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Fix, update and automate generation of detailed_gene and summary_gene tables #2 #914

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Fix, update and automate generation of detailed_gene and summary_gene tables #2 #914

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c1923e2
Fix, update and automate generation of detailed_gene and summary_gene…
pfpjs Jan 19, 2019
6cdba06
Update detailed_gene and summary_gene tables filename
pfpjs Jan 20, 2019
c0ae8ce
Fix to use GRCh37 in Ensembl biomart instead of the default GRCh38
pfpjs Jan 23, 2019
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12 changes: 6 additions & 6 deletions gemini/annotation_provenance/gene_table/README
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Ensembl biomart download:
# Ensembl gene version: Ensembl 75
# Ensembl gene version: Ensembl 95
############################################################
1) Retrieve all gene ids: query1.pl -> mart_export1
2) Retrieve CDS length: query2.pl -> mart_export2
Expand All @@ -16,11 +16,11 @@
#processing to add None for blank columns
##########################################

a) cat mart_export1 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl75_1
b) cat mart_export2 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl75_2
c) cat mart_export3 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl75_3
a) cat mart_export1 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl_1
b) cat mart_export2 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl_2
c) cat mart_export3 | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > ensembl_3
d) cat HGNC_download | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > hgnc_file
e) cat HMD_HumanPhenotype.rpt | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > HMD_HumanPhenotype
e) cat anno_files/HMD_HumanPhenotype.rpt | awk -F'\t' '{ OFS = "\t" }; {for(n=1; n<=NF; n++) sub(/^$/, "None", $n); print $0}' > HMD_HumanPhenotype
###########################################################################
# Linking CDS length to gene ids (i.e. joining on a & b)
# Connector for both these files is the ensembl transcript id
Expand Down Expand Up @@ -96,5 +96,5 @@ python combined_gene_table.py (outfiles: detailed_gene_table, summary_gene_table
"transcript_max_start","Phenotype_id")


# rm gene_table ensembl_75* ensembl_format hgnc_file HMD_HumanPhenotype
# rm gene_table ensembl_* hgnc_file HMD_HumanPhenotype

6 changes: 3 additions & 3 deletions gemini/annotation_provenance/gene_table/combined_gene_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@
from collections import defaultdict


filename = 'detailed_gene_table_v75'
filename = 'detailed_gene_table'
detailed_out = open(filename, 'w')

file = 'summary_gene_table_v75'
file = 'summary_gene_table'
summary_out = open(file, 'w')

# write out files for detailed and summary gene table
Expand All @@ -35,7 +35,7 @@
lines_seen = set()


for line in open("genic_intolerance_dataset2", 'r'):
for line in open("anno_files/genic_intolerance_dataset2", 'r'):
if line.startswith("#") is False:
field = line.strip().split("\t")
name = str(field[0])
Expand Down
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