fix paths

savvas-paragkamian · Oct 27, 2023 · 4cced0f · 4cced0f
1 parent 94257fd
commit 4cced0f
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/scripts/ena_xml_to_csv.py b/scripts/ena_xml_to_csv.py
@@ -9,7 +9,7 @@
 # Aim of this script is to transform the xml available attributes from 
 # ENA assigned to each sample of ISD Crete 2016 to csv.
 ###############################################################################
-# usage:./ena_xml_to_csv.py
+# usage:./scripts/ena_xml_to_csv.py
 ###############################################################################
 import xml.etree.ElementTree as ET
 import csv

diff --git a/scripts/get_isd_crete_2016_attributes.py b/scripts/get_isd_crete_2016_attributes.py
@@ -7,7 +7,8 @@
 ###############################################################################
 # GOAL:
 # Aim of this script is to retrieve all available attributes from 
-# ENA assigned to each sample of ISD Crete 2016.
+# ENA assigned to each sample of ISD Crete 2016. These are mentioned in
+# filereport_read_run_PRJEB21776_tsv.txt file
 ###############################################################################
 # usage:./get_isd_crete_2016_attributes.py
 ###############################################################################
@@ -53,7 +54,7 @@ def attr_request(accession):
 def write_xml(attributes,accession):
 
     # load to xml
-    newxml = "../ena_samples/" + "attributes_" + str(accession) + ".xml"
+    newxml = "../ena_samples_attr/" + "attributes_" + str(accession) + ".xml"
 
     with open(newxml, "w") as xmlFile:
         xmlFile.write(attributes)

diff --git a/scripts/get_isd_crete_2016_fastq.sh b/scripts/get_isd_crete_2016_fastq.sh
@@ -13,7 +13,7 @@ runs_accession=`gawk -F"\t" '(NR>1){split($7,fastq, ";") ; for (i in fastq){prin
     ~/isd-crete/ena_metadata/filereport_read_run_PRJEB21776_tsv.txt`
 
 # go to directory
-cd ~/isd-crete/ena_fastq
+cd ~/isd-crete/ena_data
 
 # for each ftp link wget and append to a log file
 for i in $runs_accession