Import and export fasta format for RNA, DNA and PEPTIDES

[even1024]

Background

This task covers import/export of sequences with defined monomers

These sequences in fasta are represented as a header, comment and plain string like:

>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
DIDGDGQVNYEEFVQMMTAK*

;LCBO - Prolactin precursor - Bovine
; a sample sequence in FASTA format
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*

plain string is a combination of the following symbols:

for peptides:
A - Alanine
C - Cysteine
D - Aspartic Acid
E - Glutamic Acid
F - Phenylalanine
G - Glycine
H - Histidine
I - Isoleucine
K - Lysine
L - Leucine
M - Methionine
N - Asparagine
O - Pyrrolysine
P - Proline
Q - Glutamine
R - Arginine
S - Serine
T - Threonine
U - Selenocysteine
V - Valine
W - Tryptophan
Y - Tyrosine

for RNA nucleotides:
A - AMP (Adenosine monophosphate)
C - CMP (Cytidine monophosphate)
G - GMP (Guanosine monophosphate)
U - UMP (Uridine monophosphate)
T - rTMP (Ribothymidine monophosphate)

for DNA nucleotides:
A - dAMP (Deoxyadenosine monophosphate)
C - dCMP (Deoxycytidine monophosphate)
G - dGMP (Deoxyguanosine monophosphate)
U - dUMP (Deoxyuridine monophosphate)
T - TMP (Thymidine monophosphate)

* - translation stop
- - gap of indeterminate length

Requirements:

1. FASTA file could contain one or several sequences.
   Each sequence in FASTA format is expressed in 2 or more lines of text. The first line is an identifying header, the remainder of the lines (one or more) represent the sequence itself.

• The header
  The header line starts with a greater-than symbol (">") and ends with newline. Allowed characters are "A" to "Z", "a" to
  "z", "0" to "9", "_", "-", ".", ",", ";" and "|" with SPACES between them.
• The sequence
  • DNA/RNA sequences could contain only the symbols: "A", "C", "G", "T", "U", "-"
  • Peptide sequence could contain only the symbols "A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "U", "V", "W", "Y", "*", "-"
  • Lower-case letters are accepted and are mapped into upper-case.
  • One sequence could be represented in one line or in several lines.
• Comments
  The comments line starts with the semicolon ";" symbol and ends with newline. May contain any symbol (including ">")

2. Import FASTA

• The first symbol in the FASTA file should be ">", if not the Error message should be displayed and import should not be performed.
• The header should be ignored during import.
• Comments should be ignored during import.
• Each sequence should be imported as a separate molecule. The start of the sequence is the first symbol in a line after header line, the end of the sequence is the last symbol before ">"
• If sequence contains some unallowed symbol then Error message should be displayed AND import should not be performed.
• "*" means the end of the peptide sequence.
• If " * " occurred between two letters then it should be recognized as the break in peptide chain (no bond should be created between monomers separated with the "*").
• "-" should be ignored during import.
• Import of the RNA/DNA and peptide sequences is performed according to the rules for Sequence format.
• "U" symbol for peptide should be recognized as Selenocysteine.

3. Export to FASTA

• Each molecule should be exported like separate sequence with the header "Sequence N", where N - is the number of sequence
• The header of each new sequence should be started from the new line .
• Only the sequences of the same type (DNA/RNA/Peptide) could be exported in one FASTA file.
• Complex polymer made up of different type sequences or branched polymer is not exported and system should display Error message.
• In case of molecules made up of modified monomers (peptides and nucleotides) natural analog is exported for peptide monomer and base natural analog is exported for modified nucleotides.
• [DRAFT] In case of monomer natural analog is 'X' that monomer should be ignored during export.
• CHEMs and RNA-monomers that are not a part of nucleotide or nucleoside are ignored during export.

Solution

1. Implement following functions for C API, where type can be one of "RNA", "DNA" or "PEPTIDE":

int indigoLoadFASTA(int source, const char* type);
int indigoLoadFASTAFromString(const char* string,  const char* type);
int indigoLoadFASTAFromFile(const char* filename,  const char* type);
int indigoLoadFASTAFromBuffer(const char* buffer, int size,  const char* type);
int indigoSaveFASTA(int molecule, int output, const char* type);
int indigoSaveFASTAToFile(int molecule, const char* filename, const char* type);
const char* indigoFASTA(int molecule, const char* type);

3. Add language bindings for Python, Java, C#
   python binding functions:
   def loadFASTA(self, input_string: string, sequence_type: string):
   def loadFASTAFromFile(self, input_file: string, sequence_type: string):
   def FASTA(self, sequence_type: string):
   def saveFASTA(self, output_file: string, sequence_type: string)

4. Add the following content types to WASM "loadMoleculeOrReaction" and Indigo service "convert" API:

chemical/x-rna-fasta, chemical/x-dna-fasta, chemical/x-peptide-fasta

[olganaz]

This task covers import/export of sequences with defined monomers:
Requirements:

1. A sequence in FASTA format is expressed in 2 or more lines of text. The first line is an identifying header, the remainder of the lines (one or more) represent the sequence itself.

• The header
  The header line starts with a greater-than symbol (">") and ends with newline. Allowed characters are "A" to "Z", "a" to
  "z", "0" to "9", "_", "-", ".", ",", ";" and "|" with SPACES between them.
• The sequence
  DNA/RNA sequences could contain only the symbols: "A", "C", "G", "T", "U", "-"
  Peptide sequence could contain only the symbols "A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T",
  "U", "V", "W", "Y", "*", "-"
  Lower-case letters are accepted and are mapped into upper-case. One sequence could be represented in one line or in several lines.
• Comments
  The comments line starts with the semicolon ";" symbol and ends with newline. May contain any symbol (including ">")

2. Import FASTA

• The first symbol in the FASTA file should be ">", if not the Error message should be displayed and import should not be performed.
• The header should be ignored during import.
• Comments should be ignored during import.
• Each sequence should be imported as a separate molecule. The start of the sequence is the first symbol in a line after header line, the end of the sequence is the last symbol before ">"
• If sequence contains some unallowed symbol then Error message should be displayed AND import should not be performed.
• "*" means the end of the peptide sequence
• If " * " occurred between two letters then it should be recognized as the break in peptide chain (no bond should be created between monomers separated with the "*").
• "-" should be ignored during import.
• Import of the RNA/DNA and peptide sequences is performed according to the rules for Sequence format.
• "U" symbol for peptide should be recognized as Selenocysteine.

3. Export to FASTA

• Each molecule should be exported like separate sequence with the header "Sequence N", where N - is the number of sequence

• Only the sequences of the same type (DNA/RNA/Peptide) could be exported in one FASTA file.

• Complex polymer made up of different type sequences or branched polymer is not exported and system should display Error message.

• In case of molecules made up of modified monomers (peptides and nucleotides) natural analog is exported for peptide monomer and base natural analog is exported for modified nucleotides

• CHEMs and RNA-monomers that are not a part of nucleotide or nucleoside are ignored during export.