Commit 4665c7c5 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

gzip in place

parent 773f6a44
......@@ -3,6 +3,7 @@ import multiprocessing
import os
import sys
import shlex
import gzip
curl = """curl -X POST -H "Content-Type: application/x-www-form-urlencoded" -d 'result=sample&query=secondary_sample_accession%3D%22XXXXXX%22&format=tsv' "https://www.ebi.ac.uk/ena/portal/api/search\""""
xml = "https://www.ebi.ac.uk/ena/browser/api/xml/"
......@@ -46,24 +47,36 @@ def run_command(command):
return result.stdout.decode('ascii')
def conversion(identifier):
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".conversion.ttl"): return
output_file = "./genome/" + identifier + "/" + identifier + ".conversion.ttl"
if os.path.isfile(output_file + ".gz"): return
# "-tool", "conversion", "-f", fasta.getAbsolutePath(), "-gff2rdf", "-i", gff.getAbsolutePath(), "-o", output.getAbsolutePath(), "-id", "MGYG-HGUT-00001", "-codon", "11", "-topology", "linear"
command = "java -jar ./MGnifyParser.jar -tool conversion -f ./genome/" + identifier + "/" + identifier + ".fna -gff2rdf -i ./genome/" + identifier + "/" + identifier + ".gff -id " + identifier + " -codon 11 -topology linear -o ./genome/" + identifier + "/" + identifier + ".conversion.ttl"
command = "java -jar ./MGnifyParser.jar -tool conversion -f ./genome/" + identifier + "/" + identifier + ".fna -gff2rdf -i ./genome/" + identifier + "/" + identifier + ".gff -id " + identifier + " -codon 11 -topology linear -o " + output_file
print(command)
os.system(command)
gzip(output_file)
def interproscan(identifier):
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".interproscan.ttl"): return
command = "java -jar ./MGnifyParser.jar -tool interpro -i ./genome/" + identifier + "/" + identifier + ".conversion.ttl -o ./genome/" + identifier + "/" + identifier + ".interproscan.ttl -tsv ./genome/" +identifier +"/" + identifier + "_InterProScan.tsv -version InterProScan-v5_35-74_0"
output_file = "./genome/" + identifier + "/" + identifier + ".interproscan.ttl"
if os.path.isfile(output_file + ".gz"): return
command = "java -jar ./MGnifyParser.jar -tool interpro -i ./genome/" + identifier + "/" + identifier + ".conversion.ttl -o " + output_file + " -tsv ./genome/" +identifier +"/" + identifier + "_InterProScan.tsv -version InterProScan-v5_35-74_0"
print(command)
os.system(command)
gzip(output_file)
def eggnog(identifier):
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".interproscan.eggnog.ttl"): return
command = "java -jar ./MGnifyParser.jar -tool eggnog -i ./genome/" + identifier + "/" + identifier + ".interproscan.ttl -o ./genome/" + identifier + "/" + identifier + ".interproscan.eggnog.ttl -tsv ./genome/" +identifier +"/" + identifier + "_eggNOG.tsv -v v2-db5.0"
output_file = "./genome/" + identifier + "/" + identifier + ".interproscan.eggnog.ttl"
if os.path.isfile(output_file + ".gz"): return
command = "java -jar ./MGnifyParser.jar -tool eggnog -i ./genome/" + identifier + "/" + identifier + ".interproscan.ttl -o " + output_file + " -tsv ./genome/" +identifier +"/" + identifier + "_eggNOG.tsv -v v2-db5.0"
print(command)
os.system(command)
gzip(output_file)
def gzip(file):
f_in = open(file)
f_out = gzip.open(file + '.gz', 'wb')
f_out.writelines(f_in)
f_out.close()
f_in.close()
def conversion_stage(identifier):
conversion(identifier)
......
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