cosmetic changes

README.md

@@ -106,6 +106,8 @@ Reads must be provided in FASTQ or FASTA format (can be gzipped). If you have al
 
 IsoQuant expect reads to contain polyA tails. For more reliable transcript model construction do not trim polyA tails.
 
+IsoQuant can also take aligned Illumina reads to correct long-read spliced alignments. However, short reads are _not_
+used to discover transcript models or compute abundances.
 
 <a name="sec1.2"></a>
 ## Supported reference data
@@ -116,6 +118,8 @@ Reference genome is mandatory even when BAM files are provided.
 Reference gene annotation is not mandatory, but is likely to increase precision and recall.
 It can be provided in GFF/GTF format (can be gzipped).
 In this case it will be converted to [gffutils](https://pythonhosted.org/gffutils/installation.html) database. Information on converted databases will be stored in your `~/.config/IsoQuant/db_config.json` to increase speed of future runs. You can also provide gffutils database manually. Make sure that chromosome/scaffold names are identical in FASTA file and gene annotation.
+Note, that gffutils databases may not work correctly on NFS shares. It is possible to set a designated folder for 
+the database with `--genedb_output` (different from the output directory).
 
 Pre-constructed aligner index can also be provided to increase mapping time.
 

src/dataset_processor.py

@@ -410,15 +410,15 @@ def __del__(self):
                 os.remove(self.args.gunzipped_reference)
 
     def process_all_samples(self, input_data):
-        logger.info("Processing " + proper_plural_form("sample", len(input_data.samples)))
+        logger.info("Processing " + proper_plural_form("experiment", len(input_data.samples)))
         for sample in input_data.samples:
             self.process_sample(sample)
-        logger.info("Processed " + proper_plural_form("sample", len(input_data.samples)))
+        logger.info("Processed " + proper_plural_form("experiment", len(input_data.samples)))
 
     # Run through all genes in db and count stats according to alignments given in bamfile_name
     def process_sample(self, sample):
-        logger.info("Processing sample " + sample.prefix)
-        logger.info("Sample has " + proper_plural_form("BAM file", len(sample.file_list)) + ": " + ", ".join(
+        logger.info("Processing experiment " + sample.prefix)
+        logger.info("Experiment has " + proper_plural_form("BAM file", len(sample.file_list)) + ": " + ", ".join(
             map(lambda x: x[0], sample.file_list)))
         self.args.use_technical_replicas = self.args.read_group == "file_name" and len(sample.file_list) > 1
 

src/file_utils.py

@@ -60,6 +60,7 @@ def merge_counts(counter, label, chr_ids, unaligned_reads=0):
             merged_file_handler.write("%s\t%d\n" % (v, stat_dict[v]))
         counter.reads_for_tpm = stat_dict[ "__usable"]
 
+
 def normalize_path(config_path, file_path):
     if os.path.isabs(file_path):
         return os.path.normpath(file_path)

src/gene_info.py

@@ -529,7 +529,7 @@ def set_introns_and_exons(self):
     def set_feature_properties(self, isoforms_to_feature_map, feature_profiles):
         similar_features = set()
         contained_features = set()
-        # FIXME: change to interval tree instead of brute force
+        # TODO: change to interval tree instead of brute force
         for f1 in feature_profiles.features:
             for f2 in feature_profiles.features:
                 if f1 == f2:

src/input_data_storage.py

@@ -196,7 +196,6 @@ def has_replicas(self):
         return any(len(sample.file_list) > 1 for sample in self.samples)
 
     def get_samples_from_yaml(self, yaml_file_path):
-        # TODO: allow relative paths, i.e. introduce "path fixer" for non-abosulte paths (relative to YAML file)
         sample_files = []
         experiment_names = []
         illumina_bam = []