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Step 1: eliminate all but description line of FASTA entries

First to reduce to just lines beginning with carets, i.e., leave only the description line (<---from http://stackoverflow.com/questions/7310598/remove-all-lines-without-an-character-in-notepad)

FIND:

^[^>]*$

REPLACE:

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Left-Aligned	Center Aligned	Right Aligned
col 3 is	some wordy text	$1600
col 2 is	centered	$12
zebra stripes	are neat	$1
col 3 is	some wordy text	$1600
col 2 is	centered	$12
zebra stripes	are neat	$1
col 3 is	some wordy text	$1600
col 2 is	centered	$12

fomightez

print "\n\n\n\n\nSetting up .... \n"
from Bio import Entrez
Entrez.email = "A.N.Other@example.com"     # Always tell NCBI who you are
protein_gi_numbers = ["148908191", "297793721", "48525513", "507118461"]
print "protein_gi_numbers to get are" + str(protein_gi_numbers)
taxonomy_uids = []

#ELink step
print "performing ELink step....\n"
handle = Entrez.elink(dbfrom="protein", db="taxonomy", id=protein_gi_numbers)

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#script to accompany https://www.biostars.org/p/64078/

from Bio import Entrez
Entrez.email = "A.N.Other@example.com"

protein_accn_numbers = ["ABR17211.1", "XP_002864745.1", "AAT45004.1", "XP_003642916.1" ]
protein_gi_numbers = []

print "The Accession numbers for protein sequence provided:"
print protein_accn_numbers

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#! /usr/bin/env python

# DNA_to_RNA.py
# basic version of DNA FASTA records converted to RNA, see https://github.com/fomightez/sequencework/blob/master/ConvertSeq/ConvertFASTAdnaSEQtoRNA.py for a fancier version

# adapted from start and end of latlon_3.py - from Chapter 10 PCfB
# Read in each line of the example file


# Set the input file name

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import random


numbers = range (1,50)
chosen = []

while len(chosen) < 6:
	number = random.choice(numbers)
	numbers.remove(number)
	chosen.append(number)

fomightez

>gi|429243135|ref|NM_001019799.2| Schizosaccharomyces pombe 972h- ribonuclease MRP complex subunit (predicted) (SPAC323.08), mRNA
TGTTCACATTGCTCACTCGTTGGGTGGTTTGTACGACCTATTTGTCTAGTCCAACGATATGCAGGAATTG
CAATACGATGTAGTTTTATTGCAAAAAATCGTGTATAGGAATAGAAATCAGCATCGACTAAGTGTTTGGT
GGAGACACGTACGAATGCTGCTTCGAAGACTAAAGCAGTCGCTAGATGGAAATGAAAAAGCGAAAATTGC
TATTTTAGAACAATTGCCGAAATCGTACTTTTATTTTACAAACTTAATTGCCCATGGTCAGTATCCAGCC
TTAGGGTTAGTTTTGCTGGGTATCTTAGCTCGCGTTTGGTTTGTTATGGGCGGAATAGAGTACGAAGCAA
AAATACAATCGGAAATAGTCTTTAGTCAAAAGGAGCAAAAAAAATTGGAATTACAGTCTCAAGATGACAT
AGACACTGGGACTGTTGTAGCTCGCGATGAATTGCTAGCTACGGAACCTATTTCATTGTCTATAAATCCT
GCTTCTACTAGTTATGAGAAACTGACTGTATCCTCTCCTAATTCTTTTCTCAAGAATCAAGATGAATCTC
TCTTCTTGTCTTCTTCTCCTATAACTGTTTCTCAAGGTACCAAACGTAAATCCAAAAACTCAAATTCCAC

fomightez

chr1 	21394	21394	A	G
chr2	94116	94116	A	G
chr3	41121	41121	T	C
chr4	22139	22139	A	G
chr5	181396	181396	G	A
chr7	347119	347119	A	G
chr8	99196	99196	A	G
chr10	194236	194236	C	G

fomightez

##Using SimpleHTTPServer to run JSmol locally with Chrome

adapted from Nelson Liu's post to Jmol Users' list Tue, 17 Feb 2015. It will work out of the box on both Mac and Linux machines. Windows will need Python installed and a terminal emulator (UNTESTED!!). Doesn't matter if you are already running Chrome; I didn't have luck with open -a /Applications/Google\ Chrome.app/ --args --allow-file-access-from-files when I already had Chrome running.

• Skip the first three steps if you already downloaded Jmol, unpacked it, and unpacked jsmol.zip.

• Download Jmol binary.

• Unpack binary.

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REGEX for replacing SGD fasta description line with chromosome number

recreating steps probably used in process described in ChIP-Seq example at NUCwave site

S. cerevisiae reference genome was downloaded from SGD and FASTA headers for chromosome names were replaced with chrI-chrXVI.