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  • BioPython: extracting sequence IDs from a Blast output file

    - by Jon
    Hi, I have a BLAST output file in XML format. It is 22 query sequences with 50 hits reported from each sequence. And I want to extract all the 50x22 hits. This is the code I currently have, but it only extracts the 50 hits from the first query. from Bio.Blast import NCBIXM blast_records = NCBIXML.parse(result_handle) blast_record = blast_records.next() save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w') for alignment in blast_record.alignments: for hsp in alignment.hsps: save_file.write('>%s\n' % (alignment.title,)) save_file.close() Somebody have any suggestions as to extract all the hits? I guess I have to use something else than alignments. Hope this was clear. Thanks! Jon

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  • Reading CSV files in numpy where delimiter is ","

    - by monch1962
    Hello all, I've got a CSV file with a format that looks like this: "FieldName1", "FieldName2", "FieldName3", "FieldName4" "04/13/2010 14:45:07.008", "7.59484916392", "10", "6.552373" "04/13/2010 14:45:22.010", "6.55478493312", "9", "3.5378543" ... Note that there are double quote characters at the start and end of each line in the CSV file, and the "," string is used to delimit fields within each line. When I try to read this into numpy via: import numpy as np data = np.genfromtxt(csvfile, dtype=None, delimiter=',', names=True) all the data gets read in as string values, surrounded by double-quote characters. Not unreasonable, but not much use to me as I then have to go back and convert every column to its correct type When I use delimiter='","' instead, everything works as I'd like, except for the 1st and last fields. As the start of line and end of line characters are a single double-quote character, this isn't seen as a valid delimiter for the 1st and last fields, so they get read in as e.g. "04/13/2010 14:45:07.008 and 6.552373" - note the leading and trailing double-quote characters respectively. Because of these redundant characters, numpy assumes the 1st and last fields are both String types; I don't want that to be the case Is there a way of instructing numpy to read in files formatted in this fashion as I'd like, without having to go back and "fix" the structure of the numpy array after the initial read?

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  • Avoiding thumbnail name collisions with sorl-thumbnail

    - by Owen Nelson
    Understanding that I should probably just dig into the source to come up with a solution, I'm wondering if anyone has come up with a tactic for dealing with this. In my project, I have a lot of images being generated outside of the application. I'm isolating them on the filesystem based on a model's pk. For example, a model instance with a pk of 121 might have the following images: .../thumbs/1/2/1/img.1.jpg .../thumbs/1/2/1/img.2.jpg ... .../thumbs/1/2/1/img.27.jpg Since the image filenames themselves are not guaranteed to be unique, I'm looking for a way to inform sorl (at runtime) that I'd like to prefix thumbs for this model with the instance pk value. Is this even possible without patching sorl?

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  • Django debug error

    - by Hulk
    I have the following in my model: class info(models.Model): add = models.CharField(max_length=255) name = models.CharField(max_length=255) An in the views when i say info_l = info.objects.filter(id=1) logging.debug(info_l.name) i get an error saying name doesnt exist at debug statement. 'QuerySet' object has no attribute 'name' 1.How can this be resolved. 2.Also how to query for only one field instead of selecting all like select name from info.

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  • How to deserialize an object with pyYaml using safe_load?

    - by systempuntoout
    Having a snippet like this: import yaml class User(object): def __init__(self, name, surname): self.name= name self.surname= surname user = User('spam', 'eggs') serialized_user = yaml.dump(user) #Network deserialized_user = yaml.load(serialized_user) print "name: %s, sname: %s" % (deserialized_user.name, deserialized_user.surname) Yaml docs says that it is not safe to call yaml.load with any data received from an untrusted source; so, what do i need to modify to my snippet\class to use safe_load method? Is it possible?

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  • Django1.1 model field value preprocessing before returning

    - by Satoru.Logic
    Hi, all. I have a model class like this: class Note(models.Model): author = models.ForeignKey(User, related_name='notes') content = NoteContentField(max_length=256) NoteContentField is a custom sub-class of CharField that override the to_python method in purpose of doing some twitter-text-conversion processing. class NoteContentField(models.CharField): __metaclass__ = models.SubfieldBase def to_python(self, value): value = super(NoteContentField, self).to_python(value) from ..utils import linkify return mark_safe(linkify(value)) However, this doesn't work. When I save a Note object like this: note = Note(author=request.use, content=form.cleaned_data['content']) note.save() The conversed value is saved into the database, which is not what I wanna see. What I'm trying to do is to save the raw content into the database, and only make the conversion when the content attribute is later accessed. Would you please tell me what's wrong with this? Thanks to Pierre and Daniel. I have figured out what's wrong. I thought the text-conversion code should be in either to_python or get_db_prep_value, and that's wrong. I should override both of them, make to_python do the conversion and get_db_prep_value return the unconversed value: from ..utils import linkify class NoteContentField(models.CharField): __metaclass__ = models.SubfieldBase def to_python(self, value): self._raw_value = super(NoteContentField, self).to_python(value) return mark_safe(linkify(self._raw_value)) def get_db_prep_value(self, value): return self._raw_value I wonder if there is a better way to implement this?

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  • Django access data passed to form

    - by realshadow
    Hey, I have got a choiceField in my form, where I display filtered data. To filter the data I need two arguments. The first one is not a problem, because I can take it directly from an object, but the second one is dynamically generated. Here is some code: class GroupAdd(forms.Form): def __init__(self, *args, **kwargs): self.pid = kwargs.pop('parent_id', None) super(GroupAdd, self).__init__(*args, **kwargs) parent_id = forms.IntegerField(widget=forms.HiddenInput) choices = forms.ChoiceField( choices = [ [group.node_id, group.name] for group in Objtree.objects.filter( type_id = ObjtreeTypes.objects.values_list('type_id').filter(name = 'group'), parent_id = 50 ).distinct()] + [[0, 'Add a new one'] ], widget = forms.Select( attrs = { 'id': 'group_select' } ) ) I would like to change the parent_id that is passed into the Objtree.objects.filter. As you can see I tried in the init function, as well with kwargs['initial']['parent_id'] and then calling it with self, but that doesnt work, since its out of scope... it was pretty much my last effort. I need to acccess it either trough the initial parameter or directly trough parent_id field, since it already holds its value (passed trough initial). Any help is appreciated, as I am running out of ideas.

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  • How to Convert multiple sets of Data going from left to right to top to bottom the Pythonic way?

    - by ThinkCode
    Following is a sample of sets of contacts for each company going from left to right. ID Company ContactFirst1 ContactLast1 Title1 Email1 ContactFirst2 ContactLast2 Title2 Email2 1 ABC John Doe CEO [email protected] Steve Bern CIO [email protected] How do I get them to go top to bottom as shown? ID Company Contactfirst ContactLast Title Email 1 ABC John Doe CEO [email protected] 1 ABC Steve Bern CIO [email protected] I am hoping there is a Pythonic way of solving this task. Any pointers or samples are really appreciated! p.s : In the actual file, there are 10 sets of contacts going from left to right and there are few thousand such records. It is a CSV file and I loaded into MySQL to manipulate the data.

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  • Why is Standard Input is not displayed as I type in Mac OS X Terminal application?

    - by BryanWheelock
    I'm confused by some behavior of my Mac OS X Terminal and my Django manage.py shell and pdb. When I start a new terminal, the Standard Input is displayed as I type. However, if there is an error, suddenly Standard Input does not appear on the screen. This error continues until I shut down that terminal window. The Input is still being captured as I can see the Standard Output. E.g. in pdb.set_trace() I can 'l' to display where I'm at in the code. However, the 'l' will not be displayed, just an empty prompt. This makes it hard to debug because I can't determine what I'm typing in. What could be going wrong and what can I do to fix it?

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  • [numpy] storing record arrays in object arrays

    - by Peter Prettenhofer
    I'd like to convert a list of record arrays -- dtype is (uint32, float32) -- into a numpy array of dtype np.object: X = np.array(instances, dtype = np.object) where instances is a list of arrays with data type np.dtype([('f0', '<u4'), ('f1', '<f4')]). However, the above statement results in an array whose elements are also of type np.object: X[0] array([(67111L, 1.0), (104242L, 1.0)], dtype=object) Does anybody know why? The following statement should be equivalent to the above but gives the desired result: X = np.empty((len(instances),), dtype = np.object) X[:] = instances X[0] array([(67111L, 1.0), (104242L, 1.0), dtype=[('f0', '<u4'), ('f1', '<f4')]) thanks & best regards, peter

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  • openerp client customization

    - by iamgopal
    openerp client seems to be nice and working , i would like to hack it and use it as a front end to my open erp solution. but the documentation regarding client side design or customization is poor on openerp site , is there any good reference or documentation available for further digging in to openerp client side coding ? or more : if any similar client solution available that can be plug in to any back end system. ( i.e. rich internet client )

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  • File Uploads with Turbogears 2

    - by William Chambers
    I've been trying to work out the 'best practices' way to manage file uploads with Turbogears 2 and have thus far not really found any examples. I've figured out a way to actually upload the file, but I'm not sure how reliable it us. Also, what would be a good way to get the uploaded files name? file = request.POST['file'] permanent_file = open(os.path.join(asset_dirname, file.filename.lstrip(os.sep)), 'w') shutil.copyfileobj(file.file, permanent_file) file.file.close() this_file = self.request.params["file"].filename permanent_file.close() So assuming I'm understanding correctly, would something like this avoid the core 'naming' problem? id = UUID. file = request.POST['file'] permanent_file = open(os.path.join(asset_dirname, id.lstrip(os.sep)), 'w') shutil.copyfileobj(file.file, permanent_file) file.file.close() this_file = file.filename permanent_file.close()

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  • How to limit traffic using multicast over localhost

    - by Shane Holloway
    I'm using multicast UDP over localhost to implement a loose collection of cooperative programs running on a single machine. The following code works well on Mac OSX, Windows and linux. The flaw is that the code will receive UDP packets outside of the localhost network as well. For example, sendSock.sendto(pkt, ('192.168.0.25', 1600)) is received by my test machine when sent from another box on my network. import platform, time, socket, select addr = ("239.255.2.9", 1600) sendSock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM, socket.IPPROTO_UDP) sendSock.setsockopt(socket.IPPROTO_IP, socket.IP_MULTICAST_TTL, 24) sendSock.setsockopt(socket.IPPROTO_IP, socket.IP_MULTICAST_IF, socket.inet_aton("127.0.0.1")) recvSock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM, socket.IPPROTO_UDP) recvSock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, True) if hasattr(socket, 'SO_REUSEPORT'): recvSock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEPORT, True) recvSock.bind(("0.0.0.0", addr[1])) status = recvSock.setsockopt(socket.IPPROTO_IP, socket.IP_ADD_MEMBERSHIP, socket.inet_aton(addr[0]) + socket.inet_aton("127.0.0.1")); while 1: pkt = "Hello host: {1} time: {0}".format(time.ctime(), platform.node()) print "SEND to: {0} data: {1}".format(addr, pkt) r = sendSock.sendto(pkt, addr) while select.select([recvSock], [], [], 0)[0]: data, fromAddr = recvSock.recvfrom(1024) print "RECV from: {0} data: {1}".format(fromAddr, data) time.sleep(2) I've attempted to recvSock.bind(("127.0.0.1", addr[1])), but that prevents the socket from receiving any multicast traffic. Is there a proper way to configure recvSock to only accept multicast packets from the 127/24 network, or do I need to test the address of each received packet?

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  • Django: name of many to many items in the admin interface

    - by Adam
    I have a many to many field, which I'm displaying in the django admin panel. When I add multiple items, they all come up as "ASGGroup object" in the display selector. Instead, I want them to come up as whatever the ASGGroup.name field is set to. How do I do this? My models looks like: class Thing(Model): read_groups = ManyToManyField('ASGGroup', related_name="thing_read", blank=True) class ASGGroup(Model): name = CharField(max_length=63, null=True) But what I'm seeing the m2m widget display is:

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  • django sphinx automodule -- basics

    - by haras.pl
    Hi, I have a projects with several large apps and where settings and apps files are split. directory structure goes something like that: project_name __init__.py apps __init__.py app1 app2 3rdparty __init__.py lib1 lib2 settings __init__.py installed_apps.py path.py templates.py locale.py ... urls.py every app is like that __init__.py admin __init__.py file1.py file2.py models __init__.py model1.py model2.py tests __init__.py test1.py test2.py views __init__.py view1.py view2.py urls.py how to use a sphinx to autogenerate documentation for that? I want something like that for each in settings module or INSTALLED_APPS (not starting with django.* or 3rdparty.*) give me a auto documentation output based on docstring and autogen documentation and run tests before git commit btw. I tried doing .rst files by hand with .. automodule:: module_name :members: but is sucks for such a big project, and it does not works for settings Is there an autogen method or something? I am not tied to sphinx, is there a better solution for my problem?

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  • Formatting inline many-to-many related models presented in django admin

    - by Jonathan
    I've got two django models (simplified): class Product(models.Model): name = models.TextField() price = models.IntegerField() class Invoice(models.Model): company = models.TextField() customer = models.TextField() products = models.ManyToManyField(Product) I would like to see the relevant products as a nice table (of product fields) in an Invoice page in admin and be able to link to the individual respective Product pages. My first thought was using the admin's inline - but django used a select box widget per related Product. This isn't linked to the Product pages, and also as I have thousands of products, and each select box independently downloads all the product names, it quickly becomes unreasonably slow. So I turned to using ModelAdmin.filter_horizontal as suggested here, which used a single instance of a different widget, where you have a list of all Products and another list of related Products and you can add\remove products in the later from the former. This solved the slowness, but it still doesn't show the relevant Product fields, and it ain't linkable. So, what should I do? tweak views? override ModelForms? I Googled around and couldn't find any example of such code...

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  • Django models avaoid duplicates

    - by Hulk
    In models, class Getdata(models.Model): title = models.CharField(max_length=255) state = models.CharField(max_length=2, choices=STATE, default="0") name = models.ForeignKey(School) created_by = models.ForeignKey(profile) def __unicode__(self): return self.id() In templates <form> <input type="submit" save the data/> </form> If the user clicks on the save button and the above data is saved in the table how to avoid the duplicates,i.e, if the user again clicks on the same submit button there should not be another entry for the same values.Or is it some this that has to be handeled in views Thanks..

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  • Modify headers in Pylons using Middleware

    - by Anders
    Hi all, I'm trying to modify a header using Middleware in Pylons to make my application RESTful, basically, if the user request "application/json" via GET that is what he get back. The question I have is, the variable headers is basically a long list. Looking something like this: [('Content-Type', 'text/html; charset=utf-8'), ('Pragma', 'no-cache'), ('Cache-Control', 'no-cache'), ('Content-Length','20'), ('Content-Encoding', 'gzip')] Now, I'm looking to just modify the value based on the request - but are these positions fixed? Will 'Content-Type' always be position headers[0][0]? Best Regards, Anders

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  • Rebuilding website from Django 0.96 to Django 1.2

    - by Neytiri
    I've got a website done in Django 0.96 (done in 2007), and now we are thinking about rebuilding it (not just migrating) for Django 1.2 . Can anyone point me to the new (and worth the while) widgets, plugins and other stuff for Django 1.2 (released in april 2010). I've heard of "South" and of a widget for debugging (can't remember the name), but I'm a little lost here.

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  • How to chroot Django

    - by Brian M. Hunt
    Can one run Django in a chroot? Notably, what's necessary in order to set up (for example) /var/www as a chroot'd directory and then have Django run in that chroot'd directory? Thank you - I'm grateful for any input.

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  • What is the correct way to backup ZODB blobs?

    - by joeforker
    I am using plone.app.blob to store large ZODB objects in a blobstorage directory. This reduces size pressure on Data.fs but I have not been able to find any advice on backing up this data. I am already backing up Data.fs by pointing a network backup tool at a directory of repozo backups. Should I simply point that tool at the blobstorage directory to backup my blobs? What if the database is being repacked or blobs are being added and deleted while the copy is taking place? Are there files in the blobstorage directory that must be copied over in a certain order?

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  • Calling activateWindow on QDialog sends window to background

    - by Stan
    I am debugging certain application written with C++/Qt4. On Linux it has problems that with certain window managers (gnome-wm/metacity), the main window (based on QDialog) is created in the background (it's not raised). I managed to re-create the scenario using PyQt4 and following code: from PyQt4.QtCore import * from PyQt4.QtGui import * import sys class PinDialog(QDialog): def showEvent(self, event): QDialog.showEvent(self, event) self.raise_() self.activateWindow() if __name__ == "__main__": app = QApplication(sys.argv) widget = PinDialog() app.setActiveWindow(widget) widget.exec_() sys.exit(0) If I remove self.activateWindow() the application works as expected. This seems wrong, since documentation for activateWindow does not specify any conditions under which something like this could happen. My question is: Is there any reason to have activateWindow in showEvent in the first place? If there is some reason, what would be good workaround for focusing issues?

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  • What algorithms are suitable for this simple machine learning problem?

    - by user213060
    I have a what I think is a simple machine learning question. Here is the basic problem: I am repeatedly given a new object and a list of descriptions about the object. For example: new_object: 'bob' new_object_descriptions: ['tall','old','funny']. I then have to use some kind of machine learning to find previously handled objects that had similar descriptions, for example, past_similar_objects: ['frank','steve','joe']. Next, I have an algorithm that can directly measure whether these objects are indeed similar to bob, for example, correct_objects: ['steve','joe']. The classifier is then given this feedback training of successful matches. Then this loop repeats with a new object. a Here's the pseudo-code: Classifier=new_classifier() while True: new_object,new_object_descriptions = get_new_object_and_descriptions() past_similar_objects = Classifier.classify(new_object,new_object_descriptions) correct_objects = calc_successful_matches(new_object,past_similar_objects) Classifier.train_successful_matches(object,correct_objects) But, there are some stipulations that may limit what classifier can be used: There will be millions of objects put into this classifier so classification and training needs to scale well to millions of object types and still be fast. I believe this disqualifies something like a spam classifier that is optimal for just two types: spam or not spam. (Update: I could probably narrow this to thousands of objects instead of millions, if that is a problem.) Again, I prefer speed when millions of objects are being classified, over accuracy. What are decent, fast machine learning algorithms for this purpose?

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