| Previous changeset 0:3708ff0198b7 (2017-07-18) Next changeset 2:fb8484ee54d8 (2017-10-23) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845 |
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modified:
filters.py load_db.py macros.xml query_db.py query_tabular.py query_tabular.xml sqlite_to_tabular.py |
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added:
test-data/psm_report.tsv test-data/psm_report_out1.tsv test-data/psm_report_out2.tsv |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 filters.py --- a/filters.py Tue Jul 18 09:07:07 2017 -0400 +++ b/filters.py Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| @@ -33,7 +33,8 @@ r = filter_dict['replace'] c = int(filter_dict['column']) - 1 self.func = lambda i, l: '\t'.join( - [x if j != c else re.sub(p, r, x) for j, x in enumerate(l.split('\t'))]) + [x if j != c else re.sub(p, r, x) + for j, x in enumerate(l.split('\t'))]) elif filter_dict['filter'] == 'prepend_line_num': self.func = lambda i, l: '%d\t%s' % (i, l) elif filter_dict['filter'] == 'append_line_num': |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 load_db.py --- a/load_db.py Tue Jul 18 09:07:07 2017 -0400 +++ b/load_db.py Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| b'@@ -2,11 +2,165 @@\n \n from __future__ import print_function\n \n+import re\n import sys\n \n from filters import TabularReader\n \n \n+SQLITE_KEYWORDS = [\n+ \'ABORT\',\n+ \'ACTION\',\n+ \'ADD\',\n+ \'AFTER\',\n+ \'ALL\',\n+ \'ALTER\',\n+ \'ANALYZE\',\n+ \'AND\',\n+ \'AS\',\n+ \'ASC\',\n+ \'ATTACH\',\n+ \'AUTOINCREMENT\',\n+ \'BEFORE\',\n+ \'BEGIN\',\n+ \'BETWEEN\',\n+ \'BY\',\n+ \'CASCADE\',\n+ \'CASE\',\n+ \'CAST\',\n+ \'CHECK\',\n+ \'COLLATE\',\n+ \'COLUMN\',\n+ \'COMMIT\',\n+ \'CONFLICT\',\n+ \'CONSTRAINT\',\n+ \'CREATE\',\n+ \'CROSS\',\n+ \'CURRENT_DATE\',\n+ \'CURRENT_TIME\',\n+ \'CURRENT_TIMESTAMP\',\n+ \'DATABASE\',\n+ \'DEFAULT\',\n+ \'DEFERRABLE\',\n+ \'DEFERRED\',\n+ \'DELETE\',\n+ \'DESC\',\n+ \'DETACH\',\n+ \'DISTINCT\',\n+ \'DROP\',\n+ \'EACH\',\n+ \'ELSE\',\n+ \'END\',\n+ \'ESCAPE\',\n+ \'EXCEPT\',\n+ \'EXCLUSIVE\',\n+ \'EXISTS\',\n+ \'EXPLAIN\',\n+ \'FAIL\',\n+ \'FOR\',\n+ \'FOREIGN\',\n+ \'FROM\',\n+ \'FULL\',\n+ \'GLOB\',\n+ \'GROUP\',\n+ \'HAVING\',\n+ \'IF\',\n+ \'IGNORE\',\n+ \'IMMEDIATE\',\n+ \'IN\',\n+ \'INDEX\',\n+ \'INDEXED\',\n+ \'INITIALLY\',\n+ \'INNER\',\n+ \'INSERT\',\n+ \'INSTEAD\',\n+ \'INTERSECT\',\n+ \'INTO\',\n+ \'IS\',\n+ \'ISNULL\',\n+ \'JOIN\',\n+ \'KEY\',\n+ \'LEFT\',\n+ \'LIKE\',\n+ \'LIMIT\',\n+ \'MATCH\',\n+ \'NATURAL\',\n+ \'NO\',\n+ \'NOT\',\n+ \'NOTNULL\',\n+ \'NULL\',\n+ \'OF\',\n+ \'OFFSET\',\n+ \'ON\',\n+ \'OR\',\n+ \'ORDER\',\n+ \'OUTER\',\n+ \'PLAN\',\n+ \'PRAGMA\',\n+ \'PRIMARY\',\n+ \'QUERY\',\n+ \'RAISE\',\n+ \'RECURSIVE\',\n+ \'REFERENCES\',\n+ \'REGEXP\',\n+ \'REINDEX\',\n+ \'RELEASE\',\n+ \'RENAME\',\n+ \'REPLACE\',\n+ \'RESTRICT\',\n+ \'RIGHT\',\n+ \'ROLLBACK\',\n+ \'ROW\',\n+ \'SAVEPOINT\',\n+ \'SELECT\',\n+ \'SET\',\n+ \'TABLE\',\n+ \'TEMP\',\n+ \'TEMPORARY\',\n+ \'THEN\',\n+ \'TO\',\n+ \'TRANSACTION\',\n+ \'TRIGGER\',\n+ \'UNION\',\n+ \'UNIQUE\',\n+ \'UPDATE\',\n+ \'USING\',\n+ \'VACUUM\',\n+ \'VALUES\',\n+ \'VIEW\',\n+ \'VIRTUAL\',\n+ \'WHEN\',\n+ \'WHERE\',\n+ \'WITH\',\n+ \'WITHOUT\'\n+]\n+\n+\n+def get_valid_column_name(name):\n+ valid_name = name\n+ if not name or not name.strip():\n+ return None\n+ elif name.upper() in SQLITE_KEYWORDS:\n+ valid_name = \'"%s"\' % name\n+ elif re.match(\'^[a-zA-Z]\\w*$\', name):\n+ pass\n+ elif re.match(\'^"[^"]+"$\', name):\n+ pass\n+ elif re.match(\'^\\[[^\\[\\]]*\\]$\', name):\n+ pass\n+ elif re.match("^`[^`]+`$", name):\n+ pass\n+ elif name.find(\'"\') < 0:\n+ valid_name = \'"%s"\' % name\n+ elif name.find(\'[\') < 0 and name.find(\']\') < 0:\n+ valid_name = \'[%s]\' % name\n+ elif name.find(\'`\') < 0:\n+ valid_name = \'`%s`\' % name\n+ elif name.find("\'") < 0:\n+ valid_name = "\'%s\'" % name\n+ return valid_name\n+\n+\n def getValueType(val):\n if val or 0. == val:\n try:\n@@ -23,14 +177,19 @@\n \n def get_column_def(file_path, table_name, skip=0, comment_char=\'#\',\n column_names=None, max_lines=100, load_named_columns=False,\n- filters=None):\n+ firstlinenames=False, filters=None):\n col_pref = [\'TEXT\', \'REAL\', \'INTEGER\', None]\n col_types = []\n col_idx = None\n+ col_names = []\n try:\n tr = TabularReader(file_path, skip=skip, comment_char=comment_char,\n col_idx=None, filters=filters)\n for linenum, fields in enumerate(tr):\n+ if linenum == 0 and firstlinenames:\n+ col_names = [get_valid_column_name(name) or \'c%d\' % (i + 1)\n+ for i, name in enumerate(fields)]\n+ continue\n if linenum > max_lines:\n break\n try:\n@@ -48,24 +207,24 @@\n for i, col_type in enumerate(col_types):\n if not col_type:\n col_types[i] = \'TEXT\'\n+ if not col_names:\n+ col_names = [\'c%d\' % i for i in range(1, len(col_types) + 1)]\n if column_names:\n- col_names = []\n if load_named_columns:\n col_idx = []\n+ cnames = []\n f'..b' [cn.strip() for cn in column_names.split(\',\')]):\n if cname != \'\':\n col_idx.append(i)\n- col_names.append(cname)\n+ cnames.append(cname)\n col_types = [col_types[i] for i in col_idx]\n+ col_names = cnames\n else:\n- col_names = [\'c%d\' % i for i in range(1, len(col_types) + 1)]\n for i, cname in enumerate(\n [cn.strip() for cn in column_names.split(\',\')]):\n if cname and i < len(col_names):\n col_names[i] = cname\n- else:\n- col_names = [\'c%d\' % i for i in range(1, len(col_types) + 1)]\n col_def = []\n for i, col_name in enumerate(col_names):\n col_def.append(\'%s %s\' % (col_names[i], col_types[i]))\n@@ -74,12 +233,14 @@\n \n def create_table(conn, file_path, table_name, skip=0, comment_char=\'#\',\n pkey_autoincr=None, column_names=None,\n- load_named_columns=False, filters=None,\n- unique_indexes=[], indexes=[]):\n+ load_named_columns=False, firstlinenames=False,\n+ filters=None, unique_indexes=[], indexes=[]):\n col_names, col_types, col_def, col_idx = \\\n get_column_def(file_path, table_name, skip=skip,\n comment_char=comment_char, column_names=column_names,\n- load_named_columns=load_named_columns, filters=filters)\n+ load_named_columns=load_named_columns,\n+ firstlinenames=firstlinenames,\n+ filters=filters)\n col_func = [float if t == \'REAL\' else int\n if t == \'INTEGER\' else str for t in col_types]\n table_def = \'CREATE TABLE %s (\\n %s%s\\n);\' % (\n@@ -98,19 +259,13 @@\n c.execute(table_def)\n conn.commit()\n c.close()\n- for i, index in enumerate(unique_indexes):\n- index_name = \'idx_uniq_%s_%d\' % (table_name, i)\n- index_columns = index.split(\',\')\n- create_index(conn, table_name, index_name, index_columns,\n- unique=True)\n- for i, index in enumerate(indexes):\n- index_name = \'idx_%s_%d\' % (table_name, i)\n- index_columns = index.split(\',\')\n- create_index(conn, table_name, index_name, index_columns)\n+\n c = conn.cursor()\n tr = TabularReader(file_path, skip=skip, comment_char=comment_char,\n col_idx=col_idx, filters=filters)\n for linenum, fields in enumerate(tr):\n+ if linenum == 0 and firstlinenames:\n+ continue\n data_lines += 1\n try:\n vals = [col_func[i](x)\n@@ -121,15 +276,28 @@\n file=sys.stderr)\n conn.commit()\n c.close()\n+ for i, index in enumerate(unique_indexes):\n+ index_name = \'idx_uniq_%s_%d\' % (table_name, i)\n+ index_columns = index.split(\',\')\n+ create_index(conn, table_name, index_name, index_columns,\n+ unique=True)\n+ for i, index in enumerate(indexes):\n+ index_name = \'idx_%s_%d\' % (table_name, i)\n+ index_columns = index.split(\',\')\n+ create_index(conn, table_name, index_name, index_columns)\n except Exception as e:\n exit(\'Error: %s\' % (e))\n \n \n def create_index(conn, table_name, index_name, index_columns, unique=False):\n- index_def = "CREATE %s INDEX %s on %s(%s)" % (\n+ index_def = \'CREATE %s INDEX %s on %s(%s)\' % (\n \'UNIQUE\' if unique else \'\', index_name,\n table_name, \',\'.join(index_columns))\n- c = conn.cursor()\n- c.execute(index_def)\n- conn.commit()\n- c.close()\n+ try:\n+ c = conn.cursor()\n+ c.execute(index_def)\n+ conn.commit()\n+ c.close()\n+ except Exception as e:\n+ print(\'Failed: %s err: %s\' % (index_def, e), file=sys.stderr)\n+ raise(e)\n' |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 macros.xml --- a/macros.xml Tue Jul 18 09:07:07 2017 -0400 +++ b/macros.xml Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| @@ -60,6 +60,52 @@ #end for ]]> </token> + <token name="@RESULT_HEADER@"> +<![CDATA[ + #if $query_result.header == 'yes': + #if $query_result.header_prefix: + #set $header_prefix = chr(int(str($query_result.header_prefix))) + --comment_char='$header_prefix' + #end if + #else + --no_header + #end if +]]> + </token> + <xml name="comment_char_options"> + <option value="62">></option> + <option value="64">@</option> + <option value="43">+</option> + <option value="60"><</option> + <option value="42">*</option> + <option value="45">-</option> + <option value="61">=</option> + <option value="124">|</option> + <option value="63">?</option> + <option value="36">$</option> + <option value="46">.</option> + <option value="58">:</option> + <option value="38">&</option> + <option value="37">%</option> + <option value="94">^</option> + <option value="35" selected="true">#</option> + <option value="33">!</option> + </xml> + <xml name="result_results_header_line"> + <conditional name="query_result"> + <param name="header" type="select" label="include query result column headers"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="header_prefix" type="select" optional="true" label="Prefix character for column_header line"> + <option value="">no comment character prefix</option> + <expand macro="comment_char_options" /> + </param> + </when> + <when value="no"/> + </conditional> + </xml> <xml name="macro_line_filters"> <repeat name="linefilters" title="Filter Tabular Input Lines"> <conditional name="filter"> @@ -81,23 +127,7 @@ </when> <when value="comment"> <param name="comment_char" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are skipped"> - <option value="62">></option> - <option value="64">@</option> - <option value="43">+</option> - <option value="60"><</option> - <option value="42">*</option> - <option value="45">-</option> - <option value="61">=</option> - <option value="124">|</option> - <option value="63">?</option> - <option value="36">$</option> - <option value="46">.</option> - <option value="58">:</option> - <option value="38">&</option> - <option value="37">%</option> - <option value="94">^</option> - <option value="35">#</option> - <option value="33">!</option> + <expand macro="comment_char_options" /> </param> </when> <when value="prepend_line_num"/> |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 query_db.py --- a/query_db.py Tue Jul 18 09:07:07 2017 -0400 +++ b/query_db.py Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| @@ -56,12 +56,12 @@ exit(0) -def run_query(conn, query, outputFile, no_header=False): +def run_query(conn, query, outputFile, no_header=False, comment_char='#'): cur = conn.cursor() results = cur.execute(query) if not no_header: - outputFile.write("#%s\n" % '\t'.join( - [str(col[0]) for col in cur.description])) + outputFile.write("%s%s\n" % (comment_char, '\t'.join( + [str(col[0]) for col in cur.description]))) for i, row in enumerate(results): outputFile.write("%s\n" % '\t'.join( [str(val) if val is not None else '' for val in row])) |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 query_tabular.py --- a/query_tabular.py Tue Jul 18 09:07:07 2017 -0400 +++ b/query_tabular.py Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| @@ -56,6 +56,8 @@ parser.add_option('-n', '--no_header', dest='no_header', default=False, action='store_true', help='Include a column headers line') + parser.add_option('-c', '--comment_char', dest='comment_char', default='', + help='comment character to prefix column header line') parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results') (options, args) = parser.parse_args() @@ -80,6 +82,8 @@ table['comment_char'] if 'comment_char' in table else None column_names =\ table['column_names'] if 'column_names' in table else None + firstlinenames =\ + table['firstlinenames'] if 'firstlinenames' in table else False if column_names: load_named_columns =\ table['load_named_columns']\ @@ -93,6 +97,7 @@ table['pkey_autoincr'] if 'pkey_autoincr' in table else None create_table(get_connection(options.sqlitedb), path, table_name, pkey_autoincr=pkey_autoincr, + firstlinenames=firstlinenames, column_names=column_names, skip=comment_lines, comment_char=comment_char, @@ -128,7 +133,8 @@ else: try: run_query(get_connection(options.sqlitedb), query, outputFile, - no_header=options.no_header) + no_header=options.no_header, + comment_char=options.comment_char) except Exception as e: exit('Error: %s' % (e)) |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 query_tabular.xml --- a/query_tabular.xml Tue Jul 18 09:07:07 2017 -0400 +++ b/query_tabular.xml Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="query_tabular" name="Query Tabular" version="1.0.0">\n+<tool id="query_tabular" name="Query Tabular" version="2.0.0">\n <description>using sqlite sql</description>\n \n <macros>\n@@ -26,7 +26,7 @@\n -j \'$table_json\'\n #if $sqlquery:\n -Q \'$query_file\' \n- $no_header\n+ @RESULT_HEADER@\n -o \'$output\'\n #end if\n ]]></command>\n@@ -54,6 +54,9 @@\n #if $tbl.tbl_opts.pkey_autoincr:\n #set $jtbl[\'pkey_autoincr\'] = str($tbl.tbl_opts.pkey_autoincr)\n #end if\n+ #if $tbl.tbl_opts.column_names_from_first_line:\n+ #set $jtbl[\'firstlinenames\'] = True\n+ #end if\n #if $tbl.tbl_opts.col_names:\n #set $col_names = str($tbl.tbl_opts.col_names)\n #if $tbl.tbl_opts.load_named_columns:\n@@ -104,6 +107,9 @@\n <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help>\n <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\\w*$</validator>\n </param>\n+ <param name="column_names_from_first_line" type="boolean" truevalue="True" falsevalue="False" checked="false" \n+ label="Use first line as column names"\n+ help="The names will be quoted if they are not valid SQLite column names."/>\n <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">\n <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique)\n You can override the default names by entering a comma -separated list of names, e.g. \',name1,,,name2\' would rename the second and fifth columns.\n@@ -119,8 +125,9 @@\n <repeat name="indexes" title="Table Index">\n <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>\n <param name="index_columns" type="text" value="" label="Index on Columns">\n- <help>Create an index on the column names: e,g, c1 or c2,c4</help>\n+ <help>Create an index on the column names: e.g. for default column names: c1 or c2,c4 ( use the names you gave for columns)</help>\n <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\\w*|"\\S+[^,"]*"|`\\S+[^,`]*`|[[]\\S+[^,"]*[]])(,([A-Za-z]\\w*|"\\S+.*"|`\\S+[^,`]*`|[[]\\S+[^,"]*[]])?)*$</validator>\n+ <sanitizer sanitize="False"/>\n </param>\n </repeat>\n </section>\n@@ -132,7 +139,7 @@\n <sanitizer sanitize="False"/>\n <validator type="regex" message="">^(?ims)\\s*select\\s+.*\\s+from\\s+.*$</validator>\n </param>\n- <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers from tabular output"/>\n+ <expand macro="result_results_header_line" />\n </inputs>\n <outputs>\n <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">\n@@ -391,6 +398,56 @@\n <output name="output" file="pet_normalized_query_results.tsv"/>\n </test>\n \n+ <test>\n+ <repeat name="tables">\n+ <param name="table" ftype="tabular" value="psm_report.tsv"/>\n+ <section name="input_opts">\n+ <repeat name="linefilters">\n+ <conditional name="filter">\n+ <param name="filter_type" value="select_columns"/>\n+ <param name="columns" value="1,3,2,6,14,19"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="tbl_opts">\n+ <param name="table_name" value="'..b' <param name="column_names_from_first_line" value="True"/>\n+ <param name="col_names" value="Scan"/>\n+ </section>\n+ </repeat>\n+ <param name="sqlquery" value="SELECT * from PSMs"/>\n+ <conditional name="query_result">\n+ <param name="header" value="yes"/>\n+ <param name="header_prefix" value=""/>\n+ </conditional>\n+ <output name="output" file="psm_report_out1.tsv"/>\n+ </test>\n+\n+ <test>\n+ <repeat name="tables">\n+ <param name="table" ftype="tabular" value="psm_report.tsv"/>\n+ <section name="input_opts">\n+ <repeat name="linefilters">\n+ <conditional name="filter">\n+ <param name="filter_type" value="select_columns"/>\n+ <param name="columns" value="1,3,2,6,14,19"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="tbl_opts">\n+ <param name="table_name" value="PSMs"/>\n+ <param name="column_names_from_first_line" value="True"/>\n+ <param name="col_names" value="Scan"/>\n+ </section>\n+ </repeat>\n+ <param name="sqlquery" value="SELECT Scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)" FROM PSMs WHERE NOT re_search(\', \',"Protein(s)")"/>\n+ <conditional name="query_result">\n+ <param name="header" value="yes"/>\n+ <param name="header_prefix" value=""/>\n+ </conditional>\n+ <output name="output" file="psm_report_out2.tsv"/>\n+ </test>\n+\n </tests>\n <help><![CDATA[\n =============\n@@ -406,6 +463,45 @@\n \n @LINEFILTERS_HELP@\n \n+**Table Options**\n+\n+ Specify Name for Table:\n+\n+ - By default tables will be named: t1, t2, t3, etc.\n+ \n+ - **Specify Name for Table** \n+ You can provide your own name for a database table, the name should begin with a letter and only contain letters, digits, or underscores. \n+ The name should not be a SQLite key word: https://sqlite.org/lang_keywords.html\n+\n+\n+ There are several ways to name columns in a table: \n+\n+ - By default table columns will be named: c1, c2, c3, etc.\n+\n+ - If **Use first line as column names** is selected, the first line is interpreted as column names, and not loaded into the table as a data row. \n+ Any missing column name will be assigned cn where *n* is the ordinal position of the column, \n+ e.g. a blank header for the second column would be named: c2.\n+ The column names will be quoted is they are not valid identifiers, \n+ e.g. if they are SQLite keywords, or start with a non letter character, or contain a character other than a letter, digit, or underscore.\n+ The precedent for quoting is to enclose the identifier in double quotes, \n+ else if it contains a double quote enclose in square brackets,\n+ else if it contains a square bracket enclose in grave accents.\n+ **NOTE:** that this is the first line after line filtering has been applied. \n+ If a line filter *prepend a line number column* had been used, the name of the first column would be "1".\n+ You could rename that column using **Specify Column Names**\n+\n+ - **Specify Column Names** (comma-separated list)\n+ This will override any previously assigned column names. \n+ You can also choose to only load those columns for which you provided a name, \n+ but that is better accomplished with the line filter: *select columns*. \n+\n+\n+ **Table Index**\n+\n+ Queries on larger tables can be much faster if indexes are specified. \n+ In general, specifiy an index for table columns used in joins with other tables, \n+ or on columns used in SQL query WHERE clauses or in GROUP BY clauses.\n+\n \n **Outputs**\n \n' |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 sqlite_to_tabular.py --- a/sqlite_to_tabular.py Tue Jul 18 09:07:07 2017 -0400 +++ b/sqlite_to_tabular.py Fri Aug 18 16:48:09 2017 -0400 |
| b |
| @@ -21,6 +21,8 @@ parser.add_option('-n', '--no_header', dest='no_header', default=False, action='store_true', help='Include a column headers line') + parser.add_option('-c', '--comment_char', dest='comment_char', default='', + help='comment character to prefix column header line') parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results') (options, args) = parser.parse_args() @@ -51,7 +53,8 @@ else: try: run_query(get_connection(options.sqlitedb), query, outputFile, - no_header=options.no_header) + no_header=options.no_header, + comment_char=options.comment_char) except Exception as e: exit('Error: %s' % (e)) |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 test-data/psm_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psm_report.tsv Fri Aug 18 16:48:09 2017 -0400 |
| [ |
| @@ -0,0 +1,10 @@ + + Protein(s) Sequence AAs Before AAs After Position Modified Sequence Variable Modifications Fixed Modifications Spectrum File Spectrum Title Spectrum Scan Number RT m/z Measured Charge Identification Charge Theoretical Mass Isotope Number Precursor m/z Error [ppm] Localization Confidence Probabilistic PTM score D-score Confidence [%] Validation +1 NP_116558 PYANQPTVR M IT 2 NH2-PYANQPTVR-COOH trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.04679.04679.2 4679 -1.0 523.272583 2+ 2+ 1044.53524305008 0 -4.4240452979909675 100.0 Doubtful +2 NP_443137, NP_443137_S1016F DANTQVHTLR YK; YK KM; KM 443; 443 NH2-DANTQVHTLR-COOH trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.03894.03894.2 3894 -1.0 577.799622 2+ 2+ 1153.5839841476504 0 0.6117338355350196 95.0 Doubtful +3 NP_066544_R21W SSWAGLQFPVGR TR VH 19 NH2-SSWAGLQFPVGR-COOH trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.20932.20932.2 20932 -1.0 652.843567 2+ 2+ 1303.6673198487902 0 4.029478922381296 100.0 Doubtful +4 NP_112092_rs7285167:R182C AQACNLDQSGTNVAK AR VM 179 NH2-AQAC<cmm>NLDQSGTNVAK-COOH Carbamidomethylation of C(4) trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.05257.05257.2 5257 -1.0 788.87384 2+ 2+ 1575.7311189571503 0 1.2727711831177586 100.0 Doubtful +5 NP_001273432_F75C, NP_001273433_F77C, NP_001273434_F77C, NP_006635_F75C ACNDPFIQK GR; GR; GR; GR EK; EK; EK; EK 74; 76; 76; 74 NH2-AC<cmm>NDPFIQK-COOH Carbamidomethylation of C(2) trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.09560.09560.2 9560 -1.0 546.760803 2+ 2+ 1091.50697969691 0 0.06709466946167521 94.73684210526316 Doubtful +6 NP_001028196, NP_001244919, NP_036311 LQLLPESFICK KR; KR; KR EK; EK; EK 198; 163; 277 NH2-LQLLPESFIC<cmm>K-COOH Carbamidomethylation of C(10) trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.22345.22345.2 22345 -1.0 674.370911 2+ 2+ 1346.7268088708604 0 0.3412036795550375 99.38650306748467 Doubtful +7 NP_001909_rs72973763:I239V,rs12021720:S384G DMTVPVLVSKPPVFTGK PK DK 234 NH2-DMTVPVLVSKPPVFTGK-COOH trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.20464.20464.2 20464 -1.0 908.008545 2+ 2+ 1814.0011927988103 0 0.7402290254293575 94.73684210526316 Doubtful +8 NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L FGVSSESKPEEVK FK; FK; FK; FK; FK; FK KD; KD; KD; KD; KD; KD 992; 992; 919; 919; 961; 961 NH2-FGVSSESKPEEVK-COOH trimmed_tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.mgf tgriffin_cguerrer_20150826_RP_MCF7_hipH_frac_12n28.06665.06665.2 6665 -1.0 711.858643 2+ 2+ 1421.7038244968105 0 -0.7666055674357796 100.0 Doubtful |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 test-data/psm_report_out1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psm_report_out1.tsv Fri Aug 18 16:48:09 2017 -0400 |
| b |
| @@ -0,0 +1,9 @@ +Scan Sequence Protein(s) Position m/z Precursor m/z Error +1 PYANQPTVR NP_116558 2 523.272583 -4.42404529799 +2 DANTQVHTLR NP_443137, NP_443137_S1016F 443; 443 577.799622 0.611733835535 +3 SSWAGLQFPVGR NP_066544_R21W 19 652.843567 4.02947892238 +4 AQACNLDQSGTNVAK NP_112092_rs7285167:R182C 179 788.87384 1.27277118312 +5 ACNDPFIQK NP_001273432_F75C, NP_001273433_F77C, NP_001273434_F77C, NP_006635_F75C 74; 76; 76; 74 546.760803 0.0670946694617 +6 LQLLPESFICK NP_001028196, NP_001244919, NP_036311 198; 163; 277 674.370911 0.341203679555 +7 DMTVPVLVSKPPVFTGK NP_001909_rs72973763:I239V,rs12021720:S384G 234 908.008545 0.740229025429 +8 FGVSSESKPEEVK NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L 992; 992; 919; 919; 961; 961 711.858643 -0.766605567436 |
| b |
| diff -r 3708ff0198b7 -r 8a33b442ecd9 test-data/psm_report_out2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psm_report_out2.tsv Fri Aug 18 16:48:09 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Scan m/z Precursor m/z Error Sequence Protein(s) +1 523.272583 -4.42404529799 PYANQPTVR NP_116558 +3 652.843567 4.02947892238 SSWAGLQFPVGR NP_066544_R21W +4 788.87384 1.27277118312 AQACNLDQSGTNVAK NP_112092_rs7285167:R182C +7 908.008545 0.740229025429 DMTVPVLVSKPPVFTGK NP_001909_rs72973763:I239V,rs12021720:S384G |