Merge branch 'dev'

Makefile

@@ -54,7 +54,7 @@ build:
 # Publish the package
 publish: test build
 	hatch publish
-	
+
 #REMOTE=www@biostarhandbook.com:/home/www/book/data_www/bio
 
 # Upload prebuilt data to distribution site.

src/biorun/search.py

@@ -24,7 +24,6 @@
 ENA_FIELDS = f"{ENA_API}/returnFields"
 ENA_REPORT = f"{ENA_API}/filereport"
 
-
 # The assembly summary file
 ASSEMBLY_SUMMARY_URL = 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt'
 ASSEMBLY_SUMMARY_PATH = "assembly_summary_genbank.txt"

src/biorun/search2.py

@@ -0,0 +1,80 @@
+"""
+Bio search : search for information using accession numbers
+"""
+import re
+
+# SRR numbers: SRR5260547
+SRR_PATT = re.compile(r'(ERR|SRR|DRR|SRP|ERP)\d+')
+SRR_TYPE = 'srr'
+
+# Bioproject numbers: PRJNA374918
+PRJ_PATT = re.compile(r'PRJ([A-Z])+\d+')
+PRJ_TYPE = 'bioproject'
+
+# Genbank accessions: NC_045512
+GBK_PATT = re.compile(r'(?P<letters>[a-zA-Z]+)(?P<under>_?)(?P<digits>\d+)(\.(?P<version>\d+))?')
+GBK_TYPE = 'genbank'
+
+# Ensemble ids: ENSG00000157764
+ENS_PATT = re.compile(r'ENS[A-Z]+\d+')
+ENS_TYPE = 'ensembl'
+
+# A pattern that matches words followed by a colon and the literal wordgene
+GENE_PATT = re.compile(r'(?P<word>\w+):gene', flags=re.IGNORECASE)
+GENE_TYPE = 'gene'
+
+# GEO accessions: GSM123456, GSE123456, GPL123456, GDS123456
+GEO_PATT = re.compile(r'(GSM|GSE|GPL|GDS)\d+')
+GEO_TYPE = 'geo'
+
+# NCBI assembly ids: GCF_000001405.39, GCA_000001405.15
+ASM_PATT = re.compile(r'(GCA|GCF)_\d+')
+ASM_TYPE = 'assembly'
+
+# Patterns and types.
+PATTERNS = [
+    (ASM_TYPE, ASM_PATT),
+    (GEO_TYPE, GEO_PATT),
+    (GENE_TYPE, GENE_PATT),
+    (SRR_TYPE, SRR_PATT),
+    (PRJ_TYPE, PRJ_PATT),
+    (ENS_TYPE, ENS_PATT),
+    (GBK_TYPE, GBK_PATT),
+]
+
+# ENA API urls.
+ENA_API = "https://www.ebi.ac.uk/ena/portal/api"
+ENA_FIELDS = f"{ENA_API}/returnFields"
+ENA_REPORT = f"{ENA_API}/filereport"
+
+def get_match(acc):
+    for dtype, pattern in PATTERNS:
+        if pattern.match(acc):
+            return dtype
+    return None
+
+def run(acc):
+
+    dtype = get_match(acc)
+
+
+    if not dtype:
+        print(f"# No match for: {acc}")
+    else:
+        print (acc, dtype)
+
+    print("-"* 10)
+
+
+if __name__ == '__main__':
+    accs = [
+            "NP_001191", "SRR5260547", "PRJNA374918", "HAD3:gene",
+            "ENSG00000157764", "GSM123456", "GSE123456",
+            "GCF_000001405.39",
+            "GCA_000001405",
+            "NP_001191.1", "ecoli"
+            ]
+    for acc in accs:
+        run(acc)
+
+