Dan Bolser CholoTook
CholoTook
/ convert_to_canfam_3.py
Created
June 17, 2021 11:40
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| import pathlib | |
| import csv | |
| from collections import namedtuple | |
| Marker = namedtuple('Marker', 'name, snp, chr, pos') | |
| path = pathlib.Path('Data/PlinkFormat/Samples') | |
| coord_file = 'Data/CanineHD_B.csv' |
CholoTook
/ Convert GEO SNP-Chip data to Plink .ped and .bed format .py
Last active
June 17, 2021 09:05
For some reason the people at GEO couldn't answer basic questions about data formats... GEO provides data in various format, but it isn't clear which formats are used by which tools ... </bitch> The following code snippet shows how to convert GEOs tabular data format for SNP-Chip genotype data into Plink .ped/.bed formats (with associated .bim/.…
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| import math | |
| import GEOparse | |
| import pandas_plink | |
| import xarray | |
| # The genotypes are defined as 'dosages' by pandas-plink, so we are | |
| # required to use floating point numbers in the encoding here. | |
| genotype_encoding = { | |
| 'AA': 0.0, |
CholoTook
/ dhcp.pcap-rvvv
Created
June 8, 2020 15:00
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| 10:40:05.660756 IP (tos 0x0, ttl 64, id 18018, offset 0, flags [DF], proto UDP (17), length 80) | |
| 192.168.122.10.46092 > complex2.domain: [bad udp cksum 0x75aa -> 0x27ef!] 49117+ [1au] PTR? 1.0.17.172.in-addr.arpa. ar: . OPT UDPsize=512 (52) | |
| 10:40:05.660895 IP (tos 0x0, ttl 64, id 34616, offset 0, flags [DF], proto UDP (17), length 80) | |
| complex2.domain > 192.168.122.10.46092: [bad udp cksum 0x75aa -> 0x996b!] 49117 NXDomain q: PTR? 1.0.17.172.in-addr.arpa. 0/0/1 ar: . OPT UDPsize=4096 (52) | |
| 10:40:05.661142 IP (tos 0xc0, ttl 64, id 46555, offset 0, flags [none], proto ICMP (1), length 108) | |
| 192.168.122.10 > complex2: ICMP 192.168.122.10 udp port 46092 unreachable, length 88 | |
| IP (tos 0x0, ttl 64, id 34616, offset 0, flags [DF], proto UDP (17), length 80) | |
| complex2.domain > 192.168.122.10.46092: [bad udp cksum 0x75aa -> 0x996b!] 49117 NXDomain q: PTR? 1.0.17.172.in-addr.arpa. 0/0/1 ar: . OPT UDPsize=4096 (52) | |
| 10:40:09.072930 IP (tos 0x0, ttl 64, id 18231, offset 0, flags [DF], proto UDP (17), length 84 |
CholoTook
/ filtered.pcap
Created
June 8, 2020 14:47
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| 10:40:05.660756 IP 192.168.122.10.46092 > complex2.domain: 49117+ [1au] PTR? 1.0.17.172.in-addr.arpa. (52) | |
| 10:40:05.660895 IP complex2.domain > 192.168.122.10.46092: 49117 NXDomain 0/0/1 (52) | |
| 10:40:05.661142 IP 192.168.122.10 > complex2: ICMP 192.168.122.10 udp port 46092 unreachable, length 88 | |
| 10:40:09.072930 IP 192.168.122.10.58168 > complex2.domain: 357+ [1au] PTR? 10.122.168.192.in-addr.arpa. (56) | |
| 10:40:09.073066 IP complex2.domain > 192.168.122.10.58168: 357* 1/0/1 PTR gero-clin-test. (84) | |
| 10:40:09.073316 IP 192.168.122.10 > complex2: ICMP 192.168.122.10 udp port 58168 unreachable, length 120 | |
| 10:40:09.647796 IP complex2.42265 > 229.111.112.12.3071: UDP, length 4 | |
| 10:40:09.997007 IP 192.168.122.10.35342 > complex2.domain: 45155+ [1au] PTR? 10.122.168.192.in-addr.arpa. (56) | |
| 10:40:09.997140 IP complex2.domain > 192.168.122.10.35342: 45155* 1/0/1 PTR gero-clin-test. (84) | |
| 10:40:09.998075 IP 192.168.122.10.45098 > complex2.domain: 31252+ [1au] PTR? 10.122.168.192.in-addr.arpa. (56) |
CholoTook
/ dumpxml.xml
Created
June 8, 2020 14:27
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| <domain type='kvm'> | |
| <name>geromics-clinoverse-dev-ubuntu8.04</name> | |
| <uuid>fcf20d93-6f41-4bfa-9fa0-93e457c08460</uuid> | |
| <memory unit='KiB'>4194304</memory> | |
| <currentMemory unit='KiB'>4194304</currentMemory> | |
| <vcpu placement='static'>4</vcpu> | |
| <os> | |
| <type arch='x86_64' machine='pc-i440fx-2.8'>hvm</type> | |
| <boot dev='hd'/> | |
| </os> |
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| <domain type='kvm'> | |
| <name>geromics-clinoverse-dev-ubuntu8.04</name> | |
| <uuid>fcf20d93-6f41-4bfa-9fa0-93e457c08460</uuid> | |
| <memory unit='KiB'>4194304</memory> | |
| <currentMemory unit='KiB'>4194304</currentMemory> | |
| <vcpu placement='static'>4</vcpu> | |
| <os> | |
| <type arch='x86_64' machine='pc-i440fx-2.8'>hvm</type> | |
| <boot dev='hd'/> | |
| </os> |
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| enx283737029f5c: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500 | |
| inet6 fe80::ff0d:b6b3:1c59:cb6b prefixlen 64 scopeid 0x20<link> | |
| ether 28:37:37:02:9f:5c txqueuelen 1000 (Ethernet) | |
| RX packets 0 bytes 0 (0.0 B) | |
| RX errors 0 dropped 0 overruns 0 frame 0 | |
| TX packets 165 bytes 30668 (30.6 KB) | |
| TX errors 0 dropped 0 overruns 0 carrier 0 collisions 0 | |
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| enx283737029f5c: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500 | |
| inet6 fe80::ff0d:b6b3:1c59:cb6b prefixlen 64 scopeid 0x20<link> | |
| ether 28:37:37:02:9f:5c txqueuelen 1000 (Ethernet) | |
| RX packets 0 bytes 0 (0.0 B) | |
| RX errors 0 dropped 0 overruns 0 frame 0 | |
| TX packets 165 bytes 30668 (30.6 KB) | |
| TX errors 0 dropped 0 overruns 0 carrier 0 collisions 0 | |