C++ getline, parse and take first tokens by condition
Hello,
Trying to parse a file (in FASTA format) and reformat it.
1) Each record starts with ">" and followed by words separated by space, but they are in one same line for sure;
2) Sequences are following that may be in multiple rows with possible spaces inside until the next ">".
I want to:
1) Only keep the first field (or token) of the line where ">" is found, ignore the rest of the line; i.e. keep the first word after the ">" as sequence ID;
2) Concatenate the sequences from different rows into a single string to have the second field.
The final format is a two-columns table.
My code is:
But my output is:
I am stuck, and not quite clear where it went wrong. Thanks for any help!
---------- Post updated at 06:21 PM ---------- Previous update was at 05:32 PM ----------
Modified the if block, but there is a bug for the first entry, i.e. an extra newline is printed at the beginning!
What should I do to fix this? Thanks again!
---------- Post updated 09-12-14 at 03:41 AM ---------- Previous update was 09-11-14 at 06:21 PM ----------
One of the reasons for the old problem is the leading space in some of the entries, like >seq02 . But the first newline still bugs me.
---------- Post updated at 11:31 AM ---------- Previous update was at 03:41 AM ----------
Solved the problem with a guard variable. Modified code are highlighted in bold red.
Admin, should this post be deleted as answered by myself?
Last edited by yifangt; 09-12-2014 at 12:32 PM..
Reason: found editing problem
Presumably you're using C++ rather than awk for performance reasons?
I've found that C stdio often has higher performance than C++ iostreams, sometimes surprisingly so. Especially when you're doing string-to-array conversion every single loop.
Last edited by Corona688; 09-12-2014 at 01:04 PM..
I am going back-forth with C and C++ these days, whenever I met some practical stuff I read(Too many to ask here!). I did not forget you helped me with the strtok() function in one of the posts, which is very profound and comprehensive to me, but performance is not too much of my concern at this moment.
Do you mean awk to do the job? Could you post it if you have the script handy? Thanks a lot!
Thought of combining the map<string, string> container with the program.
Store all the combined sequence entries in map< string, string>; which will be:
1) easier to print and avoid the problem like extra blank line for the first entry;
2) convenient to retrieve part of the sequences by sequence ID (i.e. the key of the map).
Here is my modified code that was compiled well with Segmentation fault when run.
The parts I was not sure are the "appending" of the parsed third and after tokens to the second token as sequence (value of map) highlighted in red FastaSeq[entryID] += sPtr;, which may be the problem for the program. Thanks a lot!
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