From 693b7d86908553de03525bfc9714a32667d57fda Mon Sep 17 00:00:00 2001
From: nschcolnicov <nico.schcolnicov@gmail.com>
Date: Wed, 6 Nov 2024 18:48:32 +0000
Subject: [PATCH] Started debugging tests

---
 data/examples/annotate/SQL_sample.db | Bin 0 -> 90112 bytes
 data/examples/annotate/mirtop.db     | Bin 0 -> 90112 bytes
 mirtop/command_line.py               |   3 +++
 mirtop/exporter/isomirs.py           |   2 +-
 mirtop/exporter/vcf.py               |   6 +++---
 mirtop/gff/read.py                   |   2 +-
 mirtop/mirna/mapper.py               |   2 ++
 7 files changed, 10 insertions(+), 5 deletions(-)
 create mode 100644 data/examples/annotate/SQL_sample.db
 create mode 100644 data/examples/annotate/mirtop.db

diff --git a/data/examples/annotate/SQL_sample.db b/data/examples/annotate/SQL_sample.db
new file mode 100644
index 0000000000000000000000000000000000000000..f8ae2c1a8f04545f888b6ede29d202729a22979b
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HcmV?d00001

diff --git a/mirtop/command_line.py b/mirtop/command_line.py
index 556db47..fb18f21 100644
--- a/mirtop/command_line.py
+++ b/mirtop/command_line.py
@@ -14,6 +14,7 @@
 from mirtop.libs import spikeins
 from mirtop.gff import update
 from mirtop.sql import sql 
+from mirtop.mirna import mapper
 import mirtop.libs.logger as mylog
 
 import time
@@ -25,6 +26,8 @@ def main(**kwargs):
                       kwargs['args'].print_debug)
     logger = mylog.getLogger(__name__)
     start = time.time()
+    if (not hasattr(kwargs["args"], "database") and ("sql" not in kwargs and "stats" not in kwargs and "update" not in kwargs)):
+        kwargs["args"].database = mapper.guess_database(kwargs["args"])
 
     if "gff" in kwargs:
         logger.info("Run annotation")
diff --git a/mirtop/exporter/isomirs.py b/mirtop/exporter/isomirs.py
index 0f633ae..139a3f7 100644
--- a/mirtop/exporter/isomirs.py
+++ b/mirtop/exporter/isomirs.py
@@ -38,7 +38,7 @@ def convert(args):
 def _convert_file(gff, args):
     sep = "\t"
     precursors = fasta.read_precursor(args.hairpin, args.sps)
-    matures = mapper.read_gtf_to_precursor(args.gtf)
+    matures = mapper.read_gtf_to_precursor(args.gtf, args.database)
     variant_header = sep.join(['mism', 'add', 't5', 't3'])
 
     gff_file = open(gff, 'r')
diff --git a/mirtop/exporter/vcf.py b/mirtop/exporter/vcf.py
index 6715cd4..3d5aaf0 100644
--- a/mirtop/exporter/vcf.py
+++ b/mirtop/exporter/vcf.py
@@ -25,7 +25,7 @@ def convert(args):
     for fn in args.files:
         out_file = op.join(args.out, "%s.vcf" % op.splitext(op.basename(fn))[0])
         logger.info("Reading %s" % fn)
-        create_vcf(fn, args.hairpin, args.gtf, out_file)
+        create_vcf(fn, args.hairpin, args.gtf, out_file, args.database)
         logger.info("VCF generated %s" % out_file)
 
 
@@ -121,7 +121,7 @@ def cigar_2_key(cigar, readseq, refseq, pos, var5p, var3p, parent_ini_pos, paren
     return(key_pos, key_var, ref, alt)
 
 
-def create_vcf(mirgff3, precursor, gtf, vcffile):
+def create_vcf(mirgff3, precursor, gtf, vcffile, database):
     """
     Args:
         'mirgff3(str)': File with mirGFF3 format that will be converted
@@ -178,7 +178,7 @@ def create_vcf(mirgff3, precursor, gtf, vcffile):
     n_noSNP = 0
     no_var = 0
     hairpins = read_precursor(precursor)
-    gff3 = read_gtf_to_precursor(gtf)
+    gff3 = read_gtf_to_precursor(gtf, database)
     gtf_dic = read_gtf_to_mirna(gtf)
     for line in range(0, len(gff3_data)):
         if not gff3_data[line]:
diff --git a/mirtop/gff/read.py b/mirtop/gff/read.py
index 7c243f8..552bd0c 100644
--- a/mirtop/gff/read.py
+++ b/mirtop/gff/read.py
@@ -20,7 +20,7 @@ def reader(args):
     args.database = database
     precursors = fasta.read_precursor(args.hairpin, args.sps)
     args.precursors = precursors
-    matures = mapper.read_gtf_to_precursor(args.gtf)
+    matures = mapper.read_gtf_to_precursor(args.gtf, args.database)
     args.matures = matures
     # TODO check numbers of miRNA and precursors read
     # TODO print message if numbers mismatch
diff --git a/mirtop/mirna/mapper.py b/mirtop/mirna/mapper.py
index 9d0d143..3840d13 100644
--- a/mirtop/mirna/mapper.py
+++ b/mirtop/mirna/mapper.py
@@ -20,6 +20,8 @@ def guess_database(args):
 
     TODO: this needs to be generic to other databases.
     """
+    if not hasattr(args, "database"):
+        args.database = None
     return _guess_database_file(args.gtf, args.database)