bio search for SRR now lists fastq urls as a list

ialbert · Apr 4, 2023 · b411b9e · b411b9e
1 parent ca69b94
commit b411b9e
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Showing 4 changed files with 31 additions and 9 deletions.
diff --git a/biorun/__init__.py b/biorun/__init__.py
@@ -5,7 +5,7 @@
 #
 import sys
 # Global package version
-VERSION = "1.5.8"
+VERSION = "1.5.9"
 
 try:
     from signal import signal, SIGPIPE, SIG_DFL

diff --git a/biorun/data/search_prjn.json b/biorun/data/search_prjn.json
@@ -17,7 +17,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/054/SRR12586154/SRR12586154_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/054/SRR12586154/SRR12586154_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/054/SRR12586154/SRR12586154_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/054/SRR12586154/SRR12586154_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 24 million reads; 7.3 billion sequenced bases"
     },
     {
@@ -38,7 +41,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/055/SRR12586155/SRR12586155_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/055/SRR12586155/SRR12586155_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/055/SRR12586155/SRR12586155_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/055/SRR12586155/SRR12586155_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 22 million reads; 6.7 billion sequenced bases"
     },
     {
@@ -59,7 +65,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/056/SRR12586156/SRR12586156_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/056/SRR12586156/SRR12586156_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/056/SRR12586156/SRR12586156_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/056/SRR12586156/SRR12586156_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 26 million reads; 7.9 billion sequenced bases"
     },
     {
@@ -80,7 +89,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/057/SRR12586157/SRR12586157_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/057/SRR12586157/SRR12586157_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/057/SRR12586157/SRR12586157_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/057/SRR12586157/SRR12586157_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 24 million reads; 7.1 billion sequenced bases"
     },
     {
@@ -101,7 +113,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/058/SRR12586158/SRR12586158_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/058/SRR12586158/SRR12586158_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/058/SRR12586158/SRR12586158_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/058/SRR12586158/SRR12586158_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 24 million reads; 7.3 billion sequenced bases"
     },
     {
@@ -122,7 +137,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Plasmodium transcription repressor AP2-O3 regulates sex-specific identity of gene expression in female gametocytes [RNA-seq]",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/059/SRR12586159/SRR12586159_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/059/SRR12586159/SRR12586159_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/059/SRR12586159/SRR12586159_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR125/059/SRR12586159/SRR12586159_2.fastq.gz"
+        ],
         "info": "2 GB, 2 GB file; 28 million reads; 8.5 billion sequenced bases"
     }
 ]
diff --git a/biorun/data/search_srr.json b/biorun/data/search_srr.json
@@ -17,7 +17,10 @@
         "instrument_platform": "ILLUMINA",
         "instrument_model": "Illumina HiSeq 2500",
         "study_title": "Zaire ebolavirus Genome sequencing",
-        "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/006/SRR1972976/SRR1972976_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/006/SRR1972976/SRR1972976_2.fastq.gz",
+        "fastq_url": [
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/006/SRR1972976/SRR1972976_1.fastq.gz",
+            "https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/006/SRR1972976/SRR1972976_2.fastq.gz"
+        ],
         "info": "699 MB, 606 MB file; 8 million reads; 1.7 billion sequenced bases"
     }
 ]
diff --git a/biorun/search.py b/biorun/search.py
@@ -162,7 +162,8 @@ def add_field(entry):
             entry["bio_error"] = f"invalid data: {exc}"
 
         info = f"{bytes_val} file; {count_val} reads; {base_val} sequenced bases"
-
+        entry['fastq_url'] = [ f"https://{u}" for u in entry['fastq_ftp'].split(";") ]
+        del entry['fastq_ftp']
         entry["info"] = info
 
         return entry