Purpose

Make sequences formatted in the same fashion as IRD.


In [156]:
import pandas as pd
import numpy as np
from Bio import SeqIO
from random import sample
from collections import defaultdict

In [166]:
ird_sequences = [s for s in SeqIO.parse('ird_seqs_name_as_accession.fasta', 'fasta')]
len(ird_sequences)


Out[166]:
21868

In [170]:
new_sequences = [s for s in SeqIO.parse('Alaska_waterfowl_79viruses_seqs_20151223.fasta', 'fasta')]
len(new_sequences)


Out[170]:
647

In [172]:
combined_sequences = []
combined_sequences.extend(ird_sequences)
combined_sequences.extend(new_sequences)
SeqIO.write(combined_sequences, '20160104_brandt Sequences.fasta', 'fasta')


Out[172]:
22515

In [ ]:
# Write the IRD-like table for the sequences. There should be 2648 rows at the end.
# The IRD tables have the following columns:
# - Segment (number)
# - Protein Name (string)
# - Sequence Accession (alphanumeric)
# - Complete Genome (Yes/No)
# - Segment Length (number)
# - Subtype (alphanumerica)
# - Collection Date (date)
# - Host Species (string)
# - Country (string)
# - State/Province (string)
# - Flu Season (alphanumeric)
# - Strain Name (alphanumeric)

In [159]:
# Read in the data
ird_df = pd.read_csv('20160104_brandt_ird.csv', parse_dates=['Collection Date'], na_filter=False)
# Clean strain name. Remove subtype from strain name, replace spaces with underscore.
ird_df['Strain Name'] = ird_df['Strain Name'].str.split('(').str[0].str.replace(' ', '_')
# Clean the Host Species names by removing "IRD" and removing "/Avian"
ird_df['Host Species'] = ird_df['Host Species'].str.split(':').str[1].str.replace('/Avian', '')
ird_df


Out[159]:
Segment Protein Name Sequence Accession Complete Genome Segment Length Subtype Collection Date Host Species Country State/Province Flu Season Strain Name
0 7 M1,M2 KU289739 Yes 1027 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
1 5 NP KU289741 Yes 1540 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
2 8 NS1,NS2 KU289742 Yes 865 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
3 3 PA,PA-N155,PA-N182,PA-X protein(+61) KU289743 Yes 2208 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
4 1 PB2 KU289745 Yes 2307 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
5 4 HA KU289738 Yes 1706 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
6 6 NA KU289740 Yes 1428 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
7 2 PB1,PB1-F2,PB1-N40 KU289744 Yes 2316 H7N3 2010-02-18 American Black Duck USA Delaware 09-10 A/American_black_duck/Delaware/A00870108/2010
8 1 PB2 CY079459 Yes 2307 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
9 8 NS1,NS2 CY079456 Yes 852 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
10 6 NA CY079454 Yes 1446 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
11 2 PB1,PB1-F2,PB1-N40 CY079458 Yes 2316 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
12 7 M1,M2 CY079453 Yes 1002 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
13 3 PA,PA-N155,PA-N182,PA-X protein(+61) CY079457 Yes 2208 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
14 5 NP CY079455 Yes 1540 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
15 4 HA CY079452 Yes 1742 H5N2 2008-10-26 American Black Duck USA Illinois 08-09 A/American_black_duck/Illinois/08OS2688/2008
16 4 HA CY097534 Yes 1719 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
17 2 PB1,PB1-F2,PB1-N40 CY097540 Yes 2316 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
18 7 M1,M2 CY097535 Yes 990 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
19 1 PB2 CY097541 Yes 2316 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
20 5 NP CY097537 Yes 1541 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
21 6 NA CY097536 Yes 1437 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
22 3 PA,PA-N155,PA-N182,PA-X protein(+61) CY097539 Yes 2201 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
23 8 NS1,NS2 CY097538 Yes 865 H8N4 2009-11-29 American Black Duck USA Illinois 09-10 A/American_black_duck/Illinois/4119/2009
24 1 PB2 KP636475 Yes 2280 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
25 5 NP KP636479 Yes 1497 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
26 2 PB1,PB1-F2,PB1-N40 KP636476 Yes 2274 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
27 4 HA KP636478 Yes 1701 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
28 6 NA KP636480 Yes 1413 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
29 7 M1,M2 KP636481 Yes 982 H3N8 2008-01-01 American Black Duck USA Maine -N/A- A/American_black_duck/Maine/44411/532/2008
... ... ... ... ... ... ... ... ... ... ... ... ...
21838 6 NA CY132959 Yes 1421 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21839 4 HA CY132957 Yes 1740 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21840 1 PB2 CY132964 Yes 2307 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21841 7 M1,M2 CY132958 Yes 1002 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21842 2 PB1,PB1-F2,PB1-N40 CY132963 Yes 2316 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21843 3 PA,PA-N155,PA-N182,PA-X protein(+61) CY132962 Yes 2151 H3N8 2010-09-26 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/10OS2778/2010
21844 6 NA CY167112 Yes 1440 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21845 8 NS1,NS2 CY167114 Yes 865 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21846 5 NP CY167113 Yes 1540 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21847 4 HA CY167110 Yes 1740 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21848 2 PB1,PB1-F2,PB1-N40 CY167116 Yes 2316 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21849 1 PB2 CY167117 Yes 2307 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21850 7 M1,M2 CY167111 Yes 1002 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21851 3 PA,PA-N155,PA-N182,PA-X protein(+61) CY167115 Yes 2196 H3N6 2011-09-24 Duck USA Wisconsin -N/A- A/wood_duck/Wisconsin/11OS2912/2011
21852 6 NA CY166655 Yes 1435 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21853 7 M1,M2 CY166654 Yes 1002 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21854 4 HA CY166653 Yes 1709 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21855 8 NS1,NS2 CY166657 Yes 865 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21856 2 PB1,PB1-F2,PB1-N40 CY166659 Yes 2304 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21857 1 PB2 CY166660 Yes 2316 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21858 5 NP CY166656 Yes 1540 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21859 3 PA,PA-N155,PA-N182,PA-X protein(+61) CY166658 Yes 2208 H11N9 2011-10-16 Duck USA Wisconsin 11-12 A/wood_duck/Wisconsin/11OS3443/2011
21860 2 PB1 GU050165 Yes 2316 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21861 7 M1,M2 GU050160 Yes 1002 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21862 1 PB2 GU050166 Yes 2316 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21863 6 NA GU050161 Yes 1383 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21864 5 NP GU050162 Yes 1540 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21865 8 NS1,NS2 GU050163 Yes 865 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21866 4 HA GU050159 Yes 1736 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007
21867 3 PA,PA-N155,PA-N182,PA-X protein(+61) GU050164 Yes 2208 H5N2 2007-01-01 Parrot USA California -N/A- A/yellow-headed_Amazon/California/500658/2007

21868 rows × 12 columns


In [160]:
# The 79 new sequences that have been added to the dataset are not in the format of the IRD. I will make them as such.
newseqs_df = pd.read_csv('Alaska_waterfowl_79viruses_metadata_20151223.csv', parse_dates=['CollectionDate'])
newseqs_df['Strain_name'] = newseqs_df['Strain_name'].str.replace(' ', '_')
newseqs_df.set_index('Strain_name')


Out[160]:
Subtype Blinded Number Organism Name provided by collaborator Updated Organism Name (names that changed are in blue) Special Note_JCVIs Complete/Draft CEIRS Sample ID UPDATED? Age Age_Brandt ... Unnamed: 26 Unnamed: 27 Unnamed: 28 Unnamed: 29 Unnamed: 30 Unnamed: 31 Unnamed: 32 Unnamed: 33 Unnamed: 34 Unnamed: 35
Strain_name
A/northern_pintail/Interior_Alaska/10BM03314/2010 H4N4 NIGSP_CEIRS_CIP105_RUNC_00058 Influenza A virus (A/northern pintail/Interior... Influenza A virus (A/northern pintail/Interior... NaN Complete 10BM03314 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/10BM12027/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00061 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 10BM12027 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/northern_pintail/Interior_Alaska/10BM12537/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00062 Influenza A virus (A/northern pintail/Interior... Influenza A virus (A/northern pintail/Interior... NaN Complete 10BM12537 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/10BM13225/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00064 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 10BM13225 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/10BM13335/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00065 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 10BM13335 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/northern_pintail/Interior_Alaska/10BM13543/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00066 Influenza A virus (A/Northern pintail/Interior... Influenza A virus (A/northern pintail/Interior... NaN Complete 10BM13543 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/northern_pintail/Interior_Alaska/10BM15017/2010 H12N5 NIGSP_CEIRS_CIP105_RUNC_00070 Influenza A virus (A/Northern pintail/Interior... Influenza A virus (A/northern pintail/Interior... NaN Complete 10BM15017 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM00293/2011 H10N5 NIGSP_CEIRS_CIP105_RUNC_00074 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM00293 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM00304/2011 H10N5 NIGSP_CEIRS_CIP105_RUNC_00075 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM00304 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM01009/2011 H12N5 NIGSP_CEIRS_CIP105_RUNC_00076 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM01009 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM01179/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00077 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM01179 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM01180/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00078 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM01180 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM01254/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00079 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM01254 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM01255/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00080 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM01255 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02089/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00081 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02089 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02099/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00082 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02099 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM02195/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00083 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM02195 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02557/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00084 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02557 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02703/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00085 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02703 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02923/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00086 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02923 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02987/2011 H2N6 NIGSP_CEIRS_CIP105_RUNC_00087 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02987 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM02991/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00088 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM02991 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM03102/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00089 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM03102 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM03165/2011 H2N9 NIGSP_CEIRS_CIP105_RUNC_00090 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM03165 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM03166/2011 H2N9 NIGSP_CEIRS_CIP105_RUNC_00091 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM03166 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM03436/2011 H2N9 NIGSP_CEIRS_CIP105_RUNC_00092 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM03436 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM03443/2011 mixed NIGSP_CEIRS_CIP105_RUNC_00093 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... Sequence data indicate that the sample was mix... Complete 11BM03443 Y After hatch year AHY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/American_green-winged_teal/Interior_Alaska/11BM03479/2011 H4N6 NIGSP_CEIRS_CIP105_RUNC_00094 Influenza A virus (A/American green-winged tea... Influenza A virus (A/American green-winged tea... NaN Complete 11BM03479 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM03577/2011 H7N3 NIGSP_CEIRS_CIP105_RUNC_00096 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM03577 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/11BM03591/2011 H2N9 NIGSP_CEIRS_CIP105_RUNC_00097 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 11BM03591 Y Hatch year HY ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
A/goose/Interior_Alaska/11PG00148/2011 H6N1 NIGSP_CEIRS_CIP105_RUNC_00163 Influenza A virus (A/goose/Interior Alaska/11P... Influenza A virus (A/goose/Interior Alaska/11P... NaN Complete 11PG00148 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/goose/Interior_Alaska/11PG00149/2011 H6N1 NIGSP_CEIRS_CIP105_RUNC_00164 Influenza A virus (A/goose/Interior Alaska/11P... Influenza A virus (A/goose/Interior Alaska/11P... NaN Complete 11PG00149 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/goose/Interior_Alaska/11PG00437/2011 H2N3 NIGSP_CEIRS_CIP105_RUNC_00165 Influenza A virus (A/goose/Interior Alaska/11P... Influenza A virus (A/goose/Interior Alaska/11P... NaN Complete 11PG00437 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/duck/Interior_Alaska/11PG00451/2011 H2N3 NIGSP_CEIRS_CIP105_RUNC_00166 Influenza A virus (A/duck/Interior Alaska/11PG... Influenza A virus (A/duck/Interior Alaska/11PG... NaN Complete 11PG00451 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/duck/Interior_Alaska/11PG00459/2011 H2N3 NIGSP_CEIRS_CIP105_RUNC_00167 Influenza A virus (A/duck/Interior Alaska/11PG... Influenza A virus (A/duck/Interior Alaska/11PG... NaN Complete 11PG00459 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/duck/Interior_Alaska/11PG00703/2011 mixed NIGSP_CEIRS_CIP105_RUNC_00169 Influenza A virus (A/duck/Interior Alaska/11PG... Influenza A virus (A/duck/Interior Alaska/11PG... Sequence data indicate that the sample was mix... Draft 11PG00703 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/duck/Interior_Alaska/11PG00704/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00170 Influenza A virus (A/duck/Interior Alaska/11PG... Influenza A virus (A/duck/Interior Alaska/11PG... NaN Complete 11PG00704 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/duck/Interior_Alaska/11PG00730/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00171 Influenza A virus (A/duck/Interior Alaska/11PG... Influenza A virus (A/duck/Interior Alaska/11PG... NaN Complete 11PG00730 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/goose/Interior_Alaska/11PG00987/2011 H3N8 NIGSP_CEIRS_CIP105_RUNC_00173 Influenza A virus (A/goose/Interior Alaska/11P... Influenza A virus (A/goose/Interior Alaska/11P... NaN Complete 11PG00987 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00034/2012 H3N8 NIGSP_CEIRS_CIP105_RUNC_00019 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00034 NaN Hatch year NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00058/2012 H8N4 NIGSP_CEIRS_CIP105_RUNC_00020 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00058 NaN Hatch year NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00059/2012 H2N9 NIGSP_CEIRS_CIP105_RUNC_00021 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00059 NaN Hatch year NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00064/2012 H2N4 NIGSP_CEIRS_CIP105_RUNC_00022 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00064 NaN After hatch year NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00076/2012 H8N4 NIGSP_CEIRS_CIP105_RUNC_00023 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00076 NaN Hatch year NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00086/2012 mixed NIGSP_CEIRS_CIP105_RUNC_00024 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... Sequence data indicate that the sample was mix... Complete 12ML00086 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00098/2012 H3N8 NIGSP_CEIRS_CIP105_RUNC_00025 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00098 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
A/mallard/Interior_Alaska/12ML00120/2012 H8N4 NIGSP_CEIRS_CIP105_RUNC_00026 Influenza A virus (A/mallard/Interior Alaska/1... Influenza A virus (A/mallard/Interior Alaska/1... NaN Complete 12ML00120 NaN Unknown NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN

92 rows × 35 columns


In [161]:
newseqs = [s for s in SeqIO.parse('Alaska_waterfowl_79viruses_seqs_20151223.fasta', 'fasta')]
len(newseqs) / 8


Out[161]:
80.875

In [162]:
segnum_name = dict()
segnum_name[1] = 'PB2'
segnum_name[2] = 'PB1'
segnum_name[3] = 'PA'
segnum_name[4] = 'HA'
segnum_name[5] = 'NP'
segnum_name[6] = 'NA'
segnum_name[7] = 'M'
segnum_name[8] = 'NS'

name_segnum = dict()
for k, v in segnum_name.items():
    name_segnum[v] = k
name_segnum


Out[162]:
{'HA': 4, 'M': 7, 'NA': 6, 'NP': 5, 'NS': 8, 'PA': 3, 'PB1': 2, 'PB2': 1}

In [163]:
newstrains_data = []
for s in newseqs:
    strain_name = s.id.split('|')[0]
    segment_name = s.id.split('|')[1]
    d = dict()
    d['Segment'] = name_segnum[segment_name]
    d['Protein Name'] = segment_name
    d['Sequence Accession'] = 'Not assigned'
    d['Complete Genome'] = 'Unconfirmed'
    d['Segment Length'] = len(s.seq)
    d['Subtype'] = newseqs_df.set_index('Strain_name').ix[strain_name]['Subtype']
    d['Collection Date'] = newseqs_df.set_index('Strain_name').ix[strain_name]['CollectionDate']
    d['Host Species'] = newseqs_df.set_index('Strain_name').ix[strain_name]['Species_final']
    d['Country'] = 'USA'
    d['State/Province'] = 'Alaska'
    d['Flu Season'] = np.nan
    d['Strain Name'] = strain_name
    newstrains_data.append(d)
newstrains_df = pd.DataFrame(newstrains_data)

In [164]:
len(newstrains_data) / 8


Out[164]:
80.875

In [165]:
final_df = ird_df.append(newstrains_df).reset_index(drop=True)

final_df['Protein Name'] = final_df['Segment'].apply(lambda x: segnum_name[x])
final_df['Sequence Accession'] = final_df['Strain Name'].str.cat(final_df['Protein Name'], sep='|')
final_df.to_csv('20160104_brandt Sequences.csv')
final_df


Out[165]:
Collection Date Complete Genome Country Flu Season Host Species Protein Name Segment Segment Length Sequence Accession State/Province Strain Name Subtype
0 2010-02-18 Yes USA 09-10 American Black Duck M 7 1027 A/American_black_duck/Delaware/A00870108/2010|M Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
1 2010-02-18 Yes USA 09-10 American Black Duck NP 5 1540 A/American_black_duck/Delaware/A00870108/2010|NP Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
2 2010-02-18 Yes USA 09-10 American Black Duck NS 8 865 A/American_black_duck/Delaware/A00870108/2010|NS Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
3 2010-02-18 Yes USA 09-10 American Black Duck PA 3 2208 A/American_black_duck/Delaware/A00870108/2010|PA Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
4 2010-02-18 Yes USA 09-10 American Black Duck PB2 1 2307 A/American_black_duck/Delaware/A00870108/2010|PB2 Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
5 2010-02-18 Yes USA 09-10 American Black Duck HA 4 1706 A/American_black_duck/Delaware/A00870108/2010|HA Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
6 2010-02-18 Yes USA 09-10 American Black Duck NA 6 1428 A/American_black_duck/Delaware/A00870108/2010|NA Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
7 2010-02-18 Yes USA 09-10 American Black Duck PB1 2 2316 A/American_black_duck/Delaware/A00870108/2010|PB1 Delaware A/American_black_duck/Delaware/A00870108/2010 H7N3
8 2008-10-26 Yes USA 08-09 American Black Duck PB2 1 2307 A/American_black_duck/Illinois/08OS2688/2008|PB2 Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
9 2008-10-26 Yes USA 08-09 American Black Duck NS 8 852 A/American_black_duck/Illinois/08OS2688/2008|NS Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
10 2008-10-26 Yes USA 08-09 American Black Duck NA 6 1446 A/American_black_duck/Illinois/08OS2688/2008|NA Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
11 2008-10-26 Yes USA 08-09 American Black Duck PB1 2 2316 A/American_black_duck/Illinois/08OS2688/2008|PB1 Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
12 2008-10-26 Yes USA 08-09 American Black Duck M 7 1002 A/American_black_duck/Illinois/08OS2688/2008|M Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
13 2008-10-26 Yes USA 08-09 American Black Duck PA 3 2208 A/American_black_duck/Illinois/08OS2688/2008|PA Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
14 2008-10-26 Yes USA 08-09 American Black Duck NP 5 1540 A/American_black_duck/Illinois/08OS2688/2008|NP Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
15 2008-10-26 Yes USA 08-09 American Black Duck HA 4 1742 A/American_black_duck/Illinois/08OS2688/2008|HA Illinois A/American_black_duck/Illinois/08OS2688/2008 H5N2
16 2009-11-29 Yes USA 09-10 American Black Duck HA 4 1719 A/American_black_duck/Illinois/4119/2009|HA Illinois A/American_black_duck/Illinois/4119/2009 H8N4
17 2009-11-29 Yes USA 09-10 American Black Duck PB1 2 2316 A/American_black_duck/Illinois/4119/2009|PB1 Illinois A/American_black_duck/Illinois/4119/2009 H8N4
18 2009-11-29 Yes USA 09-10 American Black Duck M 7 990 A/American_black_duck/Illinois/4119/2009|M Illinois A/American_black_duck/Illinois/4119/2009 H8N4
19 2009-11-29 Yes USA 09-10 American Black Duck PB2 1 2316 A/American_black_duck/Illinois/4119/2009|PB2 Illinois A/American_black_duck/Illinois/4119/2009 H8N4
20 2009-11-29 Yes USA 09-10 American Black Duck NP 5 1541 A/American_black_duck/Illinois/4119/2009|NP Illinois A/American_black_duck/Illinois/4119/2009 H8N4
21 2009-11-29 Yes USA 09-10 American Black Duck NA 6 1437 A/American_black_duck/Illinois/4119/2009|NA Illinois A/American_black_duck/Illinois/4119/2009 H8N4
22 2009-11-29 Yes USA 09-10 American Black Duck PA 3 2201 A/American_black_duck/Illinois/4119/2009|PA Illinois A/American_black_duck/Illinois/4119/2009 H8N4
23 2009-11-29 Yes USA 09-10 American Black Duck NS 8 865 A/American_black_duck/Illinois/4119/2009|NS Illinois A/American_black_duck/Illinois/4119/2009 H8N4
24 2008-01-01 Yes USA -N/A- American Black Duck PB2 1 2280 A/American_black_duck/Maine/44411/532/2008|PB2 Maine A/American_black_duck/Maine/44411/532/2008 H3N8
25 2008-01-01 Yes USA -N/A- American Black Duck NP 5 1497 A/American_black_duck/Maine/44411/532/2008|NP Maine A/American_black_duck/Maine/44411/532/2008 H3N8
26 2008-01-01 Yes USA -N/A- American Black Duck PB1 2 2274 A/American_black_duck/Maine/44411/532/2008|PB1 Maine A/American_black_duck/Maine/44411/532/2008 H3N8
27 2008-01-01 Yes USA -N/A- American Black Duck HA 4 1701 A/American_black_duck/Maine/44411/532/2008|HA Maine A/American_black_duck/Maine/44411/532/2008 H3N8
28 2008-01-01 Yes USA -N/A- American Black Duck NA 6 1413 A/American_black_duck/Maine/44411/532/2008|NA Maine A/American_black_duck/Maine/44411/532/2008 H3N8
29 2008-01-01 Yes USA -N/A- American Black Duck M 7 982 A/American_black_duck/Maine/44411/532/2008|M Maine A/American_black_duck/Maine/44411/532/2008 H3N8
... ... ... ... ... ... ... ... ... ... ... ... ...
22485 2011-09-03 Unconfirmed USA NaN Northern shoveler NA 6 1425 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22486 2011-09-03 Unconfirmed USA NaN Northern shoveler NP 5 1526 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22487 2011-09-03 Unconfirmed USA NaN Northern shoveler NS 8 865 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22488 2011-09-03 Unconfirmed USA NaN Northern shoveler PA 3 2208 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22489 2011-09-03 Unconfirmed USA NaN Northern shoveler PB1 2 2309 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22490 2011-09-03 Unconfirmed USA NaN Northern shoveler PB2 1 2295 A/northern_shoveler/Interior_Alaska/11BM03855/... Alaska A/northern_shoveler/Interior_Alaska/11BM03855/... H3N8
22491 2011-09-03 Unconfirmed USA NaN Northern shoveler HA 4 1731 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22492 2011-09-03 Unconfirmed USA NaN Northern shoveler M 7 1002 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22493 2011-09-03 Unconfirmed USA NaN Northern shoveler NA 6 1421 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22494 2011-09-03 Unconfirmed USA NaN Northern shoveler NP 5 1540 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22495 2011-09-03 Unconfirmed USA NaN Northern shoveler NS 8 865 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22496 2011-09-03 Unconfirmed USA NaN Northern shoveler PA 3 2202 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22497 2011-09-03 Unconfirmed USA NaN Northern shoveler PB1 2 2316 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22498 2011-09-03 Unconfirmed USA NaN Northern shoveler PB2 1 2295 A/northern_shoveler/Interior_Alaska/11BM03861/... Alaska A/northern_shoveler/Interior_Alaska/11BM03861/... H3N8
22499 2011-09-03 Unconfirmed USA NaN Northern shoveler HA 4 1731 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22500 2011-09-03 Unconfirmed USA NaN Northern shoveler M 7 1002 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22501 2011-09-03 Unconfirmed USA NaN Northern shoveler NA 6 1425 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22502 2011-09-03 Unconfirmed USA NaN Northern shoveler NP 5 1532 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22503 2011-09-03 Unconfirmed USA NaN Northern shoveler NS 8 865 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22504 2011-09-03 Unconfirmed USA NaN Northern shoveler PA 3 2208 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22505 2011-09-03 Unconfirmed USA NaN Northern shoveler PB1 2 2309 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22506 2011-09-03 Unconfirmed USA NaN Northern shoveler PB2 1 2295 A/northern_shoveler/Interior_Alaska/11BM03889/... Alaska A/northern_shoveler/Interior_Alaska/11BM03889/... H3N8
22507 2011-09-09 Unconfirmed USA NaN Northern shoveler HA 4 1700 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22508 2011-09-09 Unconfirmed USA NaN Northern shoveler M 7 1002 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22509 2011-09-09 Unconfirmed USA NaN Northern shoveler NA 6 1434 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22510 2011-09-09 Unconfirmed USA NaN Northern shoveler NP 5 1540 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22511 2011-09-09 Unconfirmed USA NaN Northern shoveler NS 8 865 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22512 2011-09-09 Unconfirmed USA NaN Northern shoveler PA 3 2196 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22513 2011-09-09 Unconfirmed USA NaN Northern shoveler PB1 2 2316 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6
22514 2011-09-09 Unconfirmed USA NaN Northern shoveler PB2 1 2301 A/northern_shoveler/Interior_Alaska/11ML00037/... Alaska A/northern_shoveler/Interior_Alaska/11ML00037/... H4N6

22515 rows × 12 columns


In [ ]: