensornetworkprimme/primmeRegarding any installation problems with Primme,
please refer toPrimme official.
Also, it's required to havelapackandblasinstalled in prior to Primme.Installationusing Dockerdocker run --rm -it tanlin2013/tnpyusing pip:pip install tnpyfor the latest release, orpip install git+https://github.com/tanlin2013/tnpy@mainfor the development version.DocumentationFor details abouttnpy, see thereference documentation.Getting startedDefining the Matrix Product Operator of your model as a Callable function with argumentsiteof the typeint,
e.g. the function_elem(self, site)below.
The MPO class then accepts the Callable as an input and constructs a MPO object.import numpy as np
from tnpy.operators import SpinOperators, MPO
from tnpy.finite_dmrg import FiniteDMRG

class XXZ:

    def __init__(self, N: int, delta: float) -> None:
        self.N = N
        self.delta = delta

    def _elem(self, site: int) -> np.ndarray:
        Sp, Sm, Sz, I2, O2 = SpinOperators()
        return np.array(
            [[I2, -0.5 * Sp, -0.5 * Sm, -self.delta * Sz, O2],
             [O2, O2, O2, O2, Sm],
             [O2, O2, O2, O2, Sp],
             [O2, O2, O2, O2, Sz],
             [O2, O2, O2, O2, I2]]
        )
     
    @property
    def mpo(self) -> MPO:
        return MPO(self.N, self._elem)Call the algorithm to optimize the state.N = 100  # length of spin chain
chi = 60  # virtual bond dimension 

model = XXZ(N, delta)
fdmrg = FiniteDMRG(
    mpo=model.mpo,
    chi=chi
)
fdmrg.update(tol=1e-8)Compute any physical quantities whatever you want from the obtained state.
The resulting MPS is of the typetensornetwork.FiniteMPS,
seeherefor more details.my_mps = fdmrg.mps
Package: tnqmetro
TNQMetroTNQMetro is a numerical package written in Python 3 for calculations of fundamental quantum bounds on measurement precision. Thanks to the usage of the tensor-network formalism it can beat the curse of dimensionality and provides an efficient framework to calculate bounds for finite size system as well as determine the asymptotic scaling of precision in systems where quantum enhancement amounts to a constant factor improvement over the Standard Quantum Limit. It is written in a user-friendly way so that the basic functions do not require any knowledge of tensor networks.Introduction to the package alongside simple examples can be found in the paperComputer Physics Communications274, 108282 (2022).Documentation to the package can be found on theGitHub wiki.In-depth explanation of the tensor-network based approach to calculations of fundamental quantum bounds on measurement precision can be found in the paperNature Communications11, 250 (2020).DependenciesTNQMetro requiresNumPyandnconpackage.Installationpip install tnqmetroExample of usageExample of optimization of QFI using TNQMetro for N=1000 qubits with OBC and in the asymptotic regime for the problem of phase estimation with uncorrelated dephasing noise.import numpy as np
import scipy.linalg
import tnqmetro

N = 1000 # number of sites in tensor-network (in this example one site = one qubit)
d = 2 # dimension of local Hilbert space (dimension of physical index)
h = np.arange(d)
h = np.diag(h) # local generator ("Hamiltonian")
c1 = 1. # uncorrelated noise strength parameter
aux = np.kron(h, np.eye(d)) - np.kron(np.eye(d), h)
Y = scipy.linalg.expm(-c1 * aux @ aux / 2) # local superoperator for uncorrelated dephasing noise

F_f, F_m_f, L_MPO_f, psi_MPS_f = tnqmetro.fin(N, [], h, [Y]) # finite appraoch
F_i, F_m_i, L_MPO_i, psi_MPS_i = tnqmetro.inf([], h, [Y]) # infinite appraoch
Package: tn-radio
TAMILNADU ONLINE FM RADIOIn this packagetamil nadulocal online Fm StationINSTALL PACKAGEsudo apt-get install vlcpip install tn-radioIMPORT PACKAGEPython3.7.3(default,Oct72019,12:56:13)[GCC8.3.0]onlinuxType"help","copyright","credits"or"license"formoreinformation.importtn_radioobj=tn_radio.Radio()LIST OF FM STREAMPython3.7.3(default,Oct72019,12:56:13)[GCC8.3.0]onlinuxType"help","copyright","credits"or"license"formoreinformation.importtn_radioobj=tn_radio.Radio()obj.list_fm()0OhmNamashivaya[Chennai,India]1NamakkalThedalFM[Namakkal,India]2NatrinaiFM[Tiruchirappalli,India]3PudukkottaiThedalFM[Pudukkottai,India]4முத்தமிழ்FMமேலூர்[Melur,India]5VirudhunagarThedalFM[Virudhunagar,India]SET STREAM FM INDEXPython3.7.3(default,Oct72019,12:56:13)[GCC8.3.0]onlinuxType"help","copyright","credits"or"license"formoreinformation.importtn_radioobj=tn_radio.Radio()obj.set_stream(3)PLAY FMPython3.7.3(default,Oct72019,12:56:13)[GCC8.3.0]onlinuxType"help","copyright","credits"or"license"formoreinformation.importtn_radioobj=tn_radio.Radio()obj.set_stream(3)obj.play()STOP FMobj.stop()PAUSE FMobj.pause()CHANGE FM STREAMobj.set_stream(5)
Package: tns
# Top-news-selectors (tns)A static HTML site parser for parsing the top story titles and URIs for the following websites:https://www.washingtonpost.com/http://www.foxnews.comhttp://abcnews.go.com/https://www.nytimes.com/https://www.usatoday.com/https://www.cbsnews.com/http://www.chicagotribune.com/https://www.nbcnews.com/http://www.latimes.com/https://www.npr.org/https://www.wsj.com/This parser is built on [Beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/doc/) based on the CSS selectors found inside the respective HTML documents.
These selectors were chosen based on the selectors that were present during the 30 days for the month ofNovember 2016.This package has not been tested beyond the month of November 2016, 11/01/2016 - 11/30/2016.
Use at your own risk when going beyond that range.## InstallThis package is available via pip:` $ pip install tns `## Usage`python >>> from tns import SiteParser >>> html =open('npr.html').read()>>> parser = SiteParser(html) >>> parser.npr() { 'hero_text': "foo", 'hero_link':'http://bar.com','headlines':[{'splash_title':'baz', 'link':'http://qux.com'}]} >>> parser.washingtonpost() {'hero_text': '', 'hero_link': '', 'headlines': []} `The keyshero_textandhero_linkrefer to the top most identified news post, often identified by a enlarged picture or text across the top of the page.
Headlines refer to the subsequent headlines after the hero article, wheresplash_titlerefers to the title found on the home page of the site not the actual title of the article.You can see that the second function call with parser,parser.washingtonpost(), has zero entries because the document passed to SiteParser was not intended for that parser.Each of the sites are paired to a function:`python"http://abcnews.go.com/":parser.abcnews()"https://www.cbsnews.com/":parser.cbsnews()"https://www.nbcnews.com/":parser.nbcnews()"https://www.washingtonpost.com/":parser.washingtonpost()"https://www.npr.org/":parser.npr()"http://www.latimes.com/":parser.latimes()"https://www.usatoday.com/":parser.usatoday()"https://www.wsj.com/":parser.wsj()"https://www.nytimes.com/":parser.nytimes()"http://www.foxnews.com":parser.foxnews()"http://www.chicagotribune.com/":parser.chicagotribune() `## DebuggingWhen the parser fails to find specific headlines or returns no headlines at all, this could be due to:Iframes loading content dynamicallyHeadlines being injected via JavascriptThe wrong parser is being used for the specified site
Package: tns-api
tns_apiAPI to access Transient Name Server (TNS) dataInstallationIt is recommended to installtns_apifrom pip:pipinstalltns_apior it can be installed from source in the usual way.Usage ExampleBelow are some basic examples of what the user can do with this package.Environmental VariablesFirst of all, you will need to set a.envfile in the current directory with the following variables:tns_id = 'YOUR_TNS_ID'
name = 'YOUR_BOT_NAME'
api_key = 'YOUR_API_KEY'where the values for these can be obtained by creating aBOT(for mor information, check theTNS Help page).Retrieving PropertiesAll the properties of an object can be obtained with a single line:fromtns_apiimportget_objectget_object('2004eo'){'objname':'2004eo','name_prefix':'SN','objid':2980,'object_type':{'name':'SN Ia','id':3},'redshift':None,'ra':'20:32:54.190','dec':'+09:55:42.71','radeg':308.22579,'decdeg':9.92853,'radeg_err':None,'decdeg_err':None,'hostname':'NGC 6928        ','host_redshift':None,'internal_names':None,'discoverer_internal_name':None,'discoverydate':'2004-09-17 00:00:00.000','discoverer':None,'reporter':None,'reporterid':None,'source':'bot','discoverymag':17.8,'discmagfilter':{'id':None,'name':None,'family':None},'reporting_group':{'groupid':None,'group_name':None},'discovery_data_source':{'groupid':None,'group_name':None},'public':1,'end_prop_period':None}ContributingTo contribute, either open an issue or send a pull request (prefered option). You can also contact me directly (check my profile:https://github.com/temuller).Citing TNS APIIf you make use of this code, please cite it:coming soon
Package: tnscm
TNSCMTNSCM(Tenable Nessus CLI Manager)by LimberDuck is a CLI tool which enables you to perform certain actions on Nessus by (C) Tenable, Inc. via Nessus API.Main featuresInitial version ofTNSCMlets you perform actions like:plugin family listpolicylistdeletescanlistdeleteserver infostatuslicensed IPsversionadvanced settings listuser listTo filter data to specific values you can useJMESPath.InstallationNote:It's advisable to use python virtual environment for below instructions. Read more about python virtual environment inThe Hitchhiker’s Guide to Python!Read aboutvirtualenvwrapper in The Hitchhiker’s Guide to Python!:virtualenvwrapperprovides a set of commands which makes working with virtual environments much more pleasant.InstallTNSCMpip install tnscmTo upgrade to newer version run:pip install -U tnscmRunTNSCMtnscmCommandsoption / commandpluginpolicyscanserversettingsuser--helpyesyesyesyesyesyes--listyesyesyesyes--list-familyyes--deleteyesyes--filteryesyesyesyesyes--formatyesyesyesyesyes--statusyes--ipsyes--versionyesExample filtersTo check possible keys and values by returning only first entry:--filter "[] | [0]" --format jsonTo get only name and id columns:--filter "[].{id: id, name: name}"To sort byidcolumn:--filter "sort_by([], &id)[].{id: id, name: name}"To filter returned data to these items whichnamecontainexampl:--filter "[? contains(name, 'exampl')].{id: id, name: name}"To filter returned data to these items whichnamecontainexampl1orexampl2:--filter "[? contains(name, 'exampl1') || contains(name, 'exampl2')].{id: id, name: name}"To filter returned data to item whichidis equal to number10:--filter '[?id==`10`].{id: id, name: name}'To filter returned data to item whichnameis equal to stringtest name:--filter "[?name == 'test name'].{id: id, name: name}"To filter returned data to items whichnameis different than stringtest name:--filter "[?name != 'test name'].{id: id, name: name}"MetaChange logSeeCHANGELOG.LicenceMIT:LICENSE.AuthorsDamian KrawczykcreatedTNSCM(Tenable Nessus CLI Manager)by LimberDuck.
Package: tnseq-transit
TRANSIT=======NOTE: TRANSIT v3.0+ now requires python3.6+. If you want to use TRANSIT with python2, use version < 3.0.Welcome! This is the distribution for the TRANSIT and TPP tools developed by theIoerger Labat Texas A&M University.TRANSIT is a tool for processing and statistical analysis of Tn-Seq data.
It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.TRANSIT Home page:http://saclab.tamu.edu/essentiality/transit/index.htmlTRANSIT Documentation:https://transit.readthedocs.io/en/latest/transit_overview.htmlChangelogFeaturesTRANSIT offers a variety of features including:More than10 analysis methods, including methods for determiningconditional essentialityas well asgenetic interactions.Ability to analyze datasets from libraries constructed usinghimar1 or tn5 transposons.TrackViewto help visualize read-counts across the genome.Canexport datasetsinto a variety of formats, includingIGV.Includes avariety of normalization methods.Quality Controldiagnostics, to idenfity poor quality datasets.Ability to install as apython package, to import and use in your own personal scripts.SupportFor any questions or comments, please contact Dr. Thomas Ioerger,ioerger@cs.tamu.edu.InstructionsFor full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("src/pytransit/doc" folder) or visit the following web page:https://transit.readthedocs.io/en/latest/DatasetsThe TRANSIT distribution comes with some example .wig files in the data/ directory, as well as an example annotation file (.prot_table format) in the genomes/ directory. Additional genomes may be found on the following website:http://saclab.tamu.edu/essentiality/transit/genomes/Copyright InformationSource code for TRANSIT and TPP are available open source under the terms of the GNU General Public License (Version 3.0) as published by the Free Software Foundation. For more information on this license, please see the included LICENSE.md file or visit their website at:http://www.gnu.org/licenses/gpl.html
Package: tnsgrt
tnsgrtThis package contains classes and functions that facilitate the design and analysis of tensegrity structures.
It started as a matlab toolbox many years ago written by Mauricio de Oliveira and Joseph Cessna, which is now been
ported to Python.It relies heavily onnumpy,scipy,pandas, andcvxpyfor computations.Visualization is supported viamatplotlibandvispy.InstallationInstall with pip by typing:pip install tnsgrtDocumentationSee onread the docs.
Package: tn-slack-py-module
ReadmeUpdateWhen updating this module remember to change the version in setup.cfg
when updating setup.cfg use an editor that does not autoformat due to a format requirement for this file
e.g use vim (the bug is caused on the line under package_src it needs the tab indent on the '= src' )This is a repo for a slack builder pluginBuildcurrently this is built only on pypi testpython -m buildpython -m twine upload --repository pypi dist/*
Package: tns-piler
PilerRequirementsPython >= 3.6pysamgffuitlsInstallationpipinstalltns-pilerUsageCumulative Pileups of particular genesPiler-d[GFFutilsformattedannotation]-t[EnsembltranscriptID]-o[Outlocation][Indexedbamfiles]OutputCSV with cumulative pileups for each position along the gene, no introns, first column is file name