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Tools to post-process sequence files (and some other related stuff)

Renaming of sequences within NEXUS files

The tool can be given a nexus file and a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

For instance, the following command

nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files with the specified renaming applied

The .nds file is of the form

 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files

The tool can be given a fasta file and a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated FASTA files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

For instance, the following command

fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file with the specified renaming applied.

The .nds file is of the form

 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files

The tool can generate a bunch of NEXUS files post processed with the addition of trait and/or geotag blocks. It must be given a nexus file and a configuration file. Additionally, two other files must be provided:

  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.

The configuration file points to these two as well as to other information. Example:

traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat

The tool is then called with this configuration file and the NEXUS file

nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension (here input). In this directory will be created one nexus file and one CSV file per trait. The csv file contains the trait matrix (as stored in the nexus file). If geotags are provided, one nexus file with a geotags block and one CSV file are generated as well.

input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
No description, website, or topics provided.
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2 watching
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
No description, website, or topics provided.
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2 watching
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
No description, website, or topics provided.
Resources
Readme
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Stars
1 star
Watchers
2 watching
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0 forks
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Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
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Skip to content
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History
51 Commits
Folders and files
NameName
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bin
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lib
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test
test
README.md
README.md
Repository files navigation
Tools to post-process sequence files (and some other related stuff)
Renaming of sequences within NEXUS files
The tool can be given a nexus file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated NEXUS files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
nexus --rename input.nex names.nds

will generate a file called input.renamed.nex which is the input nexus files
with the specified renaming applied
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Renaming of sequences within FASTA files
The tool can be given a fasta file and a file that gives a mapping from sequence
names (as found in the input file) to the names that should be used in the
generated FASTA files. The first word (without spaces) in each line is
interpreted as the input name and the rest as the output name.
For instance, the following command
fasta --rename input.fas names.nds

will generate a file called input.renamed.fas which is the input fasta file
with the specified renaming applied.
The .nds file is of the form
 Name0 new name 0
Name1 new name 1

Addition of traits into NEXUS files
The tool can generate a bunch of NEXUS files post processed with the addition of
trait and/or geotag blocks. It must be given a nexus file and a configuration
file. Additionally, two other files must be provided:
  • a CSV file containing some trait information. One column in this file contains the sequence names as found in the input NEXUS file. The first line of the CSV file must contain the column names.
  • a file that gives a mapping from sequence names (as found in the input file) to the names that should be used in the generated NEXUS files. The first word (without spaces) in each line is interpreted as the input name and the rest as the output name.
The configuration file points to these two as well as to other information.
Example:
traits_file: path_to_csv_file.csvname_mappings_file: path_to_name_mapping_file.nds# Name of the column containing the sequence names in the input NEXUS filekey: arb name# Column containing the decimal latitude (optional)lat: lat decimal# Column containing the decimal longitude (optional)lon: lon decimal# If lat/lon is provided, the number of clusters that popart should use to classify the sequences geographicallyncluters: 5# The trait columnstraits:
- habitat
The tool is then called with this configuration file and the NEXUS file
nexus input.nex postprocess.config

it will create a directory called like the input file, but without the extension
(here input). In this directory will be created one nexus file and one CSV
file per trait. The csv file contains the trait matrix (as stored in the nexus
file). If geotags are provided, one nexus file with a geotags block and one CSV
file are generated as well.
input/geotags.nex
input/geotags.csv
input/habitat.nex
input/habitat.csv

If a trait is unknown for a sequence, set the corresponding cell to ? in the CSV file
About
No description, website, or topics provided.
Resources
Readme
Activity
Stars
1 star
Watchers
2 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages