notebook.community

Edit and run 





In [2]:



    


import sys
sys.path.append("../VirtualEating/")



    











In [74]:



    


import al_funcs
import os
import Bio 
import re
import timeit
import copy
from Bio import SeqIO
from Bio.Blast import NCBIXML
from Bio import Restriction 
from Bio.Restriction import *
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio import SeqFeature
from Bio.SeqFeature import *
import pandas
import cPickle as pickle
from numpy import *
from pylab import *
from collections import Counter
import re
import ngsanalysis



    











In [59]:



    


reload(ngsanalysis)



    


















    
Out[59]:








<module 'ngsanalysis' from 'ngsanalysis.py'>

















In [15]:



    


# This makes a dict of the xl71 genome for score lookups
handle = open("../../Genomic Data/LAEVIS_7.1.repeatMasked.fa", 'rb')
xl71genome = SeqIO.parse(handle, "fasta", alphabet=IUPACAmbiguousDNA())
xl71genomedict = {}
for item in xl71genome:
    xl71genomedict[item.id] = item



    











In [14]:



    


bounds = pickle.load(open("boundaries of 144 pcrs used in 3mb region within scaffold102974.pkl", "rb"))



    











In [19]:



    


longscaff = xl71genomedict["Scaffold102974"]



    











In [25]:



    


# Use the boundary information to pick out the amplified regions of Scaffold102974
amplicons = []
for item in bounds:
    a = longscaff[int(item[1]):int(item[2])]
    a.name = str(item[0])
    amplicons.append(a)



    











In [32]:



    


reload(al_funcs)



    


















    
Out[32]:








<module 'al_funcs' from '../VirtualEating/al_funcs.pyc'>

















In [34]:



    


a = al_funcs.al_digesttarget(amplicons)



    











In [36]:



    


len(list(a))



    


















    
Out[36]:








1954

This sounds about right: 1954 guides in the amplicons produced. Next, load in the sequence data.





In [37]:



    


reads = list(SeqIO.parse(open("../../20150223 SeqData/RHMS004C_S3_L001_R1_001.fastq", 'rb'), "fastq"))



    











In [40]:



    


reads[1]



    


















    
Out[40]:








SeqRecord(seq=Seq('NCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAAC...TCC', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:18029:1002', name='M02248:49:000000000-ACW7V:1:1101:18029:1002', description='M02248:49:000000000-ACW7V:1:1101:18029:1002 1:N:0:3', dbxrefs=[])

















In [76]:



    


for item in reads[0:20]:
    if re.finditer("GTTTAAGAG", item.seq):
        print item



    


















    






---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-76-eae8e9180784> in <module>()
      1 for item in reads[0:20]:
----> 2     if re.finditer("GTTTAAGAG", item.seq):
      3         print item

/Users/andylane/anaconda/python.app/Contents/lib/python2.7/re.pyc in finditer(pattern, string, flags)
    184 
    185         Empty matches are included in the result."""
--> 186         return _compile(pattern, flags).finditer(string)
    187 
    188 def compile(pattern, flags=0):

TypeError: expected string or buffer
















In [69]:



    


i = iter(reads[0:100])



    











In [70]:



    


l = list(ngsanalysis.spacersonly(i))



    











In [72]:



    


[item for item in l]



    


















    
Out[72]:








[SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGATCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:17203:1002', name='M02248:49:000000000-ACW7V:1:1101:17203:1002', description='M02248:49:000000000-ACW7V:1:1101:17203:1002 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('GGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:18029:1002', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:14603:1003', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AGATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:18413:1004', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:15388:1006', name='M02248:49:000000000-ACW7V:1:1101:15388:1006', description='M02248:49:000000000-ACW7V:1:1101:15388:1006 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:19788:1010', name='M02248:49:000000000-ACW7V:1:1101:19788:1010', description='M02248:49:000000000-ACW7V:1:1101:19788:1010 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:12215:1012', name='M02248:49:000000000-ACW7V:1:1101:12215:1012', description='M02248:49:000000000-ACW7V:1:1101:12215:1012 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTATAGTGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:12034:1013', name='M02248:49:000000000-ACW7V:1:1101:12034:1013', description='M02248:49:000000000-ACW7V:1:1101:12034:1013 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TATAGGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:14520:1013', name='M02248:49:000000000-ACW7V:1:1101:14520:1013', description='M02248:49:000000000-ACW7V:1:1101:14520:1013 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:19527:1020', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AGATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:13610:1025', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:15717:1026', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16467:1032', name='M02248:49:000000000-ACW7V:1:1101:16467:1032', description='M02248:49:000000000-ACW7V:1:1101:16467:1032 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCCAACGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:17032:1033', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CTATAGGTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:10912:1033', name='M02248:49:000000000-ACW7V:1:1101:10912:1033', description='M02248:49:000000000-ACW7V:1:1101:10912:1033 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTTTAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:22176:1038', name='M02248:49:000000000-ACW7V:1:1101:22176:1038', description='M02248:49:000000000-ACW7V:1:1101:22176:1038 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('GATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:10079:1039', name='M02248:49:000000000-ACW7V:1:1101:10079:1039', description='M02248:49:000000000-ACW7V:1:1101:10079:1039 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:17483:1041', name='M02248:49:000000000-ACW7V:1:1101:17483:1041', description='M02248:49:000000000-ACW7V:1:1101:17483:1041 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TATAGGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:9370:1042', name='M02248:49:000000000-ACW7V:1:1101:9370:1042', description='M02248:49:000000000-ACW7V:1:1101:9370:1042 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('GATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16650:1047', name='M02248:49:000000000-ACW7V:1:1101:16650:1047', description='M02248:49:000000000-ACW7V:1:1101:16650:1047 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:11373:1047', name='M02248:49:000000000-ACW7V:1:1101:11373:1047', description='M02248:49:000000000-ACW7V:1:1101:11373:1047 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:16198:1049', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:15067:1049', name='M02248:49:000000000-ACW7V:1:1101:15067:1049', description='M02248:49:000000000-ACW7V:1:1101:15067:1049 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('AGATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:18890:1050', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TAGGATAGTAATCAACAGCCCCTCCTAATTCCAAC', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:11099:1051', name='M02248:49:000000000-ACW7V:1:1101:11099:1051', description='M02248:49:000000000-ACW7V:1:1101:11099:1051 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:17642:1055', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:19167:1059', name='M02248:49:000000000-ACW7V:1:1101:19167:1059', description='M02248:49:000000000-ACW7V:1:1101:19167:1059 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:20733:1068', name='M02248:49:000000000-ACW7V:1:1101:20733:1068', description='M02248:49:000000000-ACW7V:1:1101:20733:1068 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCGTCCATATCTCATGATACTAAGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:14563:1068', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('ACTCACTATGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:18799:1069', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:14905:1073', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('GATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:19498:1082', name='M02248:49:000000000-ACW7V:1:1101:19498:1082', description='M02248:49:000000000-ACW7V:1:1101:19498:1082 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TAATCAACGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:19013:1083', name='M02248:49:000000000-ACW7V:1:1101:19013:1083', description='M02248:49:000000000-ACW7V:1:1101:19013:1083 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:17783:1086', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:20292:1088', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:9843:1091', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:10846:1093', name='M02248:49:000000000-ACW7V:1:1101:10846:1093', description='M02248:49:000000000-ACW7V:1:1101:10846:1093 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:14105:1100', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('AGATGCGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:11134:1101', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:13533:1107', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16683:1111', name='M02248:49:000000000-ACW7V:1:1101:16683:1111', description='M02248:49:000000000-ACW7V:1:1101:16683:1111 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:13001:1112', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCGTCCATATCTCATGATACTAAGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:17927:1113', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16220:1114', name='M02248:49:000000000-ACW7V:1:1101:16220:1114', description='M02248:49:000000000-ACW7V:1:1101:16220:1114 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCCAACGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:13348:1119', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:17756:1119', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGCTCATAGCCACAAGCCCTCCTATTGT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:11258:1127', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:20690:1130', name='M02248:49:000000000-ACW7V:1:1101:20690:1130', description='M02248:49:000000000-ACW7V:1:1101:20690:1130 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16486:1137', name='M02248:49:000000000-ACW7V:1:1101:16486:1137', description='M02248:49:000000000-ACW7V:1:1101:16486:1137 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:12178:1138', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGATCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:16401:1138', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:9935:1139', name='M02248:49:000000000-ACW7V:1:1101:9935:1139', description='M02248:49:000000000-ACW7V:1:1101:9935:1139 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:10593:1141', name='M02248:49:000000000-ACW7V:1:1101:10593:1141', description='M02248:49:000000000-ACW7V:1:1101:10593:1141 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('TCCAACGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:13305:1144', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:20002:1145', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('ACTGTGATTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:12834:1150', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:9079:1170', name='M02248:49:000000000-ACW7V:1:1101:9079:1170', description='M02248:49:000000000-ACW7V:1:1101:9079:1170 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:20549:1172', name='M02248:49:000000000-ACW7V:1:1101:20549:1172', description='M02248:49:000000000-ACW7V:1:1101:20549:1172 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('ACTATAGCCTGGTGTTGCCCTTTATTTGTTCTGTCT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:19913:1172', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('TCACTATAGCTCATAGCCACAAGACCTCCTATTGT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:8642:1175', name='M02248:49:000000000-ACW7V:1:1101:8642:1175', description='M02248:49:000000000-ACW7V:1:1101:8642:1175 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('AGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:15298:1176', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('CACTATAGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16337:1179', name='M02248:49:000000000-ACW7V:1:1101:16337:1179', description='M02248:49:000000000-ACW7V:1:1101:16337:1179 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTATAGTTGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16721:1182', name='M02248:49:000000000-ACW7V:1:1101:16721:1182', description='M02248:49:000000000-ACW7V:1:1101:16721:1182 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('GATGCGTTGGATAGTGTAATGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:14286:1184', name='M02248:49:000000000-ACW7V:1:1101:14286:1184', description='M02248:49:000000000-ACW7V:1:1101:14286:1184 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('AGATTCTGGGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:10059:1189', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('GAACTTCGGGCTAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='M02248:49:000000000-ACW7V:1:1101:16288:1200', name='M02248:49:000000000-ACW7V:1:1101:16288:1200', description='M02248:49:000000000-ACW7V:1:1101:16288:1200 1:N:0:3', dbxrefs=[]),
 SeqRecord(seq=Seq('CTCACTATAGGATAGTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:15191:1200', description='<unknown description>', dbxrefs=[]),
 SeqRecord(seq=Seq('GTGTACTGCGGCTCCATAGACT', SingleLetterAlphabet()), id='<unknown id>', name='M02248:49:000000000-ACW7V:1:1101:15982:1200', description='<unknown description>', dbxrefs=[])]

















In [ ]:

Content source: eatingcrispr/VirtualEating

Similar notebooks:

notebook.community | gallery | about