Split multi-sequence FASTA file into list
Created: 2010-03-16 17:46:06
Splits a flat file containing multiple fasta sequences into a list of fasta sequences.
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Inputs (1)
Name |
Description |
flat_fastas |
|
Processors (6)
Name |
Type |
Description |
Split_string_into_string_list_by_regular_expression |
localworker |
ScriptList split = new ArrayList();if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); }} |
greater_than_symbol |
stringconstant |
Value> |
non_empty_fasta |
stringconstant |
Value^>$ |
Concatenate_two_strings |
localworker |
Scriptoutput = string1 + string2; |
Filter_List_of_Strings_by_regex |
localworker |
Scriptfilteredlist = new ArrayList();for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (item.matches(regex)) { filteredlist.add(item); }} |
String_List_Difference |
localworker |
ScriptList difference = new ArrayList();for (Iterator i = list1.iterator(); i.hasNext();) { Object o = i.next(); if (!list2.contains(o)) { difference.add(o); }}for (Iterator i = list2.iterator(); i.hasNext();) { Object o = i.next(); if (!list1.contains(o)) { difference.add(o); }} |
Outputs (1)
Name |
Description |
list_of_fastas |
|
Datalinks (9)
Source |
Sink |
greater_than_symbol:value |
Split_string_into_string_list_by_regular_expression:regex |
flat_fastas |
Split_string_into_string_list_by_regular_expression:string |
greater_than_symbol:value |
Concatenate_two_strings:string1 |
Split_string_into_string_list_by_regular_expression:split |
Concatenate_two_strings:string2 |
Concatenate_two_strings:output |
Filter_List_of_Strings_by_regex:stringlist |
non_empty_fasta:value |
Filter_List_of_Strings_by_regex:regex |
Filter_List_of_Strings_by_regex:filteredlist |
String_List_Difference:list1 |
Concatenate_two_strings:output |
String_List_Difference:list2 |
String_List_Difference:difference |
list_of_fastas |
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