| from irs import * | |
| from urllib import urlopen | |
| gids = ['AB019734.1', 'X86636.1', 'X86650.1', 'AB009938.1'] | |
| def rettaxids(gids): | |
| ''' Retrieves TaxIDs given a list of GeneIDs ''' | |
| # Always tell NCBI who they're messing with | |
| email = 'harekrishna@gmail.com' |
| ==> RANDOM <== | |
| CCACTGA => 19766 | |
| GAATATA => 19779 | |
| TTGCACT => 19648 | |
| ATGTCGG => 19808 | |
| GGTATGG => 19745 | |
| TTGGTAA => 19681 | |
| CTGTACG => 19721 | |
| TAACGCG => 19789 | |
| CGTGTCT => 19664 |
| [branch "master"] | |
| remote = origin | |
| merge = refs/heads/master | |
| [remote "sourceforge"] | |
| url = ssh://username@project.git.sourceforge.net/gitroot/project/project | |
| fetch = +refs/heads/*:refs/remotes/origin/* | |
| mirror = true |
| #!/usr/bin/env python | |
| # encoding: utf-8 | |
| ''' | |
| Solves Sudoku Boards In Due Time | |
| Austin G. Davis-Richardson | |
| Board.txt: | |
| 5 3 0 0 7 0 0 0 0 | |
| 6 0 0 1 9 5 0 0 0 | |
| 0 9 8 0 0 0 0 6 0 |
| #!/usr/bin/perl | |
| (my$d=q[AA GTCAGTTCCT | |
| CGCTATGTA ACACACACCA | |
| TTTGTGAGT ATGTAACATA | |
| CTCGCTGGC TATGTCAGAC | |
| AGATTGATC GATCGATAGA | |
| ATGATAGATC GAACGAGTGA | |
| TAGATAGAGT GATAGATAGA | |
| GAGAGA GATAGAACGA | |
| TC GATAGAGAGA |
| # Add lib | |
| def madlib(word1, word2): | |
| print 'the %s sat on the %s' % (word1, word2) | |
| word1 = 'cat' | |
| word2 = 'mat' |
| # SHANNON ENTROPY FUNCTION | |
| def entropy(string) | |
| entropy = 0 | |
| prob = [] | |
| string.split(//).uniq.each do |c| | |
| prob << string.count(c).to_f / string.length | |
| end | |
| prob.each do |p| | |
| entropy += p*Math.log(p)/Math.log(2.0) | |
| end |
| DESCRIPTION = ''' | |
| Duplicate filtering for FASTQ/FASTA data. | |
| If there are at least N duplicates in X basepairs, discard the read (in both pairs). | |
| usage python filter.py <sequences> <N> <X> | |
| ''' | |
| import sys | |
| from itertools import izip | |
| from collections import defaultdict |
I really love using Mendeley.
I feel like knowing about it before my classmates has given me an edge.
Especially when collaborating with others.
(the shared collection thing is awesome. Is there going to be some kind of copyright issue in the future?)
Since it's in beta, I thought now would be a good time to make suggestions:
| # "They were all engaged in manual labour, but all smiling." | |
| codon_table = { | |
| 'UUU': 'F', | |
| 'UUC': 'F', | |
| 'UUA': 'L', | |
| 'UUG': 'L', | |
| 'CUU': 'L', | |
| 'CUC': 'L', |
