fomightez

# generate output file name
def generate_output_file_name(id_of_seq_element,id_of_seq_scanned):
    '''
    Takes a file name as an argument and returns string for the name of the
    output file. The generated name is based on a prefix that can be adjusted
    under the section ' USER ADJUSTABLE VALUES ', plus the provided text in 

fomightez

# see https://gist.github.com/fomightez/ef57387b5d23106fabd4e02dab6819b4 for 
# the main ones dealing with BLAST and dataframes, search `blast` to find

# see two Jupyter notebooks in https://github.com/fomightez/blast-binder


# SEE MOE FUNCTIONAL VERSION OF THIS FUNCTION AT https://github.com/fomightez/sequencework/tree/master/blast-utilities
def BLAST_to_df(results_file):
    '''
    BLAST results to Pandas dataframe

fomightez

# This is not presently all encompassing as it was started well after my sequence work repo 
# at https://github.com/fomightez/sequencework , where much of this related code is.



# For making FASTA files/entriees out of dataframes, see 'specific dataframe contents saved as formatted text file example'
# in my useful pandas snippets gist https://gist.github.com/fomightez/ef57387b5d23106fabd4e02dab6819b4

fomightez

import time

def executeSomething():
    #code here
    print ('.')
    time.sleep(480) #60 seconds times 8 minutes

while True:
    executeSomething()

fomightez

# I like the example at https://inventwithpython.com/blog/2019/06/05/pythonic-ways-to-use-dictionaries/ better than this one I had found earlier>
##
##
def dispatch_dict(operator, x, y):
    '''
    Python to emulate switch/case statements
    
    based on https://books.google.com/books?id=C0VKDwAAQBAJ&pg=PT226&lpg=PT226&dq=%22dispatch_dict+(operator%22&source=bl&ots=Ja0bhOYv9A&sig=j7OZGsWpps97z8jHByquiYIuRBY&hl=en&sa=X&ved=2ahUKEwjW4siOl8fcAhWKTN8KHSa3ApYQ6AEwAnoECAMQAQ#v=onepage&q=%22dispatch_dict%20(operator%22&f=false
    https://twitter.com/w_cazzola/status/1023917802627973126
    https://gist.github.com/carlessanagustin/6d7584b963338426a3691d355fe28f55

fomightez

# Use `%%capture` to hush 'noisy' stdout and stderr streams, but still combine with getting `%%time` after
%%capture out_stream
%%time
---rest of a cell that does something with LOTS of output--
#In cell after, put following to get time of completion from that:
#time it took to run cell above 
for x in out_stream.stdout.split("\n")[-3:]:
    print(x)

fomightez

CLUSTAL multiple sequence alignment by MUSCLE (3.8)


STV1            -MNQEEAIFRSADMTYVQLYIPLEVIREVTFLLGKMSVFMVMDLNKDLTAFQRGYVNQLR
VPH1            MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
                  ::********:*: **:*** *: *: :: **::.:. . ***..: **** :**::*

STV1            RFDEVERMVGFLNEVVEKHAAETW-----KYILHIDDEGNDIAQPDMADLINTMEPLSLE
VPH1            RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYL----DGSGELYVPPSGSVI---------
                *:*:***   :: .:::**  : :     **:    * ..::  *  ..:*         

fomightez

# from `get_seq_following_seq_from_FASTA.py`
if __name__ == "__main__" and '__file__' in globals():
    """ This is executed when run from the command line """
    # Code with just `if __name__ == "__main__":` alone will be run if pasted
    # into a notebook. The addition of ` and '__file__' in globals()` is based
    # on https://stackoverflow.com/a/22923872/8508004
    # See also https://stackoverflow.com/a/22424821/8508004 for an option to 
    # provide arguments when prototyping a full script in the notebook.
    ###-----------------for parsing command line arguments-------------------###
    import argparse

fomightez

import difflib
from wasabi import color

def diff_strings(a, b):
    output = []
    matcher = difflib.SequenceMatcher(None, a, b)
    for opcode, a0, a1, b0, b1 in matcher.get_opcodes():
        if opcode == "equal":
            output.append(a[a0:a1])
        elif opcode == "insert":

fomightez