# HG changeset patch # User rhpvorderman # Date 1636985050 0 # Node ID c8f02bce10d02e531b82518ab8a80ac0e9209e0f # Parent dced6d52d218b76999feb1a9ccecaf0d4046d2a9 "planemo upload commit 05326cc2233eb0fa8beaf4198bd7c1519f2a0bf9" diff -r dced6d52d218 -r c8f02bce10d0 shm_clonality.htm --- a/shm_clonality.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_clonality.htm Mon Nov 15 14:04:10 2021 +0000 @@ -88,7 +88,7 @@ name="OLE_LINK107">Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. In Bioinformatics, 31 (20), pp. -33563358. [ [doi:10.1093/bioinformatics/btv359][The graphs in this tab give insight into the subclass distribution of IGG and IGA transcripts. Human C, Cα, Cγ and Cε +font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε constant genes are assigned using a custom script specifically designed for human (sub)class assignment in repertoire data as @@ -58,11 +58,11 @@ nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are then individually aligned in the right order to each input sequence. The percentage of the chunks identified in each rearrangement is calculated in the -chunk hit percentage. Cα and Cγ subclasses are very homologous and only differ in a few nucleotides. To assign subclasses the nt hit percentage is calculated. +115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. This percentage indicates how well the chunks covering the subclass specific nucleotide match with the different subclasses. Information diff -r dced6d52d218 -r c8f02bce10d0 shm_csr.xml --- a/shm_csr.xml Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_csr.xml Mon Nov 15 14:04:10 2021 +0000 @@ -1,4 +1,4 @@ - + python diff -r dced6d52d218 -r c8f02bce10d0 shm_downloads.htm --- a/shm_downloads.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_downloads.htm Mon Nov 15 14:04:10 2021 +0000 @@ -77,7 +77,7 @@ style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview table as a dataset: Allows downloading of the SHM Overview -table as a data set.

+table as a data set. 

Motif data per @@ -97,7 +97,7 @@ every sequence: links to a page showing for each transcript the sequence of the analysed region (as dependent on the sequence starts at filter), -the assigned subclass and the number of sequenced A,C,G and Ts.

+the assigned subclass and the number of sequenced A,C,G and T’s.

The data used to @@ -135,7 +135,7 @@ generate the frequency by class plot: Allows downloading the data used to generate frequency by class plot included in the -SHM frequency tab.

+SHM frequency tab.          

The data for @@ -145,7 +145,7 @@ >20% SHM. Information is provided for each subclass.

+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> 

Transition @@ -267,7 +267,7 @@

The data used to generate the aa mutation frequency plot for IGE: Provides the +style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the data used to generate the aa mutation frequency plot for all IGE sequences in the antigen selection tab.

@@ -314,7 +314,7 @@ data: Table output of the BASELINe analysis. Calculation of antigen selection as performed by BASELINe are shown for each individual IGG sequence and the sum of -all IGG sequences.

+all IGG sequences.       

Baseline IGM PDF:Sequence overlap between subclasses: Link to the overlap table as provided -under the clonality overlap tab.

+under the clonality overlap tab.        

The Change-O DB @@ -388,7 +388,7 @@ style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB defined clones summary file: Gives a summary of the total number of -clones in all sequences and their clone size.

+clones in all sequences and their clone size.          

The Change-O DB @@ -423,7 +423,7 @@

The Change-O DB file with defined clones of IGM:Downloads a table +12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the calculation of clonal relation between all IGM sequences. For each individual transcript the results of the clonal assignment as provided by Change-O are provided. Sequences with the same number in the CLONE column are diff -r dced6d52d218 -r c8f02bce10d0 shm_overview.htm --- a/shm_overview.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_overview.htm Mon Nov 15 14:04:10 2021 +0000 @@ -49,7 +49,7 @@ settings chosen on the start page of the SHM & CSR pipeline and only include details on the analysed region as determined by the setting of the sequence starts at filter. All data in this table can be downloaded via the -downloads tab.

+“downloads” tab.

Mutation diff -r dced6d52d218 -r c8f02bce10d0 shm_selection.htm --- a/shm_selection.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_selection.htm Mon Nov 15 14:04:10 2021 +0000 @@ -55,7 +55,7 @@ color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying selection in high-throughput Immunoglobulin sequencing data sets. In Nucleic Acids Research, 40 (17), -pp. e134e134. [ [doi:10.1093/nar/gks457: focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The -custom boundries are dependent on the sequence starts at filter.

+custom boundries are dependent on the ‘sequence starts at filter’.

Leader: diff -r dced6d52d218 -r c8f02bce10d0 shm_transition.htm --- a/shm_transition.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_transition.htm Mon Nov 15 14:04:10 2021 +0000 @@ -82,7 +82,7 @@ "Times New Roman","serif"'>Heatmaps visualizing for each subclass the frequency of all possible substitutions. On the x-axes the original base is shown, while the y-axes shows the new base. The darker the shade of blue, the more frequent -this type of substitution is occurring.

+this type of substitution is occurring. 

Bargraph diff -r dced6d52d218 -r c8f02bce10d0 utf8test.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utf8test.py Mon Nov 15 14:04:10 2021 +0000 @@ -0,0 +1,7 @@ +#!/usr/bin/env python3 +import sys + +with open(sys.argv[1], "rt", encoding="utf-8") as input_h: + input_h.read() + +