David C Danko dcdanko
dcdanko
/ pangea_metasub_download_example.py
Created
July 14, 2020 15:11
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import sys | |
| from pangea_api import ( | |
| Knex, | |
| User, | |
| Organization, | |
| ) | |
| username, password = sys.argv[1], sys.argv[2] | |
| knex = Knex('https://pangea.gimmebio.com') |
dcdanko
/ sequencing_compression.csv
Last active
May 22, 2020 22:05
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| BC-0332760505 | BC-0332766367 | BC-0332766553 | ||
|---|---|---|---|---|
| gzip | 7.2G | 6.8G | 2.1G | |
| bzip2 | 3.6G | 3.3G | 1.4G | |
| BAM | 6.2G | 5.9G | 1.9G | |
| blocked gzip | 5.1G | 4.8G | 1.6G | |
| blocked bzip2 | 3.3G | 3.0G | 1.3G | |
| blocked gzip (no q-scores) | 4.0G | 3.8G | 1.3G |
dcdanko
/ rabinkarp_hash.py
Created
January 30, 2019 16:13
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import click | |
| def parse_fasta(fasta): | |
| cur_line, cur_header = '', '' | |
| for line in fasta: | |
| line = line.strip().upper() | |
| if line[0] == '>': | |
| if cur_line: | |
| click.echo(cur_header, err=True) |
dcdanko
/ gist:b858f369fe4066e3b32b9891ee938a8f
Created
October 25, 2018 00:05
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ssh-rsa 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 [email protected] |
dcdanko
/ display_module.py
Last active
February 23, 2018 22:17
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| from mongoengine.errors import ValidationError | |
| from app.query_results.query_result_models import QueryResultMeta | |
| from app.response import Response | |
| class ResultModule: | |
| def name(self): | |
| raise NotImplementedError() |
dcdanko
/ sam-sample
Created
June 14, 2017 16:13
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| D00547:847:HYHNTBCXX:2:2210:13659:82197 99 NODE_1_length_1110436_cov_187.551 1 60 13S114M = 196 345 AACGCCCGATGCGGTGCATCGGGCGTTTTGAGACTGAAACAGGTGTAAACCTATTTCAGGACTAGACATAACGCGTCAGTACTGGTTAGGTTCCATCTCCAGGTCAACCTTGAAGCGTTCAGCAATG IIIIIIIIIIIIIGIIIIIIIGIIIGIGIIIIIIIIIIIIIIGGIIGIGGGGGIGIGIIIGIIGGGIIGIIGIIIIIGGGGIIIIIIIIIGGGIIGIIIGGIIGIIIIIIIIGGIIIIIIGGGGGGG NM:i:0 MD:Z:114 AS:i:114 XS:i:68 BX:Z:GGCCGATGTTTGTTGG-1 | |
| D00547:847:HYHNTBCXX:1:1202:8878:17523 99 NODE_1_length_1110436_cov_187.551 1 60 15S112M = 164 313 AAAACGCCCGATGCGGTGCATCGGGCGTTTTGAGACTGAAACAGGTGTAAACCTATTTCAGGACTAGACATAACGCGTCAGTACTGGTTAGGTTCCATCTCCAGGTCAACCTTGAAGCGTTCAGCAA GGIGIIGIG.GGIIIGAGGGGGG.GGGAGGGGGAGGGIIIIGGIAGGGGGGIIAGGGGGGGGGIIIIGIIIIGGGIGGGGGGGGIGGIGIIGGGGGIIGGGIGGGIGGGIGGGGGAAGGGGGG |
dcdanko
/ athena-error
Created
June 14, 2017 15:00
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 2017-06-14 09:44:45 - - 400 downsampled barcodes | |
| 2017-06-14 09:44:45 - - 5.475x estimated local coverage | |
| 2017-06-14 09:44:45 - - 2 min_support required | |
| 2017-06-14 09:44:46 - root-ctg:NODE_40_length_125948_cov_163.495;numreads:239831;checks:10;trunc-checks:False;asms:5;trunc-asms:False | |
| 2017-06-14 09:44:46 - - found 7 candidates | |
| 2017-06-14 09:44:46 - performing local assemblies | |
| 2017-06-14 09:44:46 - assembling with neighbor NODE_114_length_56824_cov_153.263 | |
| 2017-06-14 09:44:46 - - 7551 orig barcodes | |
| 2017-06-14 09:44:46 - - 400 downsampled barcodes | |
| 2017-06-14 09:44:46 - - 14.6305232749x estimated local coverage |
dcdanko
/ athena-config
Created
June 12, 2017 18:21
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| { | |
| "input_fqs":"/scratchLocal/cmlab/dcd3001/barcoded_only.fastq", | |
| "ctgfasta_path":"/scratchLocal/cmlab/dcd3001/athena/barcoded_metaspades/contigs.fasta", | |
| "reads_ctg_bam_path":"/scratchLocal/cmlab/dcd3001/athena/align-reads.spades-contigs.bam", | |
| "cluster_settings": { | |
| "cluster_type": "multiprocessing", | |
| "processes": 8 | |
| } | |
| } |
dcdanko
/ athena-error
Created
June 12, 2017 18:19
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ============================== index_reads ============================== | |
| 1 chunks to run. Starting... | |
| <omitted...> | |
| Traceback (most recent call last): | |
| File "/home/dcd3001/.miniconda2/bin/athena-meta", line 11, in <module> | |
| load_entry_point('athena==0.1', 'console_scripts', 'athena-meta')() | |
| File "build/bdist.linux-x86_64/egg/main.py", line 102, in main | |
| File "build/bdist.linux-x86_64/egg/main.py", line 36, in run |
dcdanko
/ metaspades_batch.sh
Created
May 16, 2017 14:27
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/bin/bash | |
| #SBATCH -N 1 | |
| #SBATCH -p RM | |
| #SBATCH --ntasks-per-node 28 | |
| EXC=/path/to/metaspades.py | |
| R1=$1 | |
| R2=$2 | |
| O=$3 |
NewerOlder