I would greatly appreciate some help with using glib functions for dynamic
memory allocation and growth.
I have a number of miRNA text input files. Each file contains a miRNA data
block followed by a variable
number of gene_transcript data blocks representing the biological property of
a miRNA to bind to many gene_transcripts, as as outlined in the following:
- miRNA data block
- gene_transcript_1
- gene_transcript_2
............................
- gene_transcript_n
A miRNA data block is made up of the following records
- miRNA identifier (mandatory)
- miRNA description (optional)
- miRNA sequence (mandatory)
A gene_trascript data block is made up of the following records
- gene_trascript identifier (mandatory)
- gene_trascript description (optional)
- gene_trascript sequence (mandatory)
Basically it reperesents a Biology natural fact. That is, a miRNA can match
many gene_transcripts.
I have already developed a function that reads into a structure either a miRNA
or a gene_transcript
data block. But I am struggling with the following tasks.
As I read a miRNA file I have to:
(1) grow a vector where I append the miRNA identifier
(2) grow a vector where I append each gene_transcript identifier
(3) grow a binary matrix whose elements are set to 1 for those (miRNA,
gene_transcript) pairs
otherwise it is set to 0
Task (1) and (2) are easily accomplished through two GArrays where the
respective identifiers are appended as they are read through function
g_array_append_val.
Task (3) is giving me a lot of headache. Basically for each newly read miRNA
identifier I allocate a column
of Integer containing as many 0-elements as the number of gene_transcripts
previously read and as many 1-elements as the number of gene_transcripts
binding to the current miRNA.
I use function g_ptr_array_new to allocate a GPtrArray. Then I use g_array_new
to allocate a column of Integer. My problem is how to pile up the pointer to
the new Integer column, returned by g_array_new, into the GPtrArray. At run
time I keep getting Segmentation Fault when I try to fill in the Integer column.
Can someone help me, please ?
Another complication at representing such Biology phenomena is that the same
gene_transcript can bind
to different miRNAs. Therefore I can read the same gene_transcript from
different miRNA files.
This case must be detected as each miRNA as well as each gene_transcript
identifier must be uniquely saved. I think I will handle this uniqueness
through a binary tree.
If it is useful I can send a few C lines that implement the scenario
illustrated above.
Thank you very much in advance.
--
Maura E.M
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