Mercurial > repos > rakesh4osdd > clsi_profile

annotate README.md @ 11:7dcc0e93288b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
author rakesh4osdd
date Wed, 30 Jun 2021 07:13:29 +0000
parents 116ebdf92e39
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
1 # clsi_profile
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
2
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
3 CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling.
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
4
7
6f4844ad364d "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 526516c07f33c30190617115ae94bac37a11f359"
rakesh4osdd
parents: 6
diff changeset
5 # ASIST: Antimicrobial Susceptibility standards
4
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
6
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
7 In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR).
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
8
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
9 **Example Input CSV file:**
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
10
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
11 Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
12 Strain_1,Phenotype_1,Resistant,Resistant,Resistant
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
13 Strain_2,Phenotype_2,Resistant,Susceptible,Resistant
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
14
11
7dcc0e93288b "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
rakesh4osdd
parents: 10
diff changeset
15 Link to the code : https://github.com/rakesh4osdd/clsi_profile , https://github.com/rakesh4osdd/asist
4
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
16
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
17
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
18 # ASIST tool suite
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
19
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents:
diff changeset
20 These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/.