Philip Tzou philiptzou
philiptzou
/ alvarez22.fas.txt
Last active
June 21, 2022 22:29
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| >T1.2522.A1 | |
| ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCTGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTAT |
philiptzou
/ make_mancon22_fasta.py
Created
June 21, 2022 18:13
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| import csv | |
| NC_045512 = ''.join(""" | |
| ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA | |
| CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC | |
| TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG | |
| TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC | |
| CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC | |
| GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG | |
| CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT |
philiptzou
/ 1_make_stevens22_fasta.py
Last active
April 15, 2022 00:24
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| import csv | |
| MT020881 = ''.join(""" | |
| ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA | |
| CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC | |
| TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG | |
| TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC | |
| CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC | |
| GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG | |
| CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT |
philiptzou
/ lynch21-accession.txt
Last active
February 9, 2022 22:33
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| Source: Figure and Appendix Table 1 | |
| EPI_ISL_2484141 | |
| EPI_ISL_2484144 | |
| EPI_ISL_2484145 | |
| EPI_ISL_2484146 | |
| EPI_ISL_2484147 | |
| EPI_ISL_2484148 | |
| EPI_ISL_2484150 | |
| EPI_ISL_2484151 | |
| EPI_ISL_2484152 |
philiptzou
/ make_morad21_fasta.py
Last active
February 8, 2022 22:36
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| import csv | |
| MN908947 = ''.join(""" | |
| ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA | |
| CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC | |
| TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG | |
| TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC | |
| CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC | |
| GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG | |
| CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT |
philiptzou
/ immune_status.csv
Created
February 8, 2022 20:09
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| ref_name | subject_name | subject_species | birth_year | immune_status | num_subjects | note | |
|---|---|---|---|---|---|---|---|
| Bronstein21 | Patient 1 | Human | 1953 | 1 | Immunocompromised | ||
| Sabin21 | P3 | Human | 1 | Household case report | |||
| Kemp21 | Septuagenarian male | Human | 1945 | 1 | prolonged infection, d1 | ||
| Jensen21 | Patient 6 | Human | 1955 | 1 | prolonged infection, d20 | ||
| Baang21 | Patient | Human | 1 | Immunocompromised | |||
| Sabin21 | P4 | Human | 1 | Household case report | |||
| Choudhary21 | ACTIV-2/A5401 trial | Human | 111 | ||||
| Kemp21 | Septuagenarian male | Human | 1945 | 1 | prolonged infection, d55 | ||
| Sabin21 | P1 | Human | 1 | Household case report |
philiptzou
/ hypermut2.py
Last active
October 27, 2023 16:27
A Python implementation of LANL Hypermut2
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| # https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html | |
| #! /usr/bin/env python | |
| """ | |
| MIT License | |
| Copyright (c) 2023 Stanford University HIVDB Team | |
| Permission is hereby granted, free of charge, to any person obtaining a copy | |
| of this software and associated documentation files (the "Software"), to deal |
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| #! /usr/bin/env python | |
| from __future__ import print_function | |
| """ | |
| The Python Debugger Pdb | |
| ======================= | |
| To use the debugger in its simplest form: | |
| >>> import pdb |
philiptzou
/ sequence_analysis_mutations_only.gql
Last active
September 24, 2018 17:41
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| inputSequence { | |
| header | |
| } | |
| mutations { | |
| text | |
| gene { name } | |
| # delete belows if you don't need mutation details | |
| consensus | |
| position |
philiptzou
/ sequence_analysis_mutation_type_only.gql
Last active
September 24, 2018 18:55
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| inputSequence { | |
| header | |
| } | |
| drugResistance { | |
| mutationsByTypes { | |
| mutationType, | |
| mutations { | |
| consensus, | |
| position, |
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