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Reading input from a text file into an array of structures in c

My definition of structure,

typedef struct { int taxid; int geneid; char goid[20]; char evidence[4]; char qualifier[20]; char goterm[50]; char pubmed; char category[20]; } gene2go;

I have a delimited text file called gene2go.txt.

Each line of this file contains taxID , geneID , goID , evidence , qualifier , goterm , pubmed and category information.

Each line of the file will be stored in the structure.

When the program starts, it first reads the contents of the input file into an array of type gene2go, I used a function called readInfo .

The program will also accept the following input arguments from the command line,

input type (1 for taxID , 2 for geneID , 3 for goID ) and search query

There is a function called listData to write a list of strings in the file "gene2go.txt" corresponding to the type of input and search query in the file "output.txt".

Here is part of my text file "gene2go.txt" ,

 3702 814629 GO:0003676 IEA - nucleic acid binding - Function 3702 814629 GO:0005575 ND - cellular_component - Component 3702 814629 GO:0005634 ISM - nucleus - Component 3702 814629 GO:0008150 ND - biological_process - Process 3702 814629 GO:0008270 IEA - zinc ion binding - Function 3702 814630 GO:0005634 ISM - nucleus - Component 3702 814636 GO:0008150 ND - biological_process - Process 3702 814637 GO:0003674 ND - molecular_function - Function 6239 177883 GO:0008150 ND - biological_process - Process 6239 177884 GO:0005575 ND - cellular_component - Component 6239 177884 GO:0008150 ND - biological_process - Process 6239 177886 GO:0004364 IDA - glutathione transferase activity 12757851 Function 6239 177886 GO:0005575 ND - cellular_component - Component 7955 555450 GO:0005634 IEA - nucleus - Component 7955 555450 GO:0006355 IEA - regulation of transcription, DNA-dependent - Process

I wrote code called ceng301.c and compiled it using the command line

gcc ceng301.c -o ceng301

but when i write

ceng301 1 3702

on the command line, I get nothing, but a flashing underscore :( instead

 3702 814629 GO:0003676 IEA - nucleic acid binding - Function 3702 814629 GO:0005575 ND - cellular_component - Component 3702 814629 GO:0005634 ISM - nucleus - Component 3702 814629 GO:0008150 ND - biological_process - Process 3702 814629 GO:0008270 IEA - zinc ion binding - Function 3702 814630 GO:0005634 ISM - nucleus - Component 3702 814636 GO:0008150 ND - biological_process - Process 3702 814637 GO:0003674 ND - molecular_function - Function

saved to output.txt

Here is the code

 #include <stdio.h> #include <stdlib.h> /* structure definition */ typedef struct { int taxid; int geneid; char goid[20]; char evidence[4]; char qualifier[20]; char goterm[50]; char *pubmed; char category[20]; } gene2go; /* function prototypes */ int readInfo( gene2go input[] ); void listData( char *inType, char *searchItem, gene2go input[], int i ); int main( int argc, char *argv[] ) { gene2go input[200]; int i; i = readInfo( input ); listData( argv[1], argv[2], input, i ); return 0; } /* read the input file*/ int readInfo( gene2go input[] ) { FILE *fin; char *inputName = "gene2go.txt"; int i = 0; fin = fopen( inputName, "r" ); if( fin == NULL ) { printf( "File cannot be opened\n" ); } /* end if */ else { while( !feof( fin ) ) { fscanf( fin, "%[^\t]", &input[i].taxid, &input[i].geneid, &input[i].goid, &input[i].evidence, &input[i].qualifier, &input[i].goterm, &input[i].pubmed, &input[i].category ); i++; } /* end while */ fclose( fin ); } /* end else */ return i; } /* end function readInfo */ void listData( char *inType, char* searchItem, gene2go input[], int i ) { FILE *fout; char *outputName = "output.txt"; int j; int inputType = atoi( inType ); fout = fopen( outputName, "w" ); switch( inputType ) { case 1: for( j = 0; j < i; j++ ) { if( input[j].taxid == atoi( searchItem ) ) { fprintf( fout, "%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n", input[i].taxid, input[i].geneid, input[i].goid, input[i].evidence, input[i].qualifier, input[i].goterm, input[i].pubmed, input[i].category ); } /* end if */ } /* end for */ break; case 2: for( j = 0; j < i; j++ ) { if( input[j].geneid == atoi( searchItem ) ) { fprintf( fout, "%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n", input[i].taxid, input[i].geneid, input[i].goid, input[i].evidence, input[i].qualifier, input[i].goterm, input[i].pubmed, input[i].category ); } /* end if */ } /* end for */ break; case 3: for( j = 0; j < i; j++ ) { if( input[j].goid == searchItem ) { fprintf( fout, "%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\n", input[i].taxid, input[i].geneid, input[i].goid, input[i].evidence, input[i].qualifier, input[i].goterm, input[i].pubmed, input[i].category ); } /* end if */ } /* end for */ break; } /* end switch */ fclose( fout ); } /* end function listData */

What should I do?

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 char mystring[100]; FILE *p = fopen ("gene2go.txt" , "r"); if (p == NULL) perror ("Error opening file"); else { if ( fgets (mystring , 100 , pFile) != NULL ) puts (mystring); pch = strtok (mystring, "\t"); while (pch != NULL) { //handle each token here and insert into struct pch = strtok (NULL, "\t"); } fclose (pFile); } return 0;

Refer to strtok , fgets

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Source: https://habr.com/ru/post/1441788/

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