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fix reportingtools html for transcripts
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@hoelzer
hoelzer committed Jan 8, 2021
1 parent f83d56c commit 84e3007
Showing 1 changed file with 60 additions and 26 deletions.
86 changes: 60 additions & 26 deletions bin/refactor_reportingtools_table.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,12 @@ def initialize(html_path, anno, add_plot_information, pvalue)
# does not work anymore because the input is now named 'annotation.gene.gtf'
#species = anno.sub('.gene.gtf','')

# check if analysis runs on transcripts instead of genes
feature_type = 'gene'
if anno.include?('.transcript.gtf')
feature_type = 'transcript'
end

$add_plots = false
$add_plots = true if add_plot_information && add_plot_information == 'add_plots'

Expand All @@ -23,6 +29,7 @@ def initialize(html_path, anno, add_plot_information, pvalue)
species = 'eco' if gene_id.start_with?('ER')
species = 'hsa' if gene_id.start_with?('ENSG')
species = 'mmu' if gene_id.start_with?('ENSMUSG')
species = 'mau' if gene_id.start_with?('ENSMAUG')
break if species != 'na'
end
end
Expand All @@ -31,19 +38,31 @@ def initialize(html_path, anno, add_plot_information, pvalue)

case species
when 'eco'
$scan_gene_id_pattern = 'ER[0-9]+_[0-9]+'
$scan_feature_id_pattern = 'ER[0-9]+_[0-9]+'
$ensembl_url = 'https://bacteria.ensembl.org/Escherichia_coli_k_12/Gene/Summary?g='
when 'hsa'
$scan_gene_id_pattern = 'ENSG[0-9]+'
$scan_feature_id_pattern = 'ENSG[0-9]+'
$ensembl_url = 'https://ensembl.org/Homo_sapiens/Gene/Summary?g='
if feature_type == 'transcript'
$scan_feature_id_pattern = 'ENST[0-9]+'
$ensembl_url = 'https://ensembl.org/Homo_sapiens/Gene/Summary?t='
end
when 'mmu'
$scan_gene_id_pattern = 'ENSMUSG[0-9]+'
$scan_feature_id_pattern = 'ENSMUSG[0-9]+'
$ensembl_url = 'https://ensembl.org/Mus_musculus/Gene/Summary?g='
if feature_type == 'transcript'
$scan_feature_id_pattern = 'ENSMUST[0-9]+'
$ensembl_url = 'https://ensembl.org/Mus_musculus/Gene/Summary?t='
end
when 'mau'
$scan_gene_id_pattern = 'ENSMAUG[0-9]+'
$scan_feature_id_pattern = 'ENSMAUG[0-9]+'
$ensembl_url = 'https://ensembl.org/Mesocricetus_auratus/Gene/Summary?g='
if feature_type == 'transcript'
$scan_feature_id_pattern = 'ENSMAUT[0-9]+'
$ensembl_url = 'https://ensembl.org/Mesocricetus_auratus/Gene/Summary?t='
end
else
$scan_gene_id_pattern = false
$scan_feature_id_pattern = false
$ensembl_url = false
end

Expand All @@ -52,25 +71,40 @@ def initialize(html_path, anno, add_plot_information, pvalue)
$id2pos = {}
gtf = File.open(anno,'r')
gtf.each do |line|

s = line.split("\t")

feature_name = 'NA'
if line.include?('gene_name')
gene_name = s[8].split('gene_name')[1].split(';')[0].gsub('"','').strip
else
gene_name = 'NA'
feature_name = s[8].split('gene_name')[1].split(';')[0].gsub('"','').strip
end
if feature_type == 'transcript' && line.include?('transcript_name')
# update feature name to transcript_name
feature_name = s[8].split('transcript_name')[1].split(';')[0].gsub('"','').strip
end

feature_id = s[8].split('gene_id')[1].split(';')[0].gsub('"','').strip
if feature_type == 'transcript' && line.include?('transcript_id')
# update feature id to transcript_name
feature_id = s[8].split('transcript_id')[1].split(';')[0].gsub('"','').strip
end
gene_id = s[8].split('gene_id')[1].split(';')[0].gsub('"','').strip

feature_biotype = 'NA'
if line.include?('gene_biotype')
gene_biotype = s[8].split('gene_biotype')[1].split(';')[0].gsub('"','').strip
else
gene_biotype = 'NA'
feature_biotype = s[8].split('gene_biotype')[1].split(';')[0].gsub('"','').strip
end
if feature_type == 'transcript' && line.include?('transcript_biotype')
# update feature biotype to transcript_name
feature_biotype = s[8].split('transcript_biotype')[1].split(';')[0].gsub('"','').strip
end

chr = s[0]
start = s[3]
stop = s[4]
strand = s[6]
$id2name[gene_id] = gene_name
$id2biotype[gene_id] = gene_biotype
$id2pos[gene_id] = [chr, start, stop, strand]
$id2name[feature_id] = feature_name
$id2biotype[feature_id] = feature_biotype
$id2pos[feature_id] = [chr, start, stop, strand]
end
gtf.close
puts "read in #{$id2name.keys.size} genes."
Expand Down Expand Up @@ -134,21 +168,21 @@ def refactor_deseq_html_table(html_path)
html_file_refac << refac_table_header(tmp_array[1], 2) << '</tr>' # second header
tmp_array[2..tmp_array.length-3].each do |row|
row_splitted = row.sub('<a href','<a target="_blank" href').split('</td>')
if $scan_gene_id_pattern
gene_id = row_splitted[0].scan(/#{$scan_gene_id_pattern}/)[0]
if $scan_feature_id_pattern
feature_id = row_splitted[0].scan(/#{$scan_feature_id_pattern}/)[0]
else
gene_id = row_splitted[0].split('"">')[1]
feature_id = row_splitted[0].split('"">')[1]
end
next unless gene_id
gene_id = gene_id.gsub('"','')
gene_name = $id2name[gene_id]
gene_biotype = $id2biotype[gene_id]
#puts gene_id
pos_part = "<td class=\"\">#{$id2pos[gene_id][0]}:#{$id2pos[gene_id][1]}-#{$id2pos[gene_id][2]} (#{$id2pos[gene_id][3]})"
next unless feature_id
feature_id = feature_id.gsub('"','')
feature_name = $id2name[feature_id]
gene_biotype = $id2biotype[feature_id]
#puts feature_id
pos_part = "<td class=\"\">#{$id2pos[feature_id][0]}:#{$id2pos[feature_id][1]}-#{$id2pos[feature_id][2]} (#{$id2pos[feature_id][3]})"
if $ensembl_url
new_row = [row_splitted[0].sub('<td class="">',"<td class=\"\"><a target=\"_blank\" href=\"#{$ensembl_url}#{gene_id};\">") + '</a>', "<td class=\"\">#{gene_name}", "<td class=\"\">#{gene_biotype}", pos_part, row_splitted[1].sub('href=','target="_blank" href=').sub('<td class="">','<td class=""><div style="width: 200px">') + '</div>', row_splitted[2], row_splitted[3], row_splitted[4]].join('</td>') << '</td>'
new_row = [row_splitted[0].sub('<td class="">',"<td class=\"\"><a target=\"_blank\" href=\"#{$ensembl_url}#{feature_id};\">") + '</a>', "<td class=\"\">#{feature_name}", "<td class=\"\">#{gene_biotype}", pos_part, row_splitted[1].sub('href=','target="_blank" href=').sub('<td class="">','<td class=""><div style="width: 200px">') + '</div>', row_splitted[2], row_splitted[3], row_splitted[4]].join('</td>') << '</td>'
else
new_row = [row_splitted[0], "<td class=\"\">#{gene_name}", "<td class=\"\">#{gene_biotype}", pos_part, row_splitted[1].sub('href=','target="_blank" href=').sub('<td class="">','<td class=""><div style="width: 200px">') + '</div>', row_splitted[2], row_splitted[3], row_splitted[4]].join('</td>') << '</td>'
new_row = [row_splitted[0], "<td class=\"\">#{feature_name}", "<td class=\"\">#{gene_biotype}", pos_part, row_splitted[1].sub('href=','target="_blank" href=').sub('<td class="">','<td class=""><div style="width: 200px">') + '</div>', row_splitted[2], row_splitted[3], row_splitted[4]].join('</td>') << '</td>'
end
html_file_refac << new_row << '</tr>'
end
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