Merge pull request #123 from rki-mf1/feat/match-from-file

Allow query parameters to be read from a file

README.md

@@ -143,7 +143,7 @@ Genomic profiles can be defined to align genomes. For this purpose, the variants
 
 The positions refer to the reference (first nucleotide in the genome is position 1). Using the option `-i` multiple variant definitions can be combined into a nucleotide, amino acid or mixed profile, which means that matching genomes must have all those variations in common. In contrast, alternative variations can be defined by multiple `-i` options. As an example, `-i S:N501Y S:E484K` matches genomes sharing the _Nelly_ **AND** _Erik_ variation while `-i S:N501Y -i S:E484K` matches to genomes that share either the _Nelly_ **OR** _Erik_ variation **OR** both. Accordingly, using the option `-e` profiles can be defined that have not to be present in the matched genomes.
 
-To filter genomes based on metadata specific options can be used (see table below). Only genomes linked to the respective metadata are then considered. Metadata values are negated when introduced by ^ (e.g. `--acc ^ID1` matches all genomes accessions but ID1). Metadata filtering is case-insensitive. To see the amount of available metadata in your database use the info tool (see section 3.5).
+To filter genomes based on metadata specific options can be used (see table below). Only genomes linked to the respective metadata are then considered. Metadata values are negated when introduced by ^ (e.g. `--acc ^ID1` matches all genomes accessions but ID1). Metadata filtering is case-insensitive. To see the amount of available metadata in your database use the info tool (see section 3.5). For many of the options multiple values can be specified on the command line (e.g. `--acc seq1 seq2`) or the query values can written one per line in a file and the file name provided (e.g. `--acc @ids.txt`).
 
 | option              | value(s)                                                              | note |
 |---------------------|-----------------------------------------------------------------------|------|

sonar.py

@@ -130,6 +130,7 @@ def parse_args():
         "remove",
         parents=[general_parser],
         help="remove genome sequences to the database.",
+        fromfile_prefix_chars="@",
     )
     parser_remove = parser_remove.add_mutually_exclusive_group()
     parser_remove.add_argument(
@@ -153,6 +154,7 @@ def parse_args():
         "match",
         parents=[general_parser],
         help="get mutations profiles for given accessions.",
+        fromfile_prefix_chars="@",
     )
     parser_match.add_argument(
         "--include",
@@ -346,6 +348,7 @@ def parse_args():
         "restore",
         parents=[general_parser],
         help="restore sequence(s) from the database.",
+        fromfile_prefix_chars="@",
     )
     parser_restore.add_argument(
         "--acc",
@@ -369,6 +372,7 @@ def parse_args():
         "var2vcf",
         parents=[general_parser],
         help="export variants from the database to vcf format.",
+        fromfile_prefix_chars="@",
     )
     parser_var2vcf.add_argument(
         "--acc",